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'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, ELISA, DB, WB and IF. Batch specific data available on the website.',
'meta_title' => 'H3K9me3 Antibody - ChIP-seq Grade (C15410056) | Diagenode',
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'name' => 'H3K9me3 Antibody - ChIP-seq Grade',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone H3 containing the trimethylated lysine 9 (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_ChIP.jpg" alt="H3K9me3 Antibody ChIP Grade" /></p>
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1 and 2 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control.<br /> <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for the ZNF510 gene and the Sat2 satellite repeat, used as positive controls, and for the EIF4A2 and GAPDH promoters, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).<br /> <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K9me1, H3K9me2, H3K9me3, H3K4me3, H3K27me3, H3K36me3, H4K20me3 modifications and the unmodified H3K9 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K9me3 modification when using 0.5 or 1 µg. With 2 µg of antibody, some recovery of the H3K27me3 nucleosome is observed.</small></p>
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<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq Grade" /></p>
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<div class="row">
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<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " /></p>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" /></p>
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<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq4000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoom-in to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B and 2C show the enrichment along the ZNF510 positive control target and at the KCNQ1 imprinted gene.</small></p>
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<p><strong></strong></p>
<p><strong></strong></p>
<p><small><strong>Figure 3. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410056) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:198,000.</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" /></p>
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<div class="small-8 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410056) with peptides containing other modifications of histone H3 and H4 and the unmodified sequence of histone H3. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 4 shows a high specificity of the antibody for the modification of interest.</small></p>
<p></p>
<p></p>
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<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western blot" /></p>
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<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot was performed on 40 µg whole cell extracts from HeLa cells (lane 1) and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K9me3 (cat. No. C15410056). The antibody was diluted 1:2,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right, the marker (in kDa) is shown on the left.</small></p>
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'description' => 'Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Trimethylation of histone H3K9 is associated with satellite repeat regions and ZNF repeat genes.',
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'reactivity' => 'Human, mouse, zebrafish, trout, Daphnia, Arabidopsis, Drosophila, silena latifolia: positive. Other species: not tested.',
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<th>Suggested dilution</th>
<th>References</th>
</tr>
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<tbody>
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<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>0.5 - 1 µg per ChIP</td>
<td>Fig 1, 2</td>
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<tr>
<td>ELISA</td>
<td>1:1,000 - 1:10,000</td>
<td>Fig 3</td>
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<tr>
<td>Dot Blotting</td>
<td>1:2,000</td>
<td>Fig 4</td>
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<td>Western Blotting</td>
<td>1:2,000</td>
<td>Fig 5</td>
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<p><small><sup>*</sup> Please note that the optimal antibody amount per IP should be determined by the end-user. We recommend testing 0.5-5 µg per IP.</small></p>',
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$meta_title = 'H3K9me3 Antibody - ChIP-seq Grade (C15410056) | Diagenode'
$product = array(
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'id' => '2216',
'antibody_id' => '120',
'name' => 'H3K9me3 Antibody - ChIP-seq Grade',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone H3 containing the trimethylated lysine 9 (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation data',
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<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_ChIP.jpg" alt="H3K9me3 Antibody ChIP Grade" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1 and 2 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control.<br /> <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for the ZNF510 gene and the Sat2 satellite repeat, used as positive controls, and for the EIF4A2 and GAPDH promoters, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).<br /> <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K9me1, H3K9me2, H3K9me3, H3K4me3, H3K27me3, H3K36me3, H4K20me3 modifications and the unmodified H3K9 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K9me3 modification when using 0.5 or 1 µg. With 2 µg of antibody, some recovery of the H3K27me3 nucleosome is observed.</small></p>
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<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq Grade" /></p>
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</div>
<div class="row">
<div class="small-12 columns">
<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " /></p>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq4000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoom-in to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B and 2C show the enrichment along the ZNF510 positive control target and at the KCNQ1 imprinted gene.</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" /></p>
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<div class="small-6 columns">
<p><strong></strong></p>
<p><strong></strong></p>
<p><small><strong>Figure 3. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410056) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:198,000.</small></p>
<p></p>
<p></p>
<p></p>
<p></p>
<p></p>
</div>
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<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410056) with peptides containing other modifications of histone H3 and H4 and the unmodified sequence of histone H3. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 4 shows a high specificity of the antibody for the modification of interest.</small></p>
<p></p>
<p></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot was performed on 40 µg whole cell extracts from HeLa cells (lane 1) and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K9me3 (cat. No. C15410056). The antibody was diluted 1:2,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right, the marker (in kDa) is shown on the left.</small></p>
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'sf_code' => 'C15410056-D001-000581',
'type' => 'FRE',
'search_order' => '03-Antibody',
'price_EUR' => '380',
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'price_JPY' => '59525',
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'slug' => 'h3k9me3-polyclonal-antibody-classic-50-ug',
'meta_title' => 'H3K9me3 Antibody - ChIP-seq Grade (C15410056) | Diagenode',
'meta_keywords' => '',
'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, ELISA, DB, WB and IF. Batch specific data available on the website.',
'modified' => '2021-10-20 09:33:57',
'created' => '2015-06-29 14:08:20',
'locale' => 'zho'
),
'Antibody' => array(
'host' => '*****',
'id' => '120',
'name' => 'H3K9me3 polyclonal antibody',
'description' => 'Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Trimethylation of histone H3K9 is associated with satellite repeat regions and ZNF repeat genes.',
'clonality' => '',
'isotype' => '',
'lot' => 'A2810P',
'concentration' => '1.85 µg/µl',
'reactivity' => 'Human, mouse, zebrafish, trout, Daphnia, Arabidopsis, Drosophila, silena latifolia: positive. Other species: not tested.',
'type' => 'Polyclonal ChIP grade, ChIP-seq grade',
'purity' => 'Affinity purified polyclonal antibody.',
'classification' => 'Classic',
'application_table' => '<table>
<thead>
<tr>
<th>Applications</th>
<th>Suggested dilution</th>
<th>References</th>
</tr>
</thead>
<tbody>
<tr>
<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>0.5 - 1 µg per ChIP</td>
<td>Fig 1, 2</td>
</tr>
<tr>
<td>ELISA</td>
<td>1:1,000 - 1:10,000</td>
<td>Fig 3</td>
</tr>
<tr>
<td>Dot Blotting</td>
<td>1:2,000</td>
<td>Fig 4</td>
</tr>
<tr>
<td>Western Blotting</td>
<td>1:2,000</td>
<td>Fig 5</td>
</tr>
</tbody>
</table>
<p><small><sup>*</sup> Please note that the optimal antibody amount per IP should be determined by the end-user. We recommend testing 0.5-5 µg per IP.</small></p>',
'storage_conditions' => 'Store at -20°C; for long storage, store at -80°C. Avoid multiple freeze-thaw cycles.',
'storage_buffer' => 'PBS containing 0.05% azide.',
'precautions' => 'This product is for research use only. Not for use in diagnostic or therapeutic procedures.',
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'slug' => '',
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'modified' => '2021-07-28 12:12:46',
'created' => '0000-00-00 00:00:00',
'select_label' => '120 - H3K9me3 polyclonal antibody (A2810P - 1.85 µg/µl - Human, mouse, zebrafish, trout, Daphnia, Arabidopsis, Drosophila, silena latifolia: positive. Other species: not tested. - Affinity purified polyclonal antibody. - Rabbit)'
),
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'modified' => '2016-02-18 20:52:54',
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'Group' => array(
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'Master' => array(
'id' => '2216',
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'name' => 'H3K9me3 Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 9</strong> (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation data',
'info1' => '<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_ChIP.jpg" alt="H3K9me3 Antibody ChIP Grade" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1 and 2 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control.<br /> <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for the ZNF510 gene and the Sat2 satellite repeat, used as positive controls, and for the EIF4A2 and GAPDH promoters, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).<br /> <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K9me1, H3K9me2, H3K9me3, H3K4me3, H3K27me3, H3K36me3, H4K20me3 modifications and the unmodified H3K9 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K9me3 modification when using 0.5 or 1 µg. With 2 µg of antibody, some recovery of the H3K27me3 nucleosome is observed.</small></p>
</div>
</div>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
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<div class="extra-spaced"></div>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-12 columns">
<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq Grade" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " /></p>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq4000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoom-in to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B and 2C show the enrichment along the ZNF510 positive control target and at the KCNQ1 imprinted gene.</small></p>
<p></p>
</div>
</div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" /></p>
</div>
<div class="small-6 columns">
<p><strong></strong></p>
<p><strong></strong></p>
<p><small><strong>Figure 3. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410056) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:198,000.</small></p>
<p></p>
<p></p>
<p></p>
<p></p>
<p></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410056) with peptides containing other modifications of histone H3 and H4 and the unmodified sequence of histone H3. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 4 shows a high specificity of the antibody for the modification of interest.</small></p>
<p></p>
<p></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot was performed on 40 µg whole cell extracts from HeLa cells (lane 1) and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K9me3 (cat. No. C15410056). The antibody was diluted 1:2,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right, the marker (in kDa) is shown on the left.</small></p>
</div>
</div>',
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'type' => 'FRE',
'search_order' => '03-Antibody',
'price_EUR' => '380',
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'slug' => 'h3k9me3-polyclonal-antibody-classic-50-ug',
'meta_title' => 'H3K9me3 Antibody - ChIP-seq Grade (C15410056) | Diagenode',
'meta_keywords' => '',
'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, ELISA, DB, WB and IF. Batch specific data available on the website.',
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'id' => '1836',
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'name' => 'iDeal ChIP-seq kit for Histones',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/ideal-chipseq-for-histones-complete-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>Don’t risk wasting your precious sequencing samples. Diagenode’s validated <strong>iDeal ChIP-seq kit for Histones</strong> has everything you need for a successful start-to-finish <strong>ChIP of histones prior to Next-Generation Sequencing</strong>. The complete kit contains all buffers and reagents for cell lysis, chromatin shearing, immunoprecipitation and DNA purification. In addition, unlike competing solutions, the kit contains positive and negative control antibodies (H3K4me3 and IgG, respectively) as well as positive and negative control PCR primers pairs (GAPDH TSS and Myoglobin exon 2, respectively) for your convenience and a guarantee of optimal results. The kit has been validated on multiple histone marks.</p>
<p> The iDeal ChIP-seq kit for Histones<strong> </strong>is perfect for <strong>cells</strong> (<strong>100,000 cells</strong> to <strong>1,000,000 cells</strong> per IP) and has been validated for <strong>tissues</strong> (<strong>1.5 mg</strong> to <strong>5 mg</strong> of tissue per IP).</p>
<p> The iDeal ChIP-seq kit is the only kit on the market validated for the major sequencing systems. Our expertise in ChIP-seq tools allows reproducible and efficient results every time.</p>
<p></p>
<p> <strong></strong></p>
<p></p>',
'label1' => 'Characteristics',
'info1' => '<ul style="list-style-type: disc;">
<li>Highly <strong>optimized</strong> protocol for ChIP-seq from cells and tissues</li>
<li><strong>Validated</strong> for ChIP-seq with multiple histones marks</li>
<li>Most <strong>complete</strong> kit available (covers all steps, including the control antibodies and primers)</li>
<li>Optimized chromatin preparation in combination with the Bioruptor ensuring the best <strong>epitope integrity</strong></li>
<li>Magnetic beads make ChIP easy, fast and more <strong>reproducible</strong></li>
<li>Combination with Diagenode ChIP-seq antibodies provides high yields with excellent <strong>specificity</strong> and <strong>sensitivity</strong></li>
<li>Purified DNA suitable for any downstream application</li>
<li>Easy-to-follow protocol</li>
</ul>
<p>Note: to obtain optimal results, this kit should be used in combination with the DiaMag1.5 - magnetic rack.</p>
<h3>ChIP-seq on cells</h3>
<p><img src="https://www.diagenode.com/img/product/kits/iDeal-kit-C01010053-figure-1.jpg" alt="Figure 1A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 1A. The high consistency of the iDeal ChIP-seq kit on the Ion Torrent™ PGM™ (Life Technologies) and GAIIx (Illumina<sup>®</sup>)</strong><br /> ChIP was performed on sheared chromatin from 1 million HelaS3 cells using the iDeal ChIP-seq kit and 1 µg of H3K4me3 positive control antibody. Two different biological samples have been analyzed using two different sequencers - GAIIx (Illumina<sup>®</sup>) and PGM™ (Ion Torrent™). The expected ChIP-seq profile for H3K4me3 on the GAPDH promoter region has been obtained.<br /> Image A shows a several hundred bp along chr12 with high similarity of read distribution despite the radically different sequencers. Image B is a close capture focusing on the GAPDH that shows that even the peak structure is similar.</p>
<p class="text-center"><strong>Perfect match between ChIP-seq data obtained with the iDeal ChIP-seq workflow and reference dataset</strong></p>
<p><img src="https://www.diagenode.com/img/product/kits/perfect-match-between-chipseq-data.png" alt="Figure 1B" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 1B.</strong> The ChIP-seq dataset from this experiment has been compared with a reference dataset from the Broad Institute. We observed a perfect match between the top 40% of Diagenode peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>
<p><img src="https://www.diagenode.com/img/product/kits/iDeal-kit-C01010053-figure-2.jpg" alt="Figure 2" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 2. Efficient and easy chromatin shearing using the Bioruptor<sup>®</sup> and Shearing buffer iS1 from the iDeal ChIP-seq kit</strong><br /> Chromatin from 1 million of Hela cells was sheared using the Bioruptor<sup>®</sup> combined with the Bioruptor<sup>®</sup> Water cooler (Cat No. BioAcc-cool) during 3 rounds of 10 cycles of 30 seconds “ON” / 30 seconds “OFF” at HIGH power setting (position H). Diagenode 1.5 ml TPX tubes (Cat No. M-50001) were used for chromatin shearing. Samples were gently vortexed before and after performing each sonication round (rounds of 10 cycles), followed by a short centrifugation at 4°C to recover the sample volume at the bottom of the tube. The sheared chromatin was then decross-linked as described in the kit manual and analyzed by agarose gel electrophoresis.</p>
<p><img src="https://www.diagenode.com/img/product/kits/iDeal-kit-C01010053-figure-3.jpg" alt="Figure 3" style="display: block; margin-left: auto; margin-right: auto;" width="264" height="320" /></p>
<p><strong>Figure 3. Validation of ChIP by qPCR: reliable results using Diagenode’s ChIP-seq grade H3K4me3 antibody, isotype control and sets of validated primers</strong><br /> Specific enrichment on positive loci (GAPDH, EIF4A2, c-fos promoter regions) comparing to no enrichment on negative loci (TSH2B promoter region and Myoglobin exon 2) was detected by qPCR. Samples were prepared using the Diagenode iDeal ChIP-seq kit. Diagenode ChIP-seq grade antibody against H3K4me3 and the corresponding isotype control IgG were used for immunoprecipitation. qPCR amplification was performed with sets of validated primers.</p>
<h3>ChIP-seq on tissue</h3>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-figure-h3k4me3.jpg" alt="Figure 4A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 4A.</strong> Chromatin Immunoprecipitation has been performed using chromatin from mouse liver tissue, the iDeal ChIP-seq kit for Histones and the Diagenode ChIP-seq-grade H3K4me3 (Cat. No. C15410003) antibody. The IP'd DNA was subsequently analysed on an Illumina® HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. This figure shows the peak distribution in a region surrounding the GAPDH positive control gene.</p>
<p><img src="https://www.diagenode.com/img/product/kits/match-of-the-top40-peaks-2.png" alt="Figure 4B" caption="false" style="display: block; margin-left: auto; margin-right: auto;" width="700" height="280" /></p>
<p><strong>Figure 4B.</strong> The ChIP-seq dataset from this experiment has been compared with a reference dataset from the Broad Institute. We observed a perfect match between the top 40% of Diagenode peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>',
'label2' => 'Species, cell lines, tissues tested',
'info2' => '<p>The iDeal ChIP-seq Kit for Histones is compatible with a broad variety of cell lines, tissues and species - some examples are shown below. Other species / cell lines / tissues can be used with this kit.</p>
<p><u>Cell lines:</u></p>
<p>Human: A549, A673, CD8+ T, Blood vascular endothelial cells, Lymphatic endothelial cells, fibroblasts, K562, MDA-MB231</p>
<p>Pig: Alveolar macrophages</p>
<p>Mouse: C2C12, primary HSPC, synovial fibroblasts, HeLa-S3, FACS sorted cells from embryonic kidneys, macrophages, mesodermal cells, myoblasts, NPC, salivary glands, spermatids, spermatocytes, skeletal muscle stem cells, stem cells, Th2</p>
<p>Hamster: CHO</p>
<p>Other cell lines / species: compatible, not tested</p>
<p><u>Tissues</u></p>
<p>Bee – brain</p>
<p>Daphnia – whole animal</p>
<p>Horse – brain, heart, lamina, liver, lung, skeletal muscles, ovary</p>
<p>Human – Erwing sarcoma tumor samples</p>
<p>Other tissues: compatible, not tested</p>
<p>Did you use the iDeal ChIP-seq for Histones Kit on other cell line / tissue / species? <a href="mailto:agnieszka.zelisko@diagenode.com?subject=Species, cell lines, tissues tested with the iDeal ChIP-seq Kit for TF&body=Dear Customer,%0D%0A%0D%0APlease, leave below your feedback about the iDeal ChIP-seq for Transcription Factors (cell / tissue type, species, other information...).%0D%0A%0D%0AThank you for sharing with us your experience !%0D%0A%0D%0ABest regards,%0D%0A%0D%0AAgnieszka Zelisko-Schmidt, PhD">Let us know!</a></p>',
'label3' => ' Additional solutions compatible with iDeal ChIP-seq Kit for Histones',
'info3' => '<p><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin EasyShear Kit - Ultra Low SDS </a>optimizes chromatin shearing, a critical step for ChIP.</p>
<p> The <a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq">MicroPlex Library Preparation Kit </a>provides easy and optimal library preparation of ChIPed samples.</p>
<p><a href="../categories/chip-seq-grade-antibodies">ChIP-seq grade anti-histone antibodies</a> provide high yields with excellent specificity and sensitivity.</p>
<p> Plus, for our IP-Star Automation users for automated ChIP, check out our <a href="../p/auto-ideal-chip-seq-kit-for-histones-x24-24-rxns">automated</a> version of this kit.</p>',
'format' => '4 chrom. prep./24 IPs',
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'description' => '<p><a href="https://www.diagenode.com/files/products/kits/truemicrochipseq-kit-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>The <b>True </b><b>MicroChIP-seq</b><b> kit </b>provides a robust ChIP protocol suitable for the investigation of histone modifications within chromatin from as few as <b>10 000 cells</b>, including <b>FACS sorted cells</b>. The kit can be used for chromatin preparation for downstream ChIP-qPCR or ChIP-seq analysis. The <b>complete kit</b> contains everything you need for start-to-finish ChIP including all validated buffers and reagents for chromatin shearing, immunoprecipitation and DNA purification for exceptional <strong>ChIP-qPCR</strong> or <strong>ChIP-seq</strong> results. In addition, positive control antibodies and negative control PCR primers are included for your convenience and assurance of result sensitivity and specificity.</p>
<p>The True MicroChIP-seq kit offers unique benefits:</p>
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<li>An <b>optimized chromatin preparation </b>protocol compatible with low number of cells (<b>10.000</b>) in combination with the Bioruptor™ shearing device</li>
<li>Most <b>complete kit </b>available (covers all steps and includes control antibodies and primers)</li>
<li><b>Magnetic beads </b>make ChIP easy, fast, and more reproducible</li>
<li>MicroChIP DiaPure columns (included in the kit) enable the <b>maximum recovery </b>of immunoprecipitation DNA suitable for any downstream application</li>
<li><b>Excellent </b><b>ChIP</b><b>-seq </b>result when combined with <a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq">MicroPlex</a><a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq"> Library Preparation kit </a>adapted for low input</li>
</ul>
<p>For fast ChIP-seq on low input – check out Diagenode’s <a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns">µ</a><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns">ChIPmentation</a><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns"> for histones</a>.</p>
<p><sub>The True MicroChIP-seq kit, Cat. No. C01010132 is an upgraded version of the kit True MicroChIP, Cat. No. C01010130, with the new validated protocols (e.g. FACS sorted cells) and MicroChIP DiaPure columns included in the kit.</sub></p>',
'label1' => 'Characteristics',
'info1' => '<ul>
<li><b>Revolutionary:</b> Only 10,000 cells needed for complete ChIP-seq procedure</li>
<li><b>Validated on</b> studies for histone marks</li>
<li><b>Automated protocol </b>for the IP-Star<sup>®</sup> Compact Automated Platform available</li>
</ul>
<p></p>
<p>The True MicroChIP-seq kit protocol has been optimized for the use of 10,000 - 100,000 cells per immunoprecipitation reaction. Regarding chromatin immunoprecipitation, three protocol variants have been optimized:<br />starting with a batch, starting with an individual sample and starting with the FACS-sorted cells.</p>
<div><button id="readmorebtn" style="background-color: #b02736; color: white; border-radius: 5px; border: none; padding: 5px;">Show Workflow</button></div>
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<div class="carrousel" style="background-position: center;">
<div class="container">
<div class="row" style="background: rgba(255,255,255,0.1);">
<div class="large-12 columns truemicro-slider" id="truemicro-slider">
<div>
<h3>High efficiency ChIP on 10,000 cells</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-histone-results.png" width="800px" /></div>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center>
<p><small><strong>Figure 1. </strong>ChIP efficiency on 10,000 cells. ChIP was performed on human Hela cells using the Diagenode antibodies <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (Cat. No. C15410003), <a href="https://www.diagenode.com/en/p/h3k27ac-polyclonal-antibody-classic-50-mg-42-ml">H3K27ac</a> (C15410174), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-classic-50-ug">H3K9me3</a> (C15410056) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-classic-50-mg-34-ml">H3K27me3</a> (C15410069). Sheared chromatin from 10,000 cells and 0.1 µg (H3K27ac), 0.25 µg (H3K4me3 and H3K27me3) or 0.5 µg (H3K9me3) of the antibody were used per IP. Corresponding amount of IgG was used as control. Quantitative PCR was performed with primers for corresponding positive and negative loci. Figure shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
</center></div>
</div>
<div>
<h3>True MicroChIP-seq protocol in a combination with MicroPlex library preparation kit results in reliable and accurate sequencing data</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><img src="https://www.diagenode.com/img/product/kits/fig2-truemicro.jpg" alt="True MicroChip results" width="800px" /></div>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center>
<p><small><strong>Figure 2.</strong> Integrative genomics viewer (IGV) visualization of ChIP-seq experiments using 50.000 of K562 cells. ChIP has been performed accordingly to True MicroChIP protocol followed by the library preparation using MicroPlex Library Preparation Kit (C05010001). The above figure shows the peaks from ChIP-seq experiments using the following antibodies: H3K4me1 (C15410194), H3K9/14ac (C15410200), H3K27ac (C15410196) and H3K36me3 (C15410192).</small></p>
</center></div>
</div>
<div>
<h3>Successful chromatin profiling from 10.000 of FACS-sorted cells</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><img src="https://www.diagenode.com/img/product/kits/fig3ab-truemicro.jpg" alt="small non coding RNA" width="800px" /></div>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center>
<p><small><strong>Figure 3.</strong> (A) Integrative genomics viewer (IGV) visualization of ChIP-seq experiments and heatmap 3kb upstream and downstream of the TSS (B) for H3K4me3. ChIP has been performed using 10.000 of FACS-sorted cells (K562) and H3K4me3 antibody (C15410003) accordingly to True MicroChIP protocol followed by the library preparation using MicroPlex Library Preparation Kit (C05010001). Data were compared to ENCODE standards.</small></p>
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'label2' => 'Additional solutions compatible with the True MicroChIP-seq Kit',
'info2' => '<p><span style="font-weight: 400;">The <a href="https://www.diagenode.com/en/p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin EasyShear Kit – High SDS</a></span><span style="font-weight: 400;"> Recommended for the optimizing chromatin shearing.</span></p>
<p><a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies"><span style="font-weight: 400;">ChIP-seq grade antibodies</span></a><span style="font-weight: 400;"> for high yields, specificity, and sensitivity.</span></p>
<p><span style="font-weight: 400;">Check the list of available </span><a href="https://www.diagenode.com/en/categories/primer-pairs"><span style="font-weight: 400;">primer pairs</span></a><span style="font-weight: 400;"> designed for high specificity to specific genomic regions.</span></p>
<p><span style="font-weight: 400;">For library preparation of immunoprecipitated samples we recommend to use the </span><b> </b><a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq"><span style="font-weight: 400;">MicroPlex Library Preparation Kit</span></a><span style="font-weight: 400;"> - validated for library preparation from picogram inputs.</span></p>
<p><span style="font-weight: 400;">For IP-Star Automation users, check out the </span><a href="https://www.diagenode.com/en/p/auto-true-microchip-kit-16-rxns"><span style="font-weight: 400;">automated version</span></a><span style="font-weight: 400;"> of this kit.</span></p>
<p><span style="font-weight: 400;">Application note: </span><a href="https://www.diagenode.com/files/application_notes/Diagenode_AATI_Joint.pdf"><span style="font-weight: 400;">Best Workflow Practices for ChIP-seq Analysis with Small Samples</span></a></p>
<p></p>',
'label3' => 'Species, cell lines, tissues tested',
'info3' => '<p>The True MicroChIP-seq kit is compatible with a broad variety of cell lines, tissues and species - some examples are shown below. Other species / cell lines / tissues can be used with this kit.</p>
<p><strong>Cell lines:</strong></p>
<p>Bovine: blastocysts,<br />Drosophila: embryos, salivary glands<br />Human: EndoC-ẞH1 cells, HeLa cells, PBMC, urothelial cells<br />Mouse: adipocytes, B cells, blastocysts, pre-B cells, BMDM cells, chondrocytes, embryonic stem cells, KH2 cells, LSK cells, macrophages, MEP cells, microglia, NK cells, oocytes, pancreatic cells, P19Cl6 cells, RPE cells,</p>
<p>Other cell lines / species: compatible, not tested</p>
<p><strong>Tissues:</strong></p>
<p>Horse: adipose tissue</p>
<p>Mice: intestine tissue</p>
<p>Other tissues: not tested</p>',
'format' => '20 rxns',
'catalog_number' => 'C01010132',
'old_catalog_number' => 'C01010130',
'sf_code' => 'C01010132-',
'type' => 'RFR',
'search_order' => '04-undefined',
'price_EUR' => '625',
'price_USD' => '680',
'price_GBP' => '575',
'price_JPY' => '97905',
'price_CNY' => '',
'price_AUD' => '1700',
'country' => 'ALL',
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'slug' => 'true-microchip-kit-x16-16-rxns',
'meta_title' => 'True MicroChIP-seq Kit | Diagenode C01010132',
'meta_keywords' => '',
'meta_description' => 'True MicroChIP-seq Kit provides a robust ChIP protocol suitable for the investigation of histone modifications within chromatin from as few as 10 000 cells, including FACS sorted cells. Compatible with ChIP-qPCR as well as ChIP-seq.',
'modified' => '2023-04-20 16:06:10',
'created' => '2015-06-29 14:08:20',
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'id' => '1927',
'antibody_id' => null,
'name' => 'MicroPlex Library Preparation Kit v2 (12 indexes)',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/MicroPlex-Libary-Prep-Kit-v2-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p><span><strong>Specifically optimized for ChIP-seq</strong></span><br /><br /><span>The MicroPlex Library Preparation™ kit is the only kit on the market which is validated for ChIP-seq and which allows the preparation of indexed libraries from just picogram inputs. In combination with the </span><a href="./true-microchip-kit-x16-16-rxns">True MicroChIP kit</a><span>, it allows for performing ChIP-seq on as few as 10,000 cells. Less input, fewer steps, fewer supplies, faster time to results! </span></p>
<p>The MicroPlex v2 kit (Cat. No. C05010012) contains all necessary reagents including single indexes for multiplexing up to 12 samples using single barcoding. For higher multiplexing (using dual indexes) check <a href="https://www.diagenode.com/en/p/microplex-lib-prep-kit-v3-48-rxns">MicroPlex Library Preparation Kits v3</a>.</p>',
'label1' => 'Characteristics',
'info1' => '<ul>
<li><strong>1 tube, 2 hours, 3 steps</strong> protocol</li>
<li><strong>Input: </strong>50 pg – 50 ng</li>
<li><strong>Reduce potential bias</strong> - few PCR amplification cycles needed</li>
<li><strong>High sensitivity ChIP-seq</strong> - low PCR duplication rate</li>
<li><strong>Great multiplexing flexibility</strong> with 12 barcodes (8 nt) included</li>
<li><strong>Validated with the <a href="https://www.diagenode.com/p/sx-8g-ip-star-compact-automated-system-1-unit" title="IP-Star Automated System">IP-Star<sup>®</sup> Automated Platform</a></strong></li>
</ul>
<h3>How it works</h3>
<center><img src="https://www.diagenode.com/img/product/kits/microplex-method-overview-v2.png" /></center>
<p style="margin-bottom: 0;"><small><strong>Microplex workflow - protocol with single indexes</strong><br />An input of 50 pg to 50 ng of fragmented dsDNA is converted into sequencing-ready libraries for Illumina® NGS platforms using a fast and simple 3-step protocol</small></p>
<ul class="accordion" data-accordion="" id="readmore" style="margin-left: 0;">
<li class="accordion-navigation"><a href="#first" style="background: #ffffff; padding: 0rem; margin: 0rem; color: #13b2a2;"><small>Read more about MicroPlex workflow</small></a>
<div id="first" class="content">
<p><small><strong>Step 1. Template Preparation</strong> provides efficient repair of the fragmented double-stranded DNA input.</small></p>
<p><small>In this step, the DNA is repaired and yields molecules with blunt ends.</small></p>
<p><small><strong>Step 2. Library Synthesis.</strong> enables ligation of MicroPlex patented stem- loop adapters.</small></p>
<p><small>In the next step, stem-loop adaptors with blocked 5’ ends are ligated with high efficiency to the 5’ end of the genomic DNA, leaving a nick at the 3’ end. The adaptors cannot ligate to each other and do not have single- strand tails, both of which contribute to non-specific background found with many other NGS preparations.</small></p>
<p><small><strong>Step 3. Library Amplification</strong> enables extension of the template, cleavage of the stem-loop adaptors, and amplification of the library. Illumina- compatible indexes are also introduced using a high-fidelity, highly- processive, low-bias DNA polymerase.</small></p>
<p><small>In the final step, the 3’ ends of the genomic DNA are extended to complete library synthesis and Illumina-compatible indexes are added through a high-fidelity amplification. Any remaining free adaptors are destroyed. Hands-on time and the risk of contamination are minimized by using a single tube and eliminating intermediate purifications.</small></p>
<p><small>Obtained libraries are purified, quantified and sized. The libraries pooling can be performed as well before sequencing.</small></p>
</div>
</li>
</ul>
<p></p>
<h3>Reliable detection of enrichments in ChIP-seq</h3>
<p><img src="https://www.diagenode.com/img/product/kits/microplex-library-prep-kit-figure-a.png" alt="Reliable detection of enrichments in ChIP-seq figure 1" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure A.</strong> ChIP has been peformed with H3K4me3 antibody, amplification of 17 pg of DNA ChIP'd from 10.000 cells and amplification of 35 pg of DNA ChIP'd from 100.000 cells (control experiment). The IP'd DNA was amplified and transformed into a sequencing-ready preparation for the Illumina plateform with the MicroPlex Library Preparation kit. The library was then analysed on an Illumina<sup>®</sup> Genome Analyzer. Cluster generation and sequencing were performed according to the manufacturer's instructions.</p>
<p><img src="https://www.diagenode.com/img/product/kits/microplex-library-prep-kit-figure-b.png" alt="Reliable detection of enrichments in ChIP-seq figure 2" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure B.</strong> We observed a perfect match between the top 40% of True MicroChIP peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>',
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'format' => '12 rxns',
'catalog_number' => 'C05010012',
'old_catalog_number' => 'C05010010',
'sf_code' => 'C05010012-',
'type' => 'FRE',
'search_order' => '04-undefined',
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'slug' => 'microplex-library-preparation-kit-v2-x12-12-indices-12-rxns',
'meta_title' => 'MicroPlex Library Preparation Kit v2 x12 (12 indices)',
'meta_keywords' => '',
'meta_description' => 'MicroPlex Library Preparation Kit v2 x12 (12 indices)',
'modified' => '2023-04-20 15:01:16',
'created' => '2015-06-29 14:08:20',
'ProductsRelated' => array(
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'id' => '2264',
'antibody_id' => '121',
'name' => 'H3K9me3 Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone<strong> H3 containing the trimethylated lysine 9</strong> (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation Data',
'info1' => '<div class="row">
<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig1.png" /></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (cat. No. C15410193) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). A titration of the antibody consisting of 0.5, 1, 2, and 5 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2a.png" width="700" /></center><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2b.png" width="700" /></center><center>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2c.png" width="700" /></center><center>D.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2d.png" width="700" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with 0.5 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410193) on sheared chromatin from 1,000,000 HeLa cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq 2000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B, 2C and 2D show the enrichment along the ZNF510 positive control target and at the H19 and KCNQ1 imprinted genes.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-CT-Fig3a.png" width="700" /></center><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-CT-Fig3b.png" width="700" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K9me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410193) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in a genomic regions on chromosome 1 containing several ZNF repeat genes and in a genomic region surrounding the KCNQ1 imprinting control gene on chromosome 11 (figure 3A and B, respectively).</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-Elisa-Fig4.png" /></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410193) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:87,000.</small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-DB-Fig5.png" /></center></div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410193) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 5 shows a high specificity of the antibody for the modification of interest.</small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-WB-Fig6.png" /></center></div>
<div class="small-8 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K9me3 (cat. No. C15410193). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-IF-Fig7.png" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br />HeLa cells were stained with the Diagenode antibody against H3K9me3 (cat. No. C15410193) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (middle) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The left panel shows staining of the nuclei with DAPI. A merge of both stainings is shown on the right.</small></p>
</div>
</div>',
'label2' => 'Target Description',
'info2' => '<p>Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Trimethylation of histone H3K9 is associated with inactive genomic regions, satellite repeats and ZNF gene repeats.</p>',
'label3' => '',
'info3' => '',
'format' => '50 μg',
'catalog_number' => 'C15410193',
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'search_order' => '03-Antibody',
'price_EUR' => '480',
'price_USD' => '470',
'price_GBP' => '430',
'price_JPY' => '75190',
'price_CNY' => '0',
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'meta_title' => 'H3K9me3 Antibody - ChIP-seq Grade (C15410193) | Diagenode',
'meta_keywords' => '',
'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, CUT&Tag, ELISA, DB, WB and IF. Specificity confirmed by Peptide array assay. Batch-specific data available on the website. Sample size available.',
'modified' => '2021-10-20 09:55:53',
'created' => '2015-06-29 14:08:20',
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(int) 4 => array(
'id' => '2173',
'antibody_id' => '115',
'name' => 'H3K4me3 Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 4</strong> (<strong>H3K4me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation data',
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<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" /></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me3</strong><br />ChIP assays were performed using human K562 cells, the Diagenode antibody against H3K4me3 (cat. No. C15410003) and optimized PCR primer pairs for qPCR. ChIP was performed with the iDeal ChIP-seq kit (cat. No. C01010051), using sheared chromatin from 500,000 cells. A titration consisting of 0.5, 1, 2 and 5 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers specific for the promoter of the active genes GAPDH and EIF4A2, used as positive controls, and for the inactive MYOD1 gene and the Sat2 satellite repeat, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p></p>
<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2a-ChIP-seq.jpg" width="800" /></center><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2b-ChIP-seq.jpg" width="800" /></center><center>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2c-ChIP-seq.jpg" width="800" /></center><center>D.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2d-ChIP-seq.jpg" width="800" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me3</strong><br />ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using 1 µg of the Diagenode antibody against H3K4me3 (cat. No. C15410003) as described above. The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2 shows the peak distribution along the complete sequence and a 600 kb region of the X-chromosome (figure 2A and B) and in two regions surrounding the GAPDH and EIF4A2 positive control genes, respectively (figure 2C and D). These results clearly show an enrichment of the H3K4 trimethylation at the promoters of active genes.</small></p>
</div>
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<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-cuttag-a.png" width="800" /></center></div>
<div class="small-12 columns"><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-cuttag-b.png" width="800" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K4me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 0.5 µg of the Diagenode antibody against H3K4me3 (cat. No. C15410003) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions surrounding the FOS gene on chromosome 14 and the ACTB gene on chromosome 7 (figure 3A and B, respectively).</small></p>
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<div class="row">
<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig3-ELISA.jpg" width="350" /></center><center></center><center></center><center></center><center></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody against H3K4me3 (cat. No. C15410003). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:11,000.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig4-DB.jpg" /></div>
<div class="small-6 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K4me3</strong><br />To test the cross reactivity of the Diagenode antibody against H3K4me3 (cat. No. C15410003), a Dot Blot analysis was performed with peptides containing other histone modifications and the unmodified H3K4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 5A shows a high specificity of the antibody for the modification of interest.</small></p>
</div>
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<div class="row">
<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig5-WB.jpg" /></div>
<div class="small-8 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K4me3</strong><br />Western blot was performed on whole cell extracts (40 µg, lane 1) from HeLa cells, and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K4me3 (cat. No. C15410003). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig6-if.jpg" /></center></div>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K4me3</strong><br />HeLa cells were stained with the Diagenode antibody against H3K4me3 (cat. No. C15410003) and with DAPI. Cells were fixed with 4% formaldehyde for 20’ and blocked with PBS/TX-100 containing 5% normal goat serum. The cells were immunofluorescently labelled with the H3K4me3 antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa568 or with DAPI (middle), which specifically labels DNA. The right picture shows a merge of both stainings.</small></p>
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'meta_description' => 'H3K4me3 (Histone H3 trimethylated at lysine 4) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, CUT&Tag, ELISA, DB, WB and IF. Specificity confirmed by Peptide array. Batch-specific data available on the website. Sample size available.',
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'description' => '<p>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 27</strong> (<strong>H3K27me3</strong>), using a KLH-conjugated synthetic peptide.</p>',
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<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig1.png" alt="H3K27me3 Antibody ChIP Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2.png" alt="H3K27me3 Antibody for ChIP" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 1 million cells. The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation. A titration consisting of 0.5, 1, 2 and 5 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control.</small></p>
<p><small><strong>Figure 1A.</strong> Quantitative PCR was performed with primers specific for the promoter of the active GAPDH and EIF4A2 genes, used as negative controls, and for the inactive TSH2B and MYT1 genes, used as positive controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
<p><small><strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K27me1, H3K27me2, H3K27me3, H3K4me3, H3K9me3 and H3K36me3 modifications and the unmodified H3K27 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K27me3 modification.</small></p>
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<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2a.png" alt="H3K27me3 Antibody ChIP-seq Grade" /></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-12 columns">
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2b.png" alt="H3K27me3 Antibody for ChIP-seq" /></p>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2c.png" alt="H3K27me3 Antibody for ChIP-seq assay" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2d.png" alt="H3K27me3 Antibody validated in ChIP-seq" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP was performed on sheared chromatin from 1 million HeLa cells using 1 µg of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2 shows the enrichment in genomic regions of chromosome 6 and 20, surrounding the TSH2B and MYT1 positive control genes (fig 2A and 2B, respectively), and in two genomic regions of chromosome 1 and X (figure 2C and D).</small></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3A.png" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3B.png" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27me3 (cat. No. C15410195) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions on chromosome and 13 and 20 (figure 3A and B, respectively).</small></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-ELISA-Fig4.png" alt="H3K27me3 Antibody ELISA Validation " /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K27me3 (Cat. No. C15410195). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:3,000.</small></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
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<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-DB-Fig5a.png" alt="H3K27me3 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) with peptides containing other modifications of histone H3 and H4 and the unmodified H3K27 sequence. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:5,000. Figure 5 shows a high specificity of the antibody for the modification of interest. Please note that the antibody also recognizes the modification if S28 is phosphorylated.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-WB-Fig6.png" alt="H3K27me3 Antibody validated in Western Blot" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27me3</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27me3 (cat. No. C15410195) diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-IF-Fig7.png" alt="H3K27me3 Antibody validated for Immunofluorescence" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27me3</strong><br />Human HeLa cells were stained with the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K27me3 antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.</small></p>
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'meta_description' => 'H3K27me3 (Histone H3 trimethylated at lysine 27) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, CUT&Tag, ELISA, DB, WB and IF. Specificity confirmed by Peptide array assay. Batch-specific data available on the website. Sample size available.',
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'name' => 'H3K27ac Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the acetylated lysine 27</strong> (<strong>H3K27ac</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation Data',
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<div class="small-6 columns">A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1a.png" width="356" /><br /> B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1b.png" width="356" /></div>
<div class="small-6 columns">
<p><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>Figure 1A ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196) and optimized PCR primer pairs for qPCR. ChIP was performed with the “Auto Histone ChIP-seq” kit on the IP-Star automated system, using sheared chromatin from 1,000,000 cells. A titration consisting of 1, 2, 5 and 10 µg of antibody per ChIP experiment was analyzed. IgG (2 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active EIF4A2 and ACTB genes, used as positive controls, and for the inactive TSH2B and MYT1 genes, used as negative controls.</p>
<p>Figure 1B ChIP assays were performed using human K562 cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196)and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 100,000 cells. A titration consisting of 0.2, 0.5, 1 and 2 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active GAPDH and EIF4A2 genes, used as positive controls, and for the coding regions of the inactive MB and MYT1 genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis)</p>
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<div class="row">
<div class="small-12 columns"><center>
<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2a.png" /></p>
</center><center>
<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2b.png" /></p>
</center><center>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2c.png" /></p>
</center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>ChIP was performed on sheared chromatin from 100,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) as described above. The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A shows the peak distribution along the complete human X-chromosome. Figure 2 B and C show the peak distribution in two regions surrounding the EIF4A2 and GAPDH positive control genes, respectively. The position of the PCR amplicon, used for validating the ChIP assay is indicated with an arrow.</p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-fig3.jpg" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (cat. No. C15410196) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions surrounding the EIF2S3 gene on the X-chromosome and the CCT5 gene on chromosome 5 (figure 3A and B, respectively).</p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-ELISA-Fig3.png" /></div>
<div class="small-6 columns">
<p><strong>Figure 4. Determination of the antibody titer</strong></p>
<p>To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:8,300.</p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-DB-Fig4.png" /></center></div>
<div class="small-8 columns">
<p><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27ac</strong><br />To test the cross reactivity of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>), a Dot Blot analysis was performed with peptides containing other histone modifications and the unmodified H3K27. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 5 shows a high specificity of the antibody for the modification of interest.</p>
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<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-WB-Fig5.png" /></center></div>
<div class="small-8 columns">
<p><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27ac</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27ac (Cat. No. C1541196). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The marker (in kDa) is shown on the left.</p>
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<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-IF-Fig6.png" /></div>
<div class="small-8 columns">
<p><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27ac</strong></p>
<p>HeLa cells were stained with the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/ TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K27ac antibody (top) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown at the bottom.</p>
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<p>Learn more about: <a href="https://www.diagenode.com/applications/western-blot">Loading control, MW marker visualization</a><em>. <br /></em></p>
<p><em></em>Check our selection of antibodies validated in Western blot.</p>',
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<p><span style="font-weight: 400;">Diagenode provides leading solutions for epigenetic research. Because ChIP-seq is a widely-used technique, we validate our antibodies in ChIP and ChIP-seq experiments (in addition to conventional methods like Western blot, Dot blot, ELISA, and immunofluorescence) to provide the highest quality antibody. We standardize our validation and production to guarantee high product quality without technical bias. Diagenode guarantees ChIP-seq grade antibody performance under our suggested conditions.</span></p>
<div class="row">
<div class="small-12 medium-9 large-9 columns">
<p><strong>ChIP-seq profile</strong> of active (H3K4me3 and H3K36me3) and inactive (H3K27me3) marks using Diagenode antibodies.</p>
<img src="https://www.diagenode.com/img/categories/antibodies/chip-seq-grade-antibodies.png" /></div>
<div class="small-12 medium-3 large-3 columns">
<p><small> ChIP was performed on sheared chromatin from 100,000 K562 cells using iDeal ChIP-seq kit for Histones (cat. No. C01010051) with 1 µg of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 µg of the antibody against H3K36me3 (cat. No. C15410192). The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. The figure shows the signal distribution along the complete sequence of human chromosome 3, a zoomin to a 10 Mb region and a further zoomin to a 1.5 Mb region. </small></p>
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<p>Diagenode’s highly validated antibodies:</p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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'description' => '<p>Histones are the main protein components of chromatin involved in the compaction of DNA into nucleosomes, the basic units of chromatin. A <strong>nucleosome</strong> consists of one pair of each of the core histones (<strong>H2A</strong>, <strong>H2B</strong>, <strong>H3</strong> and <strong>H4</strong>) forming an octameric structure wrapped by 146 base pairs of DNA. The different nucleosomes are linked by the linker histone<strong> H1, </strong>allowing for further condensation of chromatin.</p>
<p>The core histones have a globular structure with large unstructured N-terminal tails protruding from the nucleosome. They can undergo to multiple post-translational modifications (PTM), mainly at the N-terminal tails. These <strong>post-translational modifications </strong>include methylation, acetylation, phosphorylation, ubiquitinylation, citrullination, sumoylation, deamination and crotonylation. The most well characterized PTMs are <strong>methylation,</strong> <strong>acetylation and phosphorylation</strong>. Histone methylation occurs mainly on lysine (K) residues, which can be mono-, di- or tri-methylated, and on arginines (R), which can be mono-methylated and symmetrically or asymmetrically di-methylated. Histone acetylation occurs on lysines and histone phosphorylation mainly on serines (S), threonines (T) and tyrosines (Y).</p>
<p>The PTMs of the different residues are involved in numerous processes such as DNA repair, DNA replication and chromosome condensation. They influence the chromatin organization and can be positively or negatively associated with gene expression. Trimethylation of H3K4, H3K36 and H3K79, and lysine acetylation generally result in an open chromatin configuration (figure below) and are therefore associated with <strong>euchromatin</strong> and gene activation. Trimethylation of H3K9, K3K27 and H4K20, on the other hand, is enriched in <strong>heterochromatin </strong>and associated with gene silencing. The combination of different histone modifications is called the "<strong>histone code</strong>”, analogous to the genetic code.</p>
<p><img src="https://www.diagenode.com/img/categories/antibodies/histone-marks-illustration.png" /></p>
<p>Diagenode is proud to offer a large range of antibodies against histones and histone modifications. Our antibodies are highly specific and have been validated in many applications, including <strong>ChIP</strong> and <strong>ChIP-seq</strong>.</p>
<p>Diagenode’s collection includes antibodies recognizing:</p>
<ul>
<li><strong>Histone H1 variants</strong></li>
<li><strong>Histone H2A, H2A variants and histone H2A</strong> <strong>modifications</strong> (serine phosphorylation, lysine acetylation, lysine ubiquitinylation)</li>
<li><strong>Histone H2B and H2B</strong> <strong>modifications </strong>(serine phosphorylation, lysine acetylation)</li>
<li><strong>Histone H3 and H3 modifications </strong>(lysine methylation (mono-, di- and tri-methylated), lysine acetylation, serine phosphorylation, threonine phosphorylation, arginine methylation (mono-methylated, symmetrically and asymmetrically di-methylated))</li>
<li><strong>Histone H4 and H4 modifications (</strong>lysine methylation (mono-, di- and tri-methylated), lysine acetylation, arginine methylation (mono-methylated and symmetrically di-methylated), serine phosphorylation )</li>
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<p><span style="font-weight: 400;"><strong>HDAC's HAT's, HMT's and other</strong> <strong>enzymes</strong> which modify histones can be found in the category <a href="../categories/chromatin-modifying-proteins-histone-transferase">Histone modifying enzymes</a><br /></span></p>
<p><span style="font-weight: 400;"> Diagenode’s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> Expert technical support</span></li>
<li><span style="font-weight: 400;"> Sample sizes available</span></li>
<li><span style="font-weight: 400;"> 100% satisfaction guarantee</span></li>
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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
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<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
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<div class="small-12 medium-6 large-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" alt="" width="400" height="315" /> </div>
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<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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'description' => '<p>Cancers often display immune escape, but the mechanisms are incompletely understood. Herein, we identify SMYD3 as a mediator of immune escape in human papilloma virus (HPV)-negative head and neck squamous cell carcinoma (HNSCC), an aggressive disease with poor response to immunotherapy with pembrolizumab. SMYD3 depletion induces upregulation of multiple type I interferon (IFN) response and antigen presentation machinery genes in HNSCC cells. Mechanistically, SMYD3 binds to and regulates the transcription of UHRF1, encoding for a reader of H3K9me3, which binds to H3K9me3-enriched promoters of key immune-related genes, recruits DNMT1, and silences their expression. SMYD3 further maintains the repression of immune-related genes through intragenic deposition of H4K20me3. In vivo, Smyd3 depletion induces influx of CD8 T cells and increases sensitivity to anti-programmed death 1 (PD-1) therapy. SMYD3 overexpression is associated with decreased CD8 T cell infiltration and poor response to neoadjuvant pembrolizumab. These data support combining SMYD3 depletion strategies with checkpoint blockade to overcome anti-PD-1 resistance in HPV-negative HNSCC.</p>',
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'pmid' => 'https://doi.org/10.1016%2Fj.isci.2023.106795',
'doi' => '10.1016/j.isci.2023.106795',
'modified' => '2023-06-19 10:14:27',
'created' => '2023-06-13 21:11:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'id' => '4605',
'name' => 'Gene Regulatory Interactions at Lamina-Associated Domains',
'authors' => 'Madsen-Østerbye J. et al.',
'description' => '<p>The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are inactive, over ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to interact with regulatory elements remain unclear. Here, we integrate publicly available enhancer-capture Hi-C data with our own chromatin state and transcriptomic datasets to show that inferred enhancers of active genes in LADs are able to form connections with other enhancers within LADs and outside LADs. Fluorescence in situ hybridization analyses show proximity changes between differentially expressed genes in LADs and distant enhancers upon the induction of adipogenic differentiation. We also provide evidence of involvement of lamin A/C, but not lamin B1, in repressing genes at the border of an in-LAD active region within a topological domain. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with gene expression in this dynamic nuclear compartment.</p>',
'date' => '2023-01-01',
'pmid' => 'https://doi.org/10.3390%2Fgenes14020334',
'doi' => '10.3390/genes14020334',
'modified' => '2023-04-04 08:57:32',
'created' => '2023-02-21 09:59:46',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'id' => '4566',
'name' => 'Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing.',
'authors' => 'O'Geen H.et al.',
'description' => '<p>Precision epigenome editing has gained significant attention as a method to modulate gene expression without altering genetic information. However, a major limiting factor has been that the gene expression changes are often transient, unlike the life-long epigenetic changes that occur frequently in nature. Here, we systematically interrogate the ability of CRISPR/dCas9-based epigenome editors (Epi-dCas9) to engineer persistent epigenetic silencing. We elucidated cis regulatory features that contribute to the differential stability of epigenetic reprogramming, such as the active transcription histone marks H3K36me3 and H3K27ac strongly correlating with resistance to short-term repression and resistance to long-term silencing, respectively. H3K27ac inversely correlates with increased DNA methylation. Interestingly, the dependance on H3K27ac was only observed when a combination of KRAB-dCas9 and targetable DNA methyltransferases (DNMT3A-dCas9 + DNMT3L) was used, but not when KRAB was replaced with the targetable H3K27 histone methyltransferase Ezh2. In addition, programmable Ezh2/DNMT3A + L treatment demonstrated enhanced engineering of localized DNA methylation and was not sensitive to a divergent chromatin state. Our results highlight the importance of local chromatin features for heritability of programmable silencing and the differential response to KRAB- and Ezh2-based epigenetic editing platforms. The information gained in this study provides fundamental insights into understanding contextual cues to more predictably engineer persistent silencing.</p>',
'date' => '2022-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35234927',
'doi' => '10.1093/nar/gkac123',
'modified' => '2022-11-24 09:26:11',
'created' => '2022-11-24 08:49:52',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'id' => '4292',
'name' => 'The prolyl-isomerase PIN1 is essential for nuclear Lamin-Bstructure and function and protects heterochromatin under mechanicalstress.',
'authors' => 'Napoletano Francesco et al.',
'description' => '<p>Chromatin organization plays a crucial role in tissue homeostasis. Heterochromatin relaxation and consequent unscheduled mobilization of transposable elements (TEs) are emerging as key contributors of aging and aging-related pathologies, including Alzheimer's disease (AD) and cancer. However, the mechanisms governing heterochromatin maintenance or its relaxation in pathological conditions remain poorly understood. Here we show that PIN1, the only phosphorylation-specific cis/trans prolyl isomerase, whose loss is associated with premature aging and AD, is essential to preserve heterochromatin. We demonstrate that this PIN1 function is conserved from Drosophila to humans and prevents TE mobilization-dependent neurodegeneration and cognitive defects. Mechanistically, PIN1 maintains nuclear type-B Lamin structure and anchoring function for heterochromatin protein 1α (HP1α). This mechanism prevents nuclear envelope alterations and heterochromatin relaxation under mechanical stress, which is a key contributor to aging-related pathologies.</p>',
'date' => '2021-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34525372',
'doi' => '10.1016/j.celrep.2021.109694',
'modified' => '2022-05-24 09:18:40',
'created' => '2022-05-19 10:41:50',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '4174',
'name' => 'Dynamic association of the H3K64 trimethylation mark with genes encodingexported proteins in Plasmodium falciparum.',
'authors' => 'Jabeena, C A et al.',
'description' => '<p>Epigenetic modifications have emerged as critical regulators of virulence genes and stage-specific gene expression in Plasmodium falciparum. However, the specific roles of histone core epigenetic modifications in regulating the stage-specific gene expression are not well understood. In this study, we report an unconventional trimethylation at lysine 64 on histone 3 (H3K64me3) and characterize its functional relevance in P. falciparum. We show that PfSET4 and PfSET5 proteins of P. falciparum methylate H3K64 and that they prefer the nucleosome as a substrate over free histone 3 proteins. Structural analysis of PfSET5 revealed that it interacts with the nucleosome as a dimer. The H3K64me3 mark is dynamic, being enriched in the ring and trophozoite stages and drastically reduced in schizont stages. Stage-specific global ChIP-sequencing analysis of the H3K64me3 mark revealed the selective enrichment of this methyl mark on the genes of exported family proteins in the ring and trophozoite stages, and a significant reduction of the same in the schizont stages. Collectively, our data identify a novel epigenetic mark that are associated with the subset of genes encoding for exported proteins which may regulate their expression in different stages of P. falciparum.</p>',
'date' => '2021-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33839154',
'doi' => '10.1016/j.jbc.2021.100614',
'modified' => '2021-12-21 16:07:05',
'created' => '2021-12-06 15:53:19',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'id' => '4149',
'name' => 'Restricted nucleation and piRNA-mediated establishment of heterochromatinduring embryogenesis in Drosophila miranda',
'authors' => 'Wei, K. et al.',
'description' => '<p>Heterochromatin is a key architectural feature of eukaryotic genomes, crucial for silencing of repetitive elements and maintaining genome stability. Heterochromatin shows stereotypical enrichment patterns around centromeres and repetitive sequences, but the molecular details of how heterochromatin is established during embryogenesis are poorly understood. Here, we map the genome-wide distribution of H3K9me3-dependent heterochromatin in individual embryos of D. miranda at precisely staged developmental time points. We find that canonical H3K9me3 enrichment patterns are established early on before cellularization, and mature into stable and broad heterochromatin domains through development. Intriguingly, initial nucleation sites of H3K9me3 enrichment appear as early as embryonic stage3 (nuclear cycle 9) over transposable elements (TE) and progressively broaden, consistent with spreading to neighboring nucleosomes. The earliest nucleation sites are limited to specific regions of a small number of TE families and often appear over promoter regions, while late nucleation develops broadly across most TEs. Early nucleating TEs are highly targeted by maternal piRNAs and show early zygotic transcription, consistent with a model of co-transcriptional silencing of TEs by small RNAs. Interestingly, truncated TE insertions lacking nucleation sites show significantly reduced enrichment across development, suggesting that the underlying sequences play an important role in recruiting histone methyltransferases for heterochromatin</p>',
'date' => '2021-02-01',
'pmid' => 'https://doi.org/10.1101%2F2021.02.16.431328',
'doi' => '10.1101/2021.02.16.431328',
'modified' => '2021-12-14 09:28:27',
'created' => '2021-12-06 15:53:19',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'id' => '3995',
'name' => 'Epigenetic, transcriptional and phenotypic responses in Daphnia magna exposed to low-level ionizing radiation',
'authors' => 'Thaulow Jens, Song You, Lindeman Leif C., Kamstra Jorke H., Lee YeonKyeong, Xie Li, Aleström Peter, Salbu Brit, Tollefsen Knut Erik',
'description' => '<p>Ionizing radiation is known to induce oxidative stress and DNA damage as well as epigenetic effects in aquatic organisms. Epigenetic changes can be part of the adaptive responses to protect organisms from radiation-induced damage, or act as drivers of toxicity pathways leading to adverse effects. To investigate the potential roles of epigenetic mechanisms in low-dose ionizing radiation-induced stress responses, an ecologically relevant crustacean, adult Daphnia magna were chronically exposed to low and medium level external 60Co gamma radiation ranging from 0.4, 1, 4, 10, and 40 mGy/h for seven days. Biological effects at the molecular (global DNA methylation, histone modification, gene expression), cellular (reactive oxygen species formation), tissue/organ (ovary, gut and epidermal histology) and organismal (fecundity) levels were investigated using a suite of effect assessment tools. The results showed an increase in global DNA methylation associated with loci-specific alterations of histone H3K9 methylation and acetylation, and downregulation of genes involved in DNA methylation, one-carbon metabolism, antioxidant defense, DNA repair, apoptosis, calcium signaling and endocrine regulation of development and reproduction. Temporal changes of reactive oxygen species (ROS) formation were also observed with an apparent transition from ROS suppression to induction from 2-7 days after gamma exposure. The cumulative fecundity, however, was not significantly changed by the gamma exposure. On the basis of the new experimental evidence and existing knowledge, a hypothetical model was proposed to provide in-depth mechanistic understanding of the roles of epigenetic mechanisms in low dose ionizing radiation induced stress responses in D. magna.</p>',
'date' => '2020-07-18',
'pmid' => 'https://www.sciencedirect.com/science/article/pii/S0013935120308252',
'doi' => '10.1016/j.envres.2020.109930',
'modified' => '2020-09-01 14:51:16',
'created' => '2020-08-21 16:41:39',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 8 => array(
'id' => '3964',
'name' => 'The 20S proteasome activator PA28γ controls the compaction of chromatin',
'authors' => 'Didier Fesquet, David Llères, Cristina Viganò, Francisca Méchali, Séverine Boulon, Robert Feil, Olivier Coux, Catherine Bonne-Andrea, Véronique Baldin',
'description' => '<p>The nuclear PA28γ is known to activate the 20S proteasome, but its precise cellular functions remains unclear. Here, we identify PA28γ as a key factor that structures heterochromatin. We find that in human cells, a fraction of PA28γ-20S proteasome complexes localizes within HP1-linked heterochromatin foci. Our biochemical studies show that PA28γ interacts with HP1 proteins, particularly HP1β, which recruits the PA28γ-20S proteasome complexes to heterochromatin. Loss of PA28γ does not modify the localization of HP1β, its mobility within nuclear foci, or the level of H3K9 tri-methylation, but reduces H4K20 mono- and tri-methylation, modifications involved in heterochromatin establishment. Concordantly, using a quantitative FRET-based microscopy assay to monitor nanometer-scale proximity between nucleosomes in living cells, we find that PA28γ regulates nucleosome proximity within heterochromatin, and thereby controls its compaction. This function of PA28γ is independent of the 20S proteasome. Importantly, HP1β on its own is unable to drive heterochromatin compaction without PA28γ. Combined, our data reveal an unexpected chromatin structural role of PA28γ, and provide new insights into the mechanism that controls HP1β-mediated heterochromatin compaction.</p>',
'date' => '2020-05-28',
'pmid' => 'https://www.biorxiv.org/content/10.1101/716332v1.article-info',
'doi' => 'https://doi.org/10.1101/716332',
'modified' => '2020-08-12 09:44:09',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'id' => '3965',
'name' => 'Histone post-translational modifications in Silene latifolia X and Y chromosomes suggest a mammal-like dosage compensation system',
'authors' => 'Luis Rodríguez Lorenzo José, Hubinský Marcel, Vyskot Boris, Hobza Roman',
'description' => '<p>Silene latifolia is a model organism to study evolutionary young heteromorphic sex chromosome evolution in plants. Previous research indicates a Y-allele gene degeneration and a dosage compensation system already operating. Here, we propose an epigenetic approach based on analysis of several histone post-translational modifications (PTMs) to find the first epigenetic hints of the X:Y sex chromosome system regulation in S. latifolia. Through chromatin immunoprecipitation we interrogated six genes from X and Y alleles. Several histone PTMS linked to DNA methylation and transcriptional repression (H3K27me3, H3K23me, H3K9me2 and H3K9me3) and to transcriptional activation (H3K4me3 and H4K5, 8, 12, 16ac) were used. DNA enrichment (Immunoprecipitated DNA/input DNA) was analyzed and showed three main results: i) promoters of the Y allele are associated with heterochromatin marks, ii) promoters of the X allele in males are associated with activation of transcription marks and finally, iii) promoters of X alleles in females are associated with active and repressive marks. Our finding indicates a transcription activation of X allele and transcription repression of Y allele in males. In females we found a possible differential regulation (up X1, down X2) of each female X allele. These results agree with the mammal-like epigenetic dosage compensation regulation.</p>',
'date' => '2020-05-24',
'pmid' => 'https://www.sciencedirect.com/science/article/abs/pii/S0168945220301333',
'doi' => '10.1016/j.plantsci.2020.110528',
'modified' => '2020-08-12 09:42:21',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 10 => array(
'id' => '3943',
'name' => 'SETDB2 promoted breast cancer stem cell maintenance by interaction with and stabilization of ΔNp63α protein',
'authors' => 'Ying Liu, Fei Xie, Jialun Li, Jianpeng Xiao, Jie Wang, Zhaolin Mei, Hongjia Fan, Huan Fang, Sha Li, Qiuju Wu, Lin Yuan, Cuicui Liu, You Peng, Weiwei Zhao, Lulu Wang, Jiemin Wong, Jing Li, Jing Feng',
'description' => '<p>The histone H3K9 methyltransferase SETDB2 is involved in cell cycle dysregulation in acute leukemia and has oncogenic roles in gastric cancer. In our study, we found that SETDB2 plays essential roles in breast cancer stem cell maintenance. Depleted SETDB2 significantly decreased the breast cancer stem cell population and mammosphere formation in vitro and also inhibited breast tumor initiation and growth in vivo. Restoring SETDB2 expression rescued the defect in breast cancer stem cell maintenance. A mechanistic analysis showed that SETDB2 upregulated the transcription of the ΔNp63α downstream Hedgehog pathway gene. SETDB2 also interacted with and methylated ΔNp63α, and stabilized ΔNp63α protein. Restoring ΔNp63α expression rescued the breast cancer stem cell maintenance defect which mediated by SETDB2 knockdown. In conclusion, our study reveals a novel function of SETDB2 in cancer stem cell maintenance in breast cancer.</p>',
'date' => '2020-04-28',
'pmid' => 'https://www.ijbs.com/v16p2180',
'doi' => '10.7150/ijbs.43611',
'modified' => '2020-08-17 10:17:33',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 11 => array(
'id' => '3762',
'name' => 'Transit amplifying cells coordinate mouse incisor mesenchymal stem cell activation.',
'authors' => 'Walker JV, Zhuang H, Singer D, Illsley CS, Kok WL, Sivaraj KK, Gao Y, Bolton C, Liu Y, Zhao M, Grayson PRC, Wang S, Karbanová J, Lee T, Ardu S, Lai Q, Liu J, Kassem M, Chen S, Yang K, Bai Y, Tredwin C, Zambon AC, Corbeil D, Adams R, Abdallah BM, Hu B',
'description' => '<p>Stem cells (SCs) receive inductive cues from the surrounding microenvironment and cells. Limited molecular evidence has connected tissue-specific mesenchymal stem cells (MSCs) with mesenchymal transit amplifying cells (MTACs). Using mouse incisor as the model, we discover a population of MSCs neibouring to the MTACs and epithelial SCs. With Notch signaling as the key regulator, we disclose molecular proof and lineage tracing evidence showing the distinct MSCs contribute to incisor MTACs and the other mesenchymal cell lineages. MTACs can feedback and regulate the homeostasis and activation of CL-MSCs through Delta-like 1 homolog (Dlk1), which balances MSCs-MTACs number and the lineage differentiation. Dlk1's function on SCs priming and self-renewal depends on its biological forms and its gene expression is under dynamic epigenetic control. Our findings can be validated in clinical samples and applied to accelerate tooth wound healing, providing an intriguing insight of how to direct SCs towards tissue regeneration.</p>',
'date' => '2019-08-09',
'pmid' => 'http://www.pubmed.gov/31399601',
'doi' => '10.1038/s41467-019-11611-0',
'modified' => '2019-10-03 10:03:31',
'created' => '2019-10-02 16:16:55',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 12 => array(
'id' => '3715',
'name' => 'Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner.',
'authors' => 'O'Geen H, Bates SL, Carter SS, Nisson KA, Halmai J, Fink KD, Rhie SK, Farnham PJ, Segal DJ',
'description' => '<p>BACKGROUND: Rewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve in a predictable manner using targeted systems. RESULTS: Here, we report that persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). We demonstrate that the histone methyltransferase requirement can be locus specific. Co-targeting Ezh2-dCas9, but not KRAB-dCas9, with DNMT3A-dCas9 and DNMT3L induced long-term HER2 repression over at least 50 days (approximately 57 cell divisions) and triggered an epigenetic switch to a heterochromatic environment. An increase in H3K27 trimethylation and DNA methylation was stably maintained and accompanied by a sustained loss of H3K27 acetylation. Interestingly, substitution of Ezh2-dCas9 with KRAB-dCas9 enabled long-term repression at some target genes (e.g., SNURF) but not at HER2, at which H3K9me3 and DNA methylation were transiently acquired and subsequently lost. Off-target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the off-target loci tested. Conversely, robust hypermethylation was observed at HER2. We further demonstrated that Ezh2-dCas9 required full-length DNMT3L for maximal activity and that co-targeting DNMT3L was sufficient for persistent repression by Ezh2-dCas9 or KRAB-dCas9. CONCLUSIONS: These data demonstrate that targeting different combinations of histone and DNA methyltransferases is required to achieve maximal repression at different loci. Fine-tuning of targeting tools is a necessity to engineer epigenetic memory at any given locus in any given cell type.</p>',
'date' => '2019-05-03',
'pmid' => 'http://www.pubmed.gov/31053162',
'doi' => '10.1186/s13072-019-0275-8',
'modified' => '2019-07-05 13:15:49',
'created' => '2019-07-04 10:42:34',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 13 => array(
'id' => '3709',
'name' => 'Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation.',
'authors' => 'Paulsen J, Liyakat Ali TM, Nekrasov M, Delbarre E, Baudement MO, Kurscheid S, Tremethick D, Collas P',
'description' => '<p>Genomic information is selectively used to direct spatial and temporal gene expression during differentiation. Interactions between topologically associating domains (TADs) and between chromatin and the nuclear lamina organize and position chromosomes in the nucleus. However, how these genomic organizers together shape genome architecture is unclear. Here, using a dual-lineage differentiation system, we report long-range TAD-TAD interactions that form constitutive and variable TAD cliques. A differentiation-coupled relationship between TAD cliques and lamina-associated domains suggests that TAD cliques stabilize heterochromatin at the nuclear periphery. We also provide evidence of dynamic TAD cliques during mouse embryonic stem-cell differentiation and somatic cell reprogramming and of inter-TAD associations in single-cell high-resolution chromosome conformation capture (Hi-C) data. TAD cliques represent a level of four-dimensional genome conformation that reinforces the silencing of repressed developmental genes.</p>',
'date' => '2019-05-01',
'pmid' => 'http://www.pubmed.gov/31011212',
'doi' => '10.1038/s41588-019-0392-0',
'modified' => '2019-07-05 14:33:38',
'created' => '2019-07-04 10:42:34',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 14 => array(
'id' => '3692',
'name' => 'PML modulates H3.3 targeting to telomeric and centromeric repeats in mouse fibroblasts.',
'authors' => 'Spirkoski J, Shah A, Reiner AH, Collas P, Delbarre E',
'description' => '<p>Targeted deposition of histone variant H3.3 into chromatin is paramount for proper regulation of chromatin integrity, particularly in heterochromatic regions including repeats. We have recently shown that the promyelocytic leukemia (PML) protein prevents H3.3 from being deposited in large heterochromatic PML-associated domains (PADs). However, to what extent PML modulates H3.3 loading on chromatin in other areas of the genome remains unexplored. Here, we examined the impact of PML on targeting of H3.3 to genes and repeat regions that reside outside PADs. We show that loss of PML increases H3.3 deposition in subtelomeric, telomeric, pericentric and centromeric repeats in mouse embryonic fibroblasts, while other repeat classes are not affected. Expression of major satellite, minor satellite and telomeric non-coding transcripts is altered in Pml-null cells. In particular, telomeric Terra transcripts are strongly upregulated, in concordance with a marked reduction in H4K20me3 at these sites. Lastly, for most genes H3.3 enrichment or gene expression outcomes are independent of PML. Our data argue towards the importance of a PML-H3.3 axis in preserving a heterochromatin state at centromeres and telomeres.</p>',
'date' => '2019-04-16',
'pmid' => 'http://www.pubmed.gov/30850162',
'doi' => '10.1016/j.bbrc.2019.02.087',
'modified' => '2019-06-28 13:50:40',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 15 => array(
'id' => '3644',
'name' => 'Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs.',
'authors' => 'Pontis J, Planet E, Offner S, Turelli P, Duc J, Coudray A, Theunissen TW, Jaenisch R, Trono D',
'description' => '<p>Expansion of transposable elements (TEs) coincides with evolutionary shifts in gene expression. TEs frequently harbor binding sites for transcriptional regulators, thus enabling coordinated genome-wide activation of species- and context-specific gene expression programs, but such regulation must be balanced against their genotoxic potential. Here, we show that Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) control the timely and pleiotropic activation of TE-derived transcriptional cis regulators during early embryogenesis. Evolutionarily recent SVA, HERVK, and HERVH TE subgroups contribute significantly to chromatin opening during human embryonic genome activation and are KLF-stimulated enhancers in naive human embryonic stem cells (hESCs). KZFPs of corresponding evolutionary ages are simultaneously induced and repress the transcriptional activity of these TEs. Finally, the same KZFP-controlled TE-based enhancers later serve as developmental and tissue-specific enhancers. Thus, by controlling the transcriptional impact of TEs during embryogenesis, KZFPs facilitate their genome-wide incorporation into transcriptional networks, thereby contributing to human genome regulation.</p>',
'date' => '2019-03-27',
'pmid' => 'http://www.pubmed.gov/31006620',
'doi' => '10.1016/j.stem.2019.03.012',
'modified' => '2019-06-07 10:16:36',
'created' => '2019-06-06 12:11:18',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 16 => array(
'id' => '3686',
'name' => 'Gamma radiation induces locus specific changes to histone modification enrichment in zebrafish and Atlantic salmon.',
'authors' => 'Lindeman LC, Kamstra JH, Ballangby J, Hurem S, Martín LM, Brede DA, Teien HC, Oughton DH, Salbu B, Lyche JL, Aleström P',
'description' => '<p>Ionizing radiation is a recognized genotoxic agent, however, little is known about the role of the functional form of DNA in these processes. Post translational modifications on histone proteins control the organization of chromatin and hence control transcriptional responses that ultimately affect the phenotype. The purpose of this study was to investigate effects on chromatin caused by ionizing radiation in fish. Direct exposure of zebrafish (Danio rerio) embryos to gamma radiation (10.9 mGy/h for 3h) induced hyper-enrichment of H3K4me3 at the genes hnf4a, gmnn and vegfab. A similar relative hyper-enrichment was seen at the hnf4a loci of irradiated Atlantic salmon (Salmo salar) embryos (30 mGy/h for 10 days). At the selected genes in ovaries of adult zebrafish irradiated during gametogenesis (8.7 and 53 mGy/h for 27 days), a reduced enrichment of H3K4me3 was observed, which was correlated with reduced levels of histone H3 was observed. F1 embryos of the exposed parents showed hyper-methylation of H3K4me3, H3K9me3 and H3K27me3 on the same three loci, while these differences were almost negligible in F2 embryos. Our results from three selected loci suggest that ionizing radiation can affect chromatin structure and organization, and that these changes can be detected in F1 offspring, but not in subsequent generations.</p>',
'date' => '2019-01-01',
'pmid' => 'http://www.pubmed.gov/30759148',
'doi' => '10.1371/journal.pone.0212123',
'modified' => '2019-06-28 13:57:39',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 17 => array(
'id' => '3635',
'name' => 'TIP60: an actor in acetylation of H3K4 and tumor development in breast cancer.',
'authors' => 'Judes G, Dubois L, Rifaï K, Idrissou M, Mishellany F, Pajon A, Besse S, Daures M, Degoul F, Bignon YJ, Penault-Llorca F, Bernard-Gallon D',
'description' => '<p>AIM: The acetyltransferase TIP60 is reported to be downregulated in several cancers, in particular breast cancer, but the molecular mechanisms resulting from its alteration are still unclear. MATERIALS & METHODS: In breast tumors, H3K4ac enrichment and its link with TIP60 were evaluated by chromatin immunoprecipitation-qPCR and re-chromatin immunoprecipitation techniques. To assess the biological roles of TIP60 in breast cancer, two cell lines of breast cancer, MDA-MB-231 (ER-) and MCF-7 (ER+) were transfected with shRNA specifically targeting TIP60 and injected to athymic Balb-c mice. RESULTS: We identified a potential target of TIP60, H3K4. We show that an underexpression of TIP60 could contribute to a reduction of H3K4 acetylation in breast cancer. An increase in tumor development was noted in sh-TIP60 MDA-MB-231 xenografts and a slowdown of tumor growth in sh-TIP60 MCF-7 xenografts. CONCLUSION: This is evidence that the underexpression of TIP60 observed in breast cancer can promote the tumorigenesis of ER-negative tumors.</p>',
'date' => '2018-11-01',
'pmid' => 'http://www.pubmed.gov/30324811',
'doi' => '10.2217/epi-2018-0004',
'modified' => '2019-06-07 10:29:04',
'created' => '2019-06-06 12:11:18',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 18 => array(
'id' => '3556',
'name' => 'PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex.',
'authors' => 'Link S, Spitzer RMM, Sana M, Torrado M, Völker-Albert MC, Keilhauer EC, Burgold T, Pünzeler S, Low JKK, Lindström I, Nist A, Regnard C, Stiewe T, Hendrich B, Imhof A, Mann M, Mackay JP, Bartkuhn M, Hake SB',
'description' => '<p>Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified that PWWP2A tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial-facial development. Here, using in vitro assays, we show that distinct domains of PWWP2A mediate binding to free linker DNA as well as H3K36me3 nucleosomes. In vivo, PWWP2A strongly recognizes H2A.Z-containing regulatory regions and weakly binds H3K36me3-containing gene bodies. Further, PWWP2A binds to an MTA1-specific subcomplex of the NuRD complex (M1HR), which consists solely of MTA1, HDAC1, and RBBP4/7, and excludes CHD, GATAD2 and MBD proteins. Depletion of PWWP2A leads to an increase of acetylation levels on H3K27 as well as H2A.Z, presumably by impaired chromatin recruitment of M1HR. Thus, this study identifies PWWP2A as a complex chromatin-binding protein that serves to direct the deacetylase complex M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels.</p>',
'date' => '2018-10-16',
'pmid' => 'http://www.pubmed.gov/30327463',
'doi' => '10.1038/s41467-018-06665-5',
'modified' => '2019-07-22 09:17:39',
'created' => '2019-03-21 14:12:08',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 19 => array(
'id' => '3551',
'name' => 'HIV-2/SIV viral protein X counteracts HUSH repressor complex.',
'authors' => 'Ghina Chougui, Soundasse Munir-Matloob, Roy Matkovic, Michaël M Martin, Marina Morel, Hichem Lahouassa, Marjorie Leduc, Bertha Cecilia Ramirez, Lucie Etienne and Florence Margottin-Goguet',
'description' => '<p>To evade host immune defences, human immunodeficiency viruses 1 and 2 (HIV-1 and HIV-2) have evolved auxiliary proteins that target cell restriction factors. Viral protein X (Vpx) from the HIV-2/SIVsmm lineage enhances viral infection by antagonizing SAMHD1 (refs ), but this antagonism is not sufficient to explain all Vpx phenotypes. Here, through a proteomic screen, we identified another Vpx target-HUSH (TASOR, MPP8 and periphilin)-a complex involved in position-effect variegation. HUSH downregulation by Vpx is observed in primary cells and HIV-2-infected cells. Vpx binds HUSH and induces its proteasomal degradation through the recruitment of the DCAF1 ubiquitin ligase adaptor, independently from SAMHD1 antagonism. As a consequence, Vpx is able to reactivate HIV latent proviruses, unlike Vpx mutants, which are unable to induce HUSH degradation. Although antagonism of human HUSH is not conserved among all lentiviral lineages including HIV-1, it is a feature of viral protein R (Vpr) from simian immunodeficiency viruses (SIVs) of African green monkeys and from the divergent SIV of l'Hoest's monkey, arguing in favour of an ancient lentiviral species-specific vpx/vpr gene function. Altogether, our results suggest the HUSH complex as a restriction factor, active in primary CD4 T cells and counteracted by Vpx, therefore providing a molecular link between intrinsic immunity and epigenetic control.</p>',
'date' => '2018-08-01',
'pmid' => 'http://www.pubmed.gov/29891865',
'doi' => '10.1038/s41564-018-0179-6',
'modified' => '2019-02-28 10:20:23',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 20 => array(
'id' => '3470',
'name' => 'Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes.',
'authors' => 'Lomberk G, Blum Y, Nicolle R, Nair A, Gaonkar KS, Marisa L, Mathison A, Sun Z, Yan H, Elarouci N, Armenoult L, Ayadi M, Ordog T, Lee JH, Oliver G, Klee E, Moutardier V, Gayet O, Bian B, Duconseil P, Gilabert M, Bigonnet M, Garcia S, Turrini O, Delpero JR,',
'description' => '<p>Recent studies have offered ample insight into genome-wide expression patterns to define pancreatic ductal adenocarcinoma (PDAC) subtypes, although there remains a lack of knowledge regarding the underlying epigenomics of PDAC. Here we perform multi-parametric integrative analyses of chromatin immunoprecipitation-sequencing (ChIP-seq) on multiple histone modifications, RNA-sequencing (RNA-seq), and DNA methylation to define epigenomic landscapes for PDAC subtypes, which can predict their relative aggressiveness and survival. Moreover, we describe the state of promoters, enhancers, super-enhancers, euchromatic, and heterochromatic regions for each subtype. Further analyses indicate that the distinct epigenomic landscapes are regulated by different membrane-to-nucleus pathways. Inactivation of a basal-specific super-enhancer associated pathway reveals the existence of plasticity between subtypes. Thus, our study provides new insight into the epigenetic landscapes associated with the heterogeneity of PDAC, thereby increasing our mechanistic understanding of this disease, as well as offering potential new markers and therapeutic targets.</p>',
'date' => '2018-05-17',
'pmid' => 'http://www.pubmed.gov/29773832',
'doi' => '10.1038/s41467-018-04383-6',
'modified' => '2019-02-15 21:08:07',
'created' => '2019-02-14 15:01:22',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 21 => array(
'id' => '3536',
'name' => 'PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites.',
'authors' => 'Diagouraga B, Clément JAJ, Duret L, Kadlec J, de Massy B, Baudat F',
'description' => '<p>The programmed formation of hundreds of DNA double-strand breaks (DSBs) is essential for proper meiosis and fertility. In mice and humans, the location of these breaks is determined by the meiosis-specific protein PRDM9, through the DNA-binding specificity of its zinc-finger domain. PRDM9 also has methyltransferase activity. Here, we show that this activity is required for H3K4me3 and H3K36me3 deposition and for DSB formation at PRDM9-binding sites. By analyzing mice that express two PRDM9 variants with distinct DNA-binding specificities, we show that each variant generates its own set of H3K4me3 marks independently from the other variant. Altogether, we reveal several basic principles of PRDM9-dependent DSB site determination, in which an excess of sites are designated through PRDM9 binding and subsequent histone methylation, from which a subset is selected for DSB formation.</p>',
'date' => '2018-03-01',
'pmid' => 'http://www.pubmed.gov/29478809',
'doi' => '10.1016/j.molcel.2018.01.033',
'modified' => '2019-02-28 10:51:44',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 22 => array(
'id' => '3276',
'name' => 'DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease',
'authors' => 'Jeziorska D.M. et al.',
'description' => '<p>The human genome contains ∼30,000 CpG islands (CGIs). While CGIs associated with promoters nearly always remain unmethylated, many of the ∼9,000 CGIs lying within gene bodies become methylated during development and differentiation. Both promoter and intragenic CGIs may also become abnormally methylated as a result of genome rearrangements and in malignancy. The epigenetic mechanisms by which some CGIs become methylated but others, in the same cell, remain unmethylated in these situations are poorly understood. Analyzing specific loci and using a genome-wide analysis, we show that transcription running across CGIs, associated with specific chromatin modifications, is required for DNA methyltransferase 3B (DNMT3B)-mediated DNA methylation of many naturally occurring intragenic CGIs. Importantly, we also show that a subgroup of intragenic CGIs is not sensitive to this process of transcription-mediated methylation and that this correlates with their individual intrinsic capacity to initiate transcription in vivo. We propose a general model of how transcription could act as a primary determinant of the patterns of CGI methylation in normal development and differentiation, and in human disease.</p>',
'date' => '2017-09-05',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28827334',
'doi' => '',
'modified' => '2017-10-16 10:16:06',
'created' => '2017-10-16 10:16:06',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 23 => array(
'id' => '3240',
'name' => 'Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation',
'authors' => 'Pünzeler S. et al.',
'description' => '<p>Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA-based processes via poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel H2A.Z-nucleosome binder. PWWP2A is a functionally uncharacterized, vertebrate-specific protein that binds very tightly to chromatin through a concerted multivalent binding mode. Two internal protein regions mediate H2A.Z-specificity and nucleosome interaction, whereas the PWWP domain exhibits direct DNA binding. Genome-wide mapping reveals that PWWP2A binds selectively to H2A.Z-containing nucleosomes with strong preference for promoters of highly transcribed genes. In human cells, its depletion affects gene expression and impairs proliferation via a mitotic delay. While PWWP2A does not influence H2A.Z occupancy, the C-terminal tail of H2A.Z is one important mediator to recruit PWWP2A to chromatin. Knockdown of PWWP2A in <i>Xenopus</i> results in severe cranial facial defects, arising from neural crest cell differentiation and migration problems. Thus, PWWP2A is a novel H2A.Z-specific multivalent chromatin binder providing a surprising link between H2A.Z, chromosome segregation, and organ development.</p>',
'date' => '2017-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28645917',
'doi' => '',
'modified' => '2017-08-29 09:45:44',
'created' => '2017-08-29 09:45:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 24 => array(
'id' => '3216',
'name' => 'Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b',
'authors' => 'Kevin T. Ebata, Kathryn Mesh, Shichong Liu, Misha Bilenky, Alexander Fekete, Michael G. Acker, Martin Hirst, Benjamin A. Garcia and Miguel Ramalho-Santos',
'description' => '<section xmlns="" xmlns:fn="http://www.w3.org/2005/xpath-functions" xmlns:meta="http://www.springer.com/app/meta" class="Abstract" id="Abs1" lang="en">
<div class="js-CollapseSection">
<div xmlns:func="http://oscar.fig.bmc.com" xmlns="http://www.w3.org/1999/xhtml" class="AbstractSection" id="ASec1">
<h3 xmlns="" class="Heading">Background</h3>
<p id="Par1" class="Para">Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that vitamin C enhances the activity of Tet enzymes in embryonic stem (ES) cells, leading to DNA demethylation and activation of germline genes.</p>
</div>
<div xmlns:func="http://oscar.fig.bmc.com" xmlns="http://www.w3.org/1999/xhtml" class="AbstractSection" id="ASec2">
<h3 xmlns="" class="Heading">Results</h3>
<p id="Par2" class="Para">We report here that vitamin C induces a remarkably specific demethylation of histone H3 lysine 9 dimethylation (H3K9me2) in naïve ES cells. Vitamin C treatment reduces global levels of H3K9me2, but not other histone methylation marks analyzed, as measured by western blot, immunofluorescence and mass spectrometry. Vitamin C leads to widespread loss of H3K9me2 at large chromosomal domains as well as gene promoters and repeat elements. Vitamin C-induced loss of H3K9me2 occurs rapidly within 24 h and is reversible. Importantly, we found that the histone demethylases Kdm3a and Kdm3b are required for vitamin C-induced demethylation of H3K9me2. Moreover, we show that vitamin C-induced Kdm3a/b-mediated H3K9me2 demethylation and Tet-mediated DNA demethylation are independent processes at specific loci. Lastly, we document Kdm3a/b are partially required for the upregulation of germline genes by vitamin C.</p>
</div>
<div xmlns:func="http://oscar.fig.bmc.com" xmlns="http://www.w3.org/1999/xhtml" class="AbstractSection" id="ASec3">
<h3 xmlns="" class="Heading">Conclusions</h3>
<p id="Par3" class="Para">These results reveal a specific role for vitamin C in histone demethylation in ES cells and document that DNA methylation and H3K9me2 cooperate to silence germline genes in pluripotent cells.</p>
</div>
</div>
</section>',
'date' => '2017-07-12',
'pmid' => 'https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-017-0143-3',
'doi' => 'https://doi.org/10.1186/s13072-017-0143-3',
'modified' => '2017-08-23 14:47:51',
'created' => '2017-07-29 08:04:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 25 => array(
'id' => '3177',
'name' => 'Microinjection of Antibodies Targeting the Lamin A/C Histone-Binding Site Blocks Mitotic Entry and Reveals Separate Chromatin Interactions with HP1, CenpB and PML.',
'authors' => 'Dixon C.R. et al.',
'description' => '<p>Lamins form a scaffold lining the nucleus that binds chromatin and contributes to spatial genome organization; however, due to the many other functions of lamins, studies knocking out or altering the lamin polymer cannot clearly distinguish between direct and indirect effects. To overcome this obstacle, we specifically targeted the mapped histone-binding site of A/C lamins by microinjecting antibodies specific to this region predicting that this would make the genome more mobile. No increase in chromatin mobility was observed; however, interestingly, injected cells failed to go through mitosis, while control antibody-injected cells did. This effect was not due to crosslinking of the lamin polymer, as Fab fragments also blocked mitosis. The lack of genome mobility suggested other lamin-chromatin interactions. To determine what these might be, mini-lamin A constructs were expressed with or without the histone-binding site that assembled into independent intranuclear structures. HP1, CenpB and PML proteins accumulated at these structures for both constructs, indicating that other sites supporting chromatin interactions exist on lamin A. Together, these results indicate that lamin A-chromatin interactions are highly redundant and more diverse than generally acknowledged and highlight the importance of trying to experimentally separate their individual functions.</p>',
'date' => '2017-03-25',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28346356',
'doi' => '',
'modified' => '2017-05-17 10:39:58',
'created' => '2017-05-17 10:39:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 26 => array(
'id' => '3172',
'name' => 'Decoupling of DNA methylation and activity of intergenic LINE-1 promoters in colorectal cancer',
'authors' => 'Vafadar-Isfahani N. et al.',
'description' => '<p>Hypomethylation of LINE-1 repeats in cancer has been proposed as the main mechanism behind their activation; this assumption, however, was based on findings from early studies that were biased toward young and transpositionally active elements. Here, we investigate the relationship between methylation of 2 intergenic, transpositionally inactive LINE-1 elements and expression of the LINE-1 chimeric transcript (LCT) 13 and LCT14 driven by their antisense promoters (L1-ASP). Our data from DNA modification, expression, and 5'RACE analyses suggest that colorectal cancer methylation in the regions analyzed is not always associated with LCT repression. Consistent with this, in HCT116 colorectal cancer cells lacking DNA methyltransferases DNMT1 or DNMT3B, LCT13 expression decreases, while cells lacking both DNMTs or treated with the DNMT inhibitor 5-azacytidine (5-aza) show no change in LCT13 expression. Interestingly, levels of the H4K20me3 histone modification are inversely associated with LCT13 and LCT14 expression. Moreover, at these LINE-1s, H4K20me3 levels rather than DNA methylation seem to be good predictor of their sensitivity to 5-aza treatment. Therefore, by studying individual LINE-1 promoters we have shown that in some cases these promoters can be active without losing methylation; in addition, we provide evidence that other factors (e.g., H4K20me3 levels) play prominent roles in their regulation.</p>',
'date' => '2017-03-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28300471',
'doi' => '',
'modified' => '2017-05-10 16:26:24',
'created' => '2017-05-10 16:26:24',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 27 => array(
'id' => '3152',
'name' => 'H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements',
'authors' => 'Zink L.M. et al.',
'description' => '<p>Histone chaperones prevent promiscuous histone interactions before chromatin assembly. They guarantee faithful deposition of canonical histones and functionally specialized histone variants into chromatin in a spatial- and temporally-restricted manner. Here, we identify the binding partners of the primate-specific and H3.3-related histone variant H3.Y using several quantitative mass spectrometry approaches, and biochemical and cell biological assays. We find the HIRA, but not the DAXX/ATRX, complex to recognize H3.Y, explaining its presence in transcriptionally active euchromatic regions. Accordingly, H3.Y nucleosomes are enriched in the transcription-promoting FACT complex and depleted of repressive post-translational histone modifications. H3.Y mutational gain-of-function screens reveal an unexpected combinatorial amino acid sequence requirement for histone H3.3 interaction with DAXX but not HIRA, and for H3.3 recruitment to PML nuclear bodies. We demonstrate the importance and necessity of specific H3.3 core and C-terminal amino acids in discriminating between distinct chaperone complexes. Further, chromatin immunoprecipitation sequencing experiments reveal that in contrast to euchromatic HIRA-dependent deposition sites, human DAXX/ATRX-dependent regions of histone H3 variant incorporation are enriched in heterochromatic H3K9me3 and simple repeat sequences. These data demonstrate that H3.Y's unique amino acids allow a functional distinction between HIRA and DAXX binding and its consequent deposition into open chromatin.</p>',
'date' => '2017-02-21',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28334823',
'doi' => '',
'modified' => '2017-03-31 14:13:36',
'created' => '2017-03-31 14:13:36',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 28 => array(
'id' => '3100',
'name' => 'Muscle catabolic capacities and global hepatic epigenome are modified in juvenile rainbow trout fed different vitamin levels at first feeding',
'authors' => 'Panserat S. et al.',
'description' => '<p>Based on the concept of nutritional programming in mammals, we tested whether a short term hyper or hypo vitamin stimulus during first-feeding could induce long-lasting changes in nutrient metabolism in rainbow trout. Trout alevins received during the 4 first weeks of exogenous feeding a diet either without supplemental vitamins (NOSUP), a diet supplemented with a vitamin premix to satisfy the minimal requirement in all the vitamins (NRC) or a diet with a vitamin premix corresponding to an optimal vitamin nutrition (OVN). Following a common rearing period on the control diet, all three groups were then evaluated in terms of metabolic marker gene expressions at the end of the feeding period (day 119). Whereas no gene modifications for proteins involved in energy and lipid metabolism were observed in whole alevins (short-term effect), some of these genes showed a long-term molecular adaptation in the muscle of juveniles (long-term effect). Indeed, muscle of juveniles subjected at an early feeding of the OVN diet displayed up-regulated expression of markers of lipid catabolism (3-hydroxyacyl-CoA dehydrogenase – HOAD - enzyme) and mitochondrial energy metabolism (Citrate synthase - <em>cs</em>, Ubiquitinol cytochrome <em>c</em> reductase core protein 2 - QCR2, cytochrome oxidase 4 - COX4, ATP synthase form 5 - ATP5A) compared to fish fed the NOSUP diet. Moreover, some key enzymes involved in glucose catabolism (Muscle Pyruvate kinase - PKM) and amino acid catabolism (Glutamate dehydrogenase - GDH3) were also up regulated in muscle of juvenile fish fed with the OVN diet at first-feeding compared to fish fed the NOSUP diet. We researched if these permanently modified gene expressions could be related to global modifications of epigenetic marks (global DNA methylation and global histone acetylation and methylation). There was no variation of the epigenetic marks in muscle. However, we found changes in hepatic DNA methylation, global H3 acetylation and H3K4 methylation, dependent on the vitamin intake at early life. In summary, our data show, for the first time in fish, that a short-term vitamin-stimulus during early life may durably influence muscle energy and lipid metabolism as well as some hepatic epigenetic marks in rainbow trout.</p>',
'date' => '2017-02-01',
'pmid' => 'http://www.sciencedirect.com/science/article/pii/S0044848616309693',
'doi' => '',
'modified' => '2017-01-03 15:01:50',
'created' => '2017-01-03 15:01:50',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 29 => array(
'id' => '2825',
'name' => 'Oestrogen receptor β regulates epigenetic patterns at specific genomic loci through interaction with thymine DNA glycosylase.',
'authors' => 'Liu Y, Duong W, Krawczyk C, Bretschneider N, Borbély G, Varshney M, Zinser C, Schär P, Rüegg J.',
'description' => '<div class="">
<h4>BACKGROUND:</h4>
<p><abstracttext label="BACKGROUND" nlmcategory="BACKGROUND">DNA methylation is one way to encode epigenetic information and plays a crucial role in regulating gene expression during embryonic development. DNA methylation marks are established by the DNA methyltransferases and, recently, a mechanism for active DNA demethylation has emerged involving the ten-eleven translocator proteins and thymine DNA glycosylase (TDG). However, so far it is not clear how these enzymes are recruited to, and regulate DNA methylation at, specific genomic loci. A number of studies imply that sequence-specific transcription factors are involved in targeting DNA methylation and demethylation processes. Oestrogen receptor beta (ERβ) is a ligand-inducible transcription factor regulating gene expression in response to the female sex hormone oestrogen. Previously, we found that ERβ deficiency results in changes in DNA methylation patterns at two gene promoters, implicating an involvement of ERβ in DNA methylation. In this study, we set out to explore this involvement on a genome-wide level, and to investigate the underlying mechanisms of this function.</abstracttext></p>
<h4>RESULTS:</h4>
<p><abstracttext label="RESULTS" nlmcategory="RESULTS">Using reduced representation bisulfite sequencing, we compared genome-wide DNA methylation in mouse embryonic fibroblasts derived from wildtype and ERβ knock-out mice, and identified around 8000 differentially methylated positions (DMPs). Validation and further characterisation of selected DMPs showed that differences in methylation correlated with changes in expression of the nearest gene. Additionally, re-introduction of ERβ into the knock-out cells could reverse hypermethylation and reactivate expression of some of the genes. We also show that ERβ is recruited to regions around hypermethylated DMPs. Finally, we demonstrate here that ERβ interacts with TDG and that TDG binds ERβ-dependently to hypermethylated DMPs.</abstracttext></p>
<h4>CONCLUSION:</h4>
<p><abstracttext label="CONCLUSION" nlmcategory="CONCLUSIONS">We provide evidence that ERβ plays a role in regulating DNA methylation at specific genomic loci, likely as the result of its interaction with TDG at these regions. Our findings imply a novel function of ERβ, beyond direct transcriptional control, in regulating DNA methylation at target genes. Further, they shed light on the question how DNA methylation is regulated at specific genomic loci by supporting a concept in which sequence-specific transcription factors can target factors that regulate DNA methylation patterns.</abstracttext></p>
</div>',
'date' => '2016-02-16',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/26889208',
'doi' => '10.1186/s13072-016-0055-7.',
'modified' => '2016-02-22 10:05:14',
'created' => '2016-02-22 10:05:14',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 30 => array(
'id' => '2909',
'name' => 'Epigenetic priming of inflammatory response genes by high glucose in adipose progenitor cells',
'authors' => 'Rønningen T, Shah A, Reiner AH, Collas P, Moskaug JØ',
'description' => '<p>Cellular metabolism confers wide-spread epigenetic modifications required for regulation of transcriptional networks that determine cellular states. Mesenchymal stromal cells are responsive to metabolic cues including circulating glucose levels and modulate inflammatory responses. We show here that long term exposure of undifferentiated human adipose tissue stromal cells (ASCs) to high glucose upregulates a subset of inflammation response (IR) genes and alters their promoter histone methylation patterns in a manner consistent with transcriptional de-repression. Modeling of chromatin states from combinations of histone modifications in nearly 500 IR genes unveil three overarching chromatin configurations reflecting repressive, active, and potentially active states in promoter and enhancer elements. Accordingly, we show that adipogenic differentiation in high glucose predominantly upregulates IR genes. Our results indicate that elevated extracellular glucose levels sensitize in ASCs an IR gene expression program which is exacerbated during adipocyte differentiation. We propose that high glucose exposure conveys an epigenetic 'priming' of IR genes, favoring a transcriptional inflammatory response upon adipogenic stimulation. Chromatin alterations at IR genes by high glucose exposure may play a role in the etiology of metabolic diseases.</p>',
'date' => '2015-11-27',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/26462465',
'doi' => '10.1016/j.bbrc.2015.10.030',
'modified' => '2016-05-09 22:54:48',
'created' => '2016-05-09 22:54:48',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 31 => array(
'id' => '2874',
'name' => 'Polycomb RING1A- and RING1B-dependent histone H2A monoubiquitylation at pericentromeric regions promotes S-phase progression',
'authors' => 'Bravo M, Nicolini F, Starowicz K, Barroso S, Calés C, Aguilera A, Vidal M',
'description' => '<p>The functions of polycomb products extend beyond their well-known activity as transcriptional regulators to include genome duplication processes. Polycomb activities during DNA replication and DNA damage repair are unclear, particularly without induced replicative stress. We have used a cellular model of conditionally inactive polycomb E3 ligases (RING1A and RING1B), which monoubiquitylate lysine 119 of histone H2A (H2AK119Ub), to examine DNA replication in unperturbed cells. We identify slow elongation and fork stalling during DNA replication that is associated with the accumulation of mid and late S-phase cells. Signs of replicative stress and colocalisation of double-strand breaks with chromocenters, the sites of coalesced pericentromeric heterocromatic (PCH) domains, were enriched in cells at mid S-phase, the stage at which PCH is replicated. Altered replication was rescued by targeted monoubiquitylation of PCH through methyl-CpG binding domain protein 1. The acute senescence associated with the depletion of RING1 proteins, which is mediated by p21 (also known as CDKN1A) upregulation, could be uncoupled from a response to DNA damage. These findings link cell proliferation and the polycomb proteins RING1A and RING1B to S-phase progression through a specific function in PCH replication.</p>',
'date' => '2015-08-13',
'pmid' => 'http://jcs.biologists.org/content/128/19/3660',
'doi' => '10.1242/jcs.173021 ',
'modified' => '2016-03-29 16:29:38',
'created' => '2016-03-29 16:29:38',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 32 => array(
'id' => '2725',
'name' => 'Erosion of X Chromosome Inactivation in Human Pluripotent Cells Initiates with XACT Coating and Depends on a Specific Heterochromatin Landscape.',
'authors' => 'Vallot C, Ouimette JF, Makhlouf M, Féraud O, Pontis J, Côme J, Martinat C, Bennaceur-Griscelli A, Lalande M, Rougeulle C',
'description' => 'Human pluripotent stem cells (hPSCs) display extensive epigenetic instability, particularly on the X chromosome. In this study, we show that, in hPSCs, the inactive X chromosome has a specific heterochromatin landscape that predisposes it to erosion of X chromosome inactivation (XCI), a process that occurs spontaneously in hPSCs. Heterochromatin remodeling and gene reactivation occur in a non-random fashion and are confined to specific H3K27me3-enriched domains, leaving H3K9me3-marked regions unaffected. Using single-cell monitoring of XCI erosion, we show that this instability only occurs in pluripotent cells. We also provide evidence that loss of XIST expression is not the primary cause of XCI instability and that gene reactivation from the inactive X (Xi) precedes loss of XIST coating. Notably, expression and coating by the long non-coding RNA XACT are early events in XCI erosion and, therefore, may play a role in mediating this process.',
'date' => '2015-05-07',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25921272',
'doi' => '',
'modified' => '2015-07-24 15:39:05',
'created' => '2015-07-24 15:39:05',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 33 => array(
'id' => '2575',
'name' => 'Embryonic stem cell differentiation requires full length Chd1.',
'authors' => 'Piatti P, Lim CY, Nat R, Villunger A, Geley S, Shue YT, Soratroi C, Moser M, Lusser A',
'description' => 'The modulation of chromatin dynamics by ATP-dependent chromatin remodeling factors has been recognized as an important mechanism to regulate the balancing of self-renewal and pluripotency in embryonic stem cells (ESCs). Here we have studied the effects of a partial deletion of the gene encoding the chromatin remodeling factor Chd1 that generates an N-terminally truncated version of Chd1 in mouse ESCs in vitro as well as in vivo. We found that a previously uncharacterized serine-rich region (SRR) at the N-terminus is not required for chromatin assembly activity of Chd1 but that it is subject to phosphorylation. Expression of Chd1 lacking this region in ESCs resulted in aberrant differentiation properties of these cells. The self-renewal capacity and ESC chromatin structure, however, were not affected. Notably, we found that newly established ESCs derived from Chd1(Δ2/Δ2) mutant mice exhibited similar differentiation defects as in vitro generated mutant ESCs, even though the N-terminal truncation of Chd1 was fully compatible with embryogenesis and post-natal life in the mouse. These results underscore the importance of Chd1 for the regulation of pluripotency in ESCs and provide evidence for a hitherto unrecognized critical role of the phosphorylated N-terminal SRR for full functionality of Chd1.',
'date' => '2015-01-26',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25620209',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 34 => array(
'id' => '2513',
'name' => 'The histone demethylase enzyme KDM3A is a key estrogen receptor regulator in breast cancer.',
'authors' => 'Wade MA, Jones D, Wilson L, Stockley J, Coffey K, Robson CN, Gaughan L',
'description' => '<p>Endocrine therapy has successfully been used to treat estrogen receptor (ER)-positive breast cancer, but this invariably fails with cancers becoming refractory to treatment. Emerging evidence has suggested that fluctuations in ER co-regulatory protein expression may facilitate resistance to therapy and be involved in breast cancer progression. To date, a small number of enzymes that control methylation status of histones have been identified as co-regulators of ER signalling. We have identified the histone H3 lysine 9 mono- and di-methyl demethylase enzyme KDM3A as a positive regulator of ER activity. Here, we demonstrate that depletion of KDM3A by RNAi abrogates the recruitment of the ER to cis-regulatory elements within target gene promoters, thereby inhibiting estrogen-induced gene expression changes. Global gene expression analysis of KDM3A-depleted cells identified gene clusters associated with cell growth. Consistent with this, we show that knockdown of KDM3A reduces ER-positive cell proliferation and demonstrate that KDM3A is required for growth in a model of endocrine therapy-resistant disease. Crucially, we show that KDM3A catalytic activity is required for both ER-target gene expression and cell growth, demonstrating that developing compounds which target demethylase enzymatic activity may be efficacious in treating both ER-positive and endocrine therapy-resistant disease.</p>',
'date' => '2015-01-09',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25488809',
'doi' => '',
'modified' => '2016-05-03 11:59:18',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 35 => array(
'id' => '2502',
'name' => 'TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells.',
'authors' => 'Fasching L, Kapopoulou A, Sachdeva R, Petri R, Jönsson ME, Männe C, Turelli P, Jern P, Cammas F, Trono D, Jakobsson J',
'description' => '<p>TRIM28 is a corepressor that mediates transcriptional silencing by establishing local heterochromatin. Here, we show that deletion of TRIM28 in neural progenitor cells (NPCs) results in high-level expression of two groups of endogenous retroviruses (ERVs): IAP1 and MMERVK10C. We find that NPCs use TRIM28-mediated histone modifications to dynamically regulate transcription and silencing of ERVs, which is in contrast to other somatic cell types using DNA methylation. We also show that derepression of ERVs influences transcriptional dynamics in NPCs through the activation of nearby genes and the expression of long noncoding RNAs. These findings demonstrate a unique dynamic transcriptional regulation of ERVs in NPCs. Our results warrant future studies on the role of ERVs in the healthy and diseased brain.</p>',
'date' => '2015-01-06',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25543143',
'doi' => '',
'modified' => '2017-06-22 13:34:19',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 36 => array(
'id' => '2492',
'name' => 'Cryosectioning the intestinal crypt-villus axis: an ex vivo method to study the dynamics of epigenetic modifications from stem cells to differentiated cells',
'authors' => 'Vincent A, Kazmierczak C, Duchêne B, Jonckheere N, Leteurtre E, Van Seuningen I',
'description' => 'The intestinal epithelium is a particularly attractive biological adult model to study epigenetic mechanisms driving adult stem cell renewal and cell differentiation. Since epigenetic modifications are dynamic, we have developed an original ex vivo approach to study the expression and epigenetic profiles of key genes associated with either intestinal cell pluripotency or differentiation by isolating cryosections of the intestinal crypt-villus axis. Gene expression, DNA methylation and histone modifications were studied by qRT-PCR, Methylation Specific-PCR and micro-Chromatin Immunoprecipitation, respectively. Using this approach, it was possible to identify segment-specific methylation and chromatin profiles. We show that (i) expression of intestinal stem cell markers (Lgr5, Ascl2) exclusively in the crypt is associated with active histone marks, (ii) promoters of all pluripotency genes studied and transcription factors involved in intestinal cell fate (Cdx2) harbour a bivalent chromatin pattern in the crypts, (iii) expression of differentiation markers (Muc2, Sox9) along the crypt-villus axis is associated with DNA methylation. Hence, using an original model of cryosectioning along the crypt-villus axis that allows in situ detection of dynamic epigenetic modifications, we demonstrate that regulation of pluripotency and differentiation markers in healthy intestinal mucosa involves different and specific epigenetic mechanisms.',
'date' => '2014-12-27',
'pmid' => 'http://www.sciencedirect.com/science/article/pii/S1873506114001585',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 37 => array(
'id' => '2215',
'name' => 'Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation.',
'authors' => 'Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ',
'description' => 'Artificial transcription factors (ATFs) and genomic nucleases based on a DNA binding platform consisting of multiple zinc finger domains are currently being developed for clinical applications. However, no genome-wide investigations into their binding specificity have been performed. We have created six-finger ATFs to target two different 18 nt regions of the human SOX2 promoter; each ATF is constructed such that it contains or lacks a super KRAB domain (SKD) that interacts with a complex containing repressive histone methyltransferases. ChIP-seq analysis of the effector-free ATFs in MCF7 breast cancer cells identified thousands of binding sites, mostly in promoter regions; the addition of an SKD domain increased the number of binding sites ∼5-fold, with a majority of the new sites located outside of promoters. De novo motif analyses suggest that the lack of binding specificity is due to subsets of the finger domains being used for genomic interactions. Although the ATFs display widespread binding, few genes showed expression differences; genes repressed by the ATF-SKD have stronger binding sites and are more enriched for a 12 nt motif. Interestingly, epigenetic analyses indicate that the transcriptional repression caused by the ATF-SKD is not due to changes in active histone modifications.',
'date' => '2014-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25122745',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 38 => array(
'id' => '2664',
'name' => 'The PML-associated protein DEK regulates the balance of H3.3 loading on chromatin and is important for telomere integrity.',
'authors' => 'Ivanauskiene K, Delbarre E, McGhie JD, Küntziger T, Wong LH, Collas P',
'description' => 'Histone variant H3.3 is deposited in chromatin at active sites, telomeres, and pericentric heterochromatin by distinct chaperones, but the mechanisms of regulation and coordination of chaperone-mediated H3.3 loading remain largely unknown. We show here that the chromatin-associated oncoprotein DEK regulates differential HIRA- and DAAX/ATRX-dependent distribution of H3.3 on chromosomes in somatic cells and embryonic stem cells. Live cell imaging studies show that nonnucleosomal H3.3 normally destined to PML nuclear bodies is re-routed to chromatin after depletion of DEK. This results in HIRA-dependent widespread chromatin deposition of H3.3 and H3.3 incorporation in the foci of heterochromatin in a process requiring the DAXX/ATRX complex. In embryonic stem cells, loss of DEK leads to displacement of PML bodies and ATRX from telomeres, redistribution of H3.3 from telomeres to chromosome arms and pericentric heterochromatin, induction of a fragile telomere phenotype, and telomere dysfunction. Our results indicate that DEK is required for proper loading of ATRX and H3.3 on telomeres and for telomeric chromatin architecture. We propose that DEK acts as a "gatekeeper" of chromatin, controlling chromatin integrity by restricting broad access to H3.3 by dedicated chaperones. Our results also suggest that telomere stability relies on mechanisms ensuring proper histone supply and routing.',
'date' => '2014-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25049225',
'doi' => '',
'modified' => '2015-07-24 15:39:05',
'created' => '2015-07-24 15:39:05',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 39 => array(
'id' => '2338',
'name' => 'The specific alteration of histone methylation profiles by DZNep during early zebrafish development.',
'authors' => 'Ostrup O, Reiner AH, Aleström P, Collas P',
'description' => '<p>Early embryo development constitutes a unique opportunity to study acquisition of epigenetic marks, including histone methylation. This study investigates the in vivo function and specificity of 3-deazaneplanocin A (DZNep), a promising anti-cancer drug that targets polycomb complex genes. One- to two-cell stage embryos were cultured with DZNep, and subsequently evaluated at the post-mid blastula transition stage for H3K27me3, H3K4me3 and H3K9me3 occupancy and enrichment at promoters using ChIP-chip microarrays. DZNep affected promoter enrichment of H3K27me3 and H3K9me3, whereas H3K4me3 remained stable. Interestingly, DZNep induced a loss of H3K27me3 and H3K9me3 from a substantial number of promoters but did not prevent de novo acquisition of these marks on others, indicating gene-specific targeting of its action. Loss/gain of H3K27me3 on promoters did not result in changes in gene expression levels until 24h post-fertilization. In contrast, genes gaining H3K9me3 displayed strong and constant down-regulation upon DZNep treatment. H3K9me3 enrichment on these gene promoters was observed not only in the proximal area as expected, but also over the transcription start site. Altered H3K9me3 profiles were associated with severe neuronal and cranial phenotypes at day 4-5 post-fertilization. Thus, DZNep was shown to affect enrichment patterns of H3K27me3 and H3K9me3 at promoters in a gene-specific manner.</p>',
'date' => '2014-09-28',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25260724',
'doi' => '',
'modified' => '2016-04-08 09:43:32',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 40 => array(
'id' => '2226',
'name' => 'KMTase Set7/9 is a critical regulator of E2F1 activity upon genotoxic stress.',
'authors' => 'Lezina L, Aksenova V, Ivanova T, Purmessur N, Antonov AV, Tentler D, Fedorova O, Garabadgiu AV, Talianidis I, Melino G, Barlev NA',
'description' => 'During the recent years lysine methyltransferase Set7/9 ((Su(var)-3-9, Enhancer-of-Zeste, Trithorax) domain containing protein 7/9) has emerged as an important regulator of different transcription factors. In this study, we report a novel function for Set7/9 as a critical co-activator of E2 promoter-binding factor 1 (E2F1)-dependent transcription in response to DNA damage. By means of various biochemical, cell biology, and bioinformatics approaches, we uncovered that cell-cycle progression through the G1/S checkpoint of tumour cells upon DNA damage is defined by the threshold of expression of both E2F1 and Set7/9. The latter affects the activity of E2F1 by indirectly modulating histone modifications in the promoters of E2F1-dependent genes. Moreover, Set7/9 differentially affects E2F1 transcription targets: it promotes cell proliferation via expression of the CCNE1 gene and represses apoptosis by inhibiting the TP73 gene. Our biochemical screening of the panel of lung tumour cell lines suggests that these two factors are critically important for transcriptional upregulation of the CCNE1 gene product and hence successful progression through cell cycle. These findings identify Set7/9 as a potential biomarker in tumour cells with overexpressed E2F1 activity.Cell Death and Differentiation advance online publication, 15 August 2014; doi:10.1038/cdd.2014.108.',
'date' => '2014-08-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25124555',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 41 => array(
'id' => '2206',
'name' => 'The histone variant composition of centromeres is controlled by the pericentric heterochromatin state during the cell cycle.',
'authors' => 'Boyarchuk E, Filipescu D, Vassias I, Cantaloube S, Almouzni G',
'description' => 'Correct chromosome segregation requires a unique chromatin environment at centromeres and in their vicinity. Here, we address how the deposition of canonical H2A and H2A.Z histone variants is controlled at pericentric heterochromatin (PHC). Whereas in euchromatin newly synthesized H2A and H2A.Z are deposited throughout the cell cycle, we reveal two discrete waves of deposition at PHC - during mid to late S phase in a replication-dependent manner for H2A and during G1 phase for H2A.Z. This G1 cell cycle restriction is lost when heterochromatin features are altered, leading to the accumulation of H2A.Z at the domain. Interestingly, compromising PHC integrity also impacts upon neighboring centric chromatin, increasing the amount of centromeric CENP-A without changing the timing of its deposition. We conclude that the higher-order chromatin structure at the pericentric domain influences dynamics at the nucleosomal level within centromeric chromatin. The two different modes of rearrangement of the PHC during the cell cycle provide distinct opportunities to replenish one or the other H2A variant, highlighting PHC integrity as a potential signal to regulate the deposition timing and stoichiometry of histone variants at the centromere.',
'date' => '2014-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24906798',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 42 => array(
'id' => '2081',
'name' => 'RNAi-Mediated Gene silencing in Zebrafish Triggered by Convergent Transcription.',
'authors' => 'Andrews OE, Cha DJ, Wei C, Patton JG',
'description' => 'RNAi based strategies to induce gene silencing are commonly employed in numerous model organisms but have not been extensively used in zebrafish. We found that introduction of transgenes containing convergent transcription units in zebrafish embryos induced stable transcriptional gene silencing (TGS) in cis and trans for reporter (mCherry) and endogenous (One-Eyed Pinhead (OEP) and miR-27a/b) genes. Convergent transcription enabled detection of both sense and antisense transcripts and silencing was suppressed upon Dicer knockdown, indicating processing of double stranded RNA. By ChIP analyses, increased silencing was accompanied by enrichment of the heterochromatin mark H3K9me3 in the two convergently arranged promoters and in the intervening reading frame. Our work demonstrates that convergent transcription can induce gene silencing in zebrafish providing another tool to create specific temporal and spatial control of gene expression.',
'date' => '2014-06-09',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24909225',
'doi' => '',
'modified' => '2015-07-24 15:39:02',
'created' => '2015-07-24 15:39:02',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 43 => array(
'id' => '1888',
'name' => 'Transcriptional Derepression of the ERVWE1 Locus following Influenza A Virus Infection.',
'authors' => 'Li F, Nellåker C, Sabunciyan S, Yolken RH, Jones-Brando L, Johansson AS, Owe-Larsson B, Karlsson H',
'description' => 'UNLABELLED: Syncytin-1, a fusogenic protein encoded by a human endogenous retrovirus of the W family (HERV-W) element (ERVWE1), is expressed in the syncytiotrophoblast layer of the placenta. This locus is transcriptionally repressed in adult tissues through promoter CpG methylation and suppressive histone modifications. Whereas syncytin-1 appears to be crucial for the development and functioning of the human placenta, its ectopic expression has been associated with pathological conditions, such as multiple sclerosis and schizophrenia. We previously reported on the transactivation of HERV-W elements, including ERVWE1, during influenza A/WSN/33 virus infection in a range of human cell lines. Here we report the results of quantitative PCR analyses of transcripts encoding syncytin-1 in both cell lines and primary fibroblast cells. We observed that spliced ERVWE1 transcripts and those encoding the transcription factor glial cells missing 1 (GCM1), acting as an enhancer element upstream of ERVWE1, are prominently upregulated in response to influenza A/WSN/33 virus infection in nonplacental cells. Knockdown of GCM1 by small interfering RNA followed by infection suppressed the transactivation of ERVWE1. While the infection had no influence on CpG methylation in the ERVWE1 promoter, chromatin immunoprecipitation assays detected decreased H3K9 trimethylation (H3K9me3) and histone methyltransferase SETDB1 levels along with influenza virus proteins associated with ERVWE1 and other HERV-W loci in infected CCF-STTG1 cells. The present findings suggest that an exogenous influenza virus infection can transactivate ERVWE1 by increasing transcription of GCM1 and reducing H3K9me3 in this region and in other regions harboring HERV-W elements. IMPORTANCE: Syncytin-1, a protein encoded by the env gene in the HERV-W locus ERVWE1, appears to be crucial for the development and functioning of the human placenta and is transcriptionally repressed in nonplacental tissues. Nevertheless, its ectopic expression has been associated with pathological conditions, such as multiple sclerosis and schizophrenia. In the present paper, we report findings suggesting that an exogenous influenza A virus infection can transactivate ERVWE1 by increasing the transcription of GCM1 and reducing the repressive histone mark H3K9me3 in this region and in other regions harboring HERV-W elements. These observations have implications of potential relevance for viral pathogenesis and for conditions associated with the aberrant transcription of HERV-W loci.',
'date' => '2014-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24478419',
'doi' => '',
'modified' => '2015-07-24 15:39:02',
'created' => '2015-07-24 15:39:02',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 44 => array(
'id' => '1723',
'name' => 'HDAC inhibitor confers radiosensitivity to prostate stem-like cells.',
'authors' => 'Frame FM, Pellacani D, Collins AT, Simms MS, Mann VM, Jones G, Meuth M, Bristow RG, Maitland NJ',
'description' => 'Background:Radiotherapy can be an effective treatment for prostate cancer, but radiorecurrent tumours do develop. Considering prostate cancer heterogeneity, we hypothesised that primitive stem-like cells may constitute the radiation-resistant fraction.Methods:Primary cultures were derived from patients undergoing resection for prostate cancer or benign prostatic hyperplasia. After short-term culture, three populations of cells were sorted, reflecting the prostate epithelial hierarchy, namely stem-like cells (SCs, α2β1integrin(hi)/CD133(+)), transit-amplifying (TA, α2β1integrin(hi)/CD133(-)) and committed basal (CB, α2β1integrin(lo)) cells. Radiosensitivity was measured by colony-forming efficiency (CFE) and DNA damage by comet assay and DNA damage foci quantification. Immunofluorescence and flow cytometry were used to measure heterochromatin. The HDAC (histone deacetylase) inhibitor Trichostatin A was used as a radiosensitiser.Results:Stem-like cells had increased CFE post irradiation compared with the more differentiated cells (TA and CB). The SC population sustained fewer lethal double-strand breaks than either TA or CB cells, which correlated with SCs being less proliferative and having increased levels of heterochromatin. Finally, treatment with an HDAC inhibitor sensitised the SCs to radiation.Interpretation:Prostate SCs are more radioresistant than more differentiated cell populations. We suggest that the primitive cells survive radiation therapy and that pre-treatment with HDAC inhibitors may sensitise this resistant fraction.',
'date' => '2013-12-10',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24220693',
'doi' => '',
'modified' => '2015-07-24 15:39:01',
'created' => '2015-07-24 15:39:01',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 45 => array(
'id' => '1516',
'name' => 'Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes.',
'authors' => 'Lund E, Oldenburg AR, Delbarre E, Freberg CT, Duband-Goulet I, Eskeland R, Buendia B, Collas P',
'description' => 'The nuclear lamina is implicated in the organization of the eukaryotic nucleus. Association of nuclear lamins with the genome occurs through large chromatin domains including mostly, but not exclusively, repressed genes. How lamin interactions with regulatory elements modulate gene expression in different cellular contexts is unknown. We show here that in human adipose tissue stem cells, lamin A/C interacts with distinct spatially restricted subpromoter regions, both within and outside peripheral and intra-nuclear lamin-rich domains. These localized interactions are associated with distinct transcriptional outcomes in a manner dependent on local chromatin modifications. Down-regulation of lamin A/C leads to dissociation of lamin A/C from promoters and remodels repressive and permissive histone modifications by enhancing transcriptional permissiveness, but is not sufficient to elicit gene activation. Adipogenic differentiation resets a large number of lamin-genome associations globally and at subpromoter levels and redefines associated transcription outputs. We propose that lamin A/C acts as a modulator of local gene expression outcome through interaction with adjustable sites on promoters, and that these position-dependent transcriptional readouts may be reset upon differentiation.',
'date' => '2013-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23861385',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 46 => array(
'id' => '1595',
'name' => 'Long range epigenetic silencing is a trans-species mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells.',
'authors' => 'Forn M, Muñoz M, Tauriello DV, Merlos-Suárez A, Rodilla V, Bigas A, Batlle E, Jordà M, Peinado MA',
'description' => 'DNA methylation and chromatin remodeling are frequently implicated in the silencing of genes involved in carcinogenesis. Long Range Epigenetic Silencing (LRES) is a mechanism of gene inactivation that affects multiple contiguous CpG islands and has been described in different human cancer types. However, it is unknown whether there is a coordinated regulation of the genes embedded in these regions in normal cells and in early stages of tumor progression. To better characterize the molecular events associated with the regulation and remodeling of these regions we analyzed two regions undergoing LRES in human colon cancer in the mouse model. We demonstrate that LRES also occurs in murine cancer in vivo and mimics the molecular features of the human phenomenon, namely, downregulation of gene expression, acquisition of inactive histone marks, and DNA hypermethylation of specific CpG islands. The genes embedded in these regions showed a dynamic and autonomous regulation during mouse intestinal cell differentiation, indicating that, in the framework considered here, the coordinated regulation in LRES is restricted to cancer. Unexpectedly, benign adenomas in Apc(Min/+) mice showed overexpression of most of the genes affected by LRES in cancer, which suggests that the repressive remodeling of the region is a late event. Chromatin immunoprecipitation analysis of the transcriptional insulator CTCF in mouse colon cancer cells revealed disrupted chromatin domain boundaries as compared with normal cells. Malignant regression of cancer cells by in vitro differentiation resulted in partial reversion of LRES and gain of CTCF binding. We conclude that genes in LRES regions are plastically regulated in cell differentiation and hyperproliferation, but are constrained to a coordinated repression by abolishing boundaries and the autonomous regulation of chromatin domains in cancer cells.',
'date' => '2013-08-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24035705',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 47 => array(
'id' => '1486',
'name' => 'Transgene- and locus-dependent imprinting reveals allele-specific chromosome conformations.',
'authors' => 'Lonfat N, Montavon T, Jebb D, Tschopp P, Nguyen Huynh TH, Zakany J, Duboule D',
'description' => 'When positioned into the integrin α-6 gene, an Hoxd9lacZ reporter transgene displayed parental imprinting in mouse embryos. While the expression from the paternal allele was comparable with patterns seen for the same transgene when present at the neighboring HoxD locus, almost no signal was scored at this integration site when the transgene was inherited from the mother, although the Itga6 locus itself is not imprinted. The transgene exhibited maternal allele-specific DNA hypermethylation acquired during oogenesis, and its expression silencing was reversible on passage through the male germ line. Histone modifications also corresponded to profiles described at known imprinted loci. Chromosome conformation analyses revealed distinct chromatin microarchitectures, with a more compact structure characterizing the maternally inherited repressed allele. Such genetic analyses of well-characterized transgene insertions associated with a de novo-induced parental imprint may help us understand the molecular determinants of imprinting.',
'date' => '2013-07-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23818637',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 48 => array(
'id' => '1425',
'name' => 'Expression of a large LINE-1-driven antisense RNA is linked to epigenetic silencing of the metastasis suppressor gene TFPI-2 in cancer.',
'authors' => 'Cruickshanks HA, Vafadar-Isfahani N, Dunican DS, Lee A, Sproul D, Lund JN, Meehan RR, Tufarelli C',
'description' => 'LINE-1 retrotransposons are abundant repetitive elements of viral origin, which in normal cells are kept quiescent through epigenetic mechanisms. Activation of LINE-1 occurs frequently in cancer and can enable LINE-1 mobilization but also has retrotransposition-independent consequences. We previously reported that in cancer, aberrantly active LINE-1 promoters can drive transcription of flanking unique sequences giving rise to LINE-1 chimeric transcripts (LCTs). Here, we show that one such LCT, LCT13, is a large transcript (>300 kb) running antisense to the metastasis-suppressor gene TFPI-2. We have modelled antisense RNA expression at TFPI-2 in transgenic mouse embryonic stem (ES) cells and demonstrate that antisense RNA induces silencing and deposition of repressive histone modifications implying a causal link. Consistent with this, LCT13 expression in breast and colon cancer cell lines is associated with silencing and repressive chromatin at TFPI-2. Furthermore, we detected LCT13 transcripts in 56% of colorectal tumours exhibiting reduced TFPI-2 expression. Our findings implicate activation of LINE-1 elements in subsequent epigenetic remodelling of surrounding genes, thus hinting a novel retrotransposition-independent role for LINE-1 elements in malignancy.',
'date' => '2013-05-23',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23703216',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 49 => array(
'id' => '1497',
'name' => 'Histone lysine trimethylation or acetylation can be modulated by phytoestrogen, estrogen or anti-HDAC in breast cancer cell lines.',
'authors' => 'Dagdemir A, Durif J, Ngollo M, Bignon YJ, Bernard-Gallon D',
'description' => '<p>AIM: The isoflavones genistein, daidzein and equol (daidzein metabolite) have been reported to interact with epigenetic modifications, specifically hypermethylation of tumor suppressor genes. The objective of this study was to analyze and understand the mechanisms by which phytoestrogens act on chromatin in breast cancer cell lines. MATERIALS & METHODS: Two breast cancer cell lines, MCF-7 and MDA-MB 231, were treated with genistein (18.5 µM), daidzein (78.5 µM), equol (12.8 µM), 17β-estradiol (10 nM) and suberoylanilide hydroxamic acid (1 µM) for 48 h. A control with untreated cells was performed. 17β-estradiol and an anti-HDAC were used to compare their actions with phytoestrogens. The chromatin immunoprecipitation coupled with quantitative PCR was used to follow soy phytoestrogen effects on H3 and H4 histones on H3K27me3, H3K9me3, H3K4me3, H4K8ac and H3K4ac marks, and we selected six genes (EZH2, BRCA1, ERα, ERβ, SRC3 and P300) for analysis. RESULTS: Soy phytoestrogens induced a decrease in trimethylated marks and an increase in acetylating marks studied at six selected genes. CONCLUSION: We demonstrated that soy phytoestrogens tend to modify transcription through the demethylation and acetylation of histones in breast cancer cell lines.</p>',
'date' => '2013-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23414320',
'doi' => '',
'modified' => '2016-05-03 12:17:35',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 50 => array(
'id' => '1179',
'name' => 'Epigenetic Regulation of Nestin Expression During Neurogenic Differentiation of Adipose Tissue Stem Cells.',
'authors' => 'Boulland JL, Mastrangelopoulou M, Boquest AC, Jakobsen R, Noer A, Glover JC, Collas P.',
'description' => 'Adipose-tissue-derived stem cells (ASCs) have received considerable attention due to their easy access, expansion potential, and differentiation capacity. ASCs are believed to have the potential to differentiate into neurons. However, the mechanisms by which this may occur remain largely unknown. Here, we show that culturing ASCs under active proliferation conditions greatly improves their propensity to differentiate toward osteogenic, adipogenic, and neurogenic lineages. Neurogenic-induced ASCs express early neurogenic genes as well as markers of mature neurons, including voltage-gated ion channels. Nestin, highly expressed in neural progenitors, is upregulated by mitogenic stimulation of ASCs, and as in neural progenitors, then repressed during neurogenic differentiation. Nestin gene (NES) expression under these conditions appears to be regulated by epigenetic mechanisms. The neural-specific, but not muscle-specific, enhancer regions of NES are DNA demethylated by mitogenic stimulation, and remethylated upon neurogenic differentiation. We observe dynamic changes in histone H3K4, H3K9, and H3K27 methylation on the NES locus before and during neurogenic differentiation that are consistent with epigenetic processes involved in the regulation of NES expression. We suggest that ASCs are epigenetically prepatterned to differentiate toward a neural lineage and that this prepatterning is enhanced by demethylation of critical NES enhancer elements upon mitogenic stimulation preceding neurogenic differentiation. Our findings provide molecular evidence that the differentiation repertoire of ASCs may extend beyond mesodermal lineages.',
'date' => '2012-12-21',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/23140086',
'doi' => '',
'modified' => '2015-07-24 15:38:59',
'created' => '2015-07-24 15:38:59',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 51 => array(
'id' => '752',
'name' => 'The histone demethylase Kdm3a is essential to progression through differentiation.',
'authors' => 'Herzog M, Josseaux E, Dedeurwaerder S, Calonne E, Volkmar M, Fuks F',
'description' => 'Histone demethylation has important roles in regulating gene expression and forms part of the epigenetic memory system that regulates cell fate and identity by still poorly understood mechanisms. Here, we examined the role of histone demethylase Kdm3a during cell differentiation, showing that Kdm3a is essential for differentiation into parietal endoderm-like (PE) cells in the F9 mouse embryonal carcinoma model. We identified a number of target genes regulated by Kdm3a during endoderm differentiation; among the most dysregulated were the three developmental master regulators Dab2, Pdlim4 and FoxQ1. We show that dysregulation of the expression of these genes correlates with Kdm3a H3K9me2 demethylase activity. We further demonstrate that either Dab2 depletion or Kdm3a depletion prevents F9 cells from fully differentiating into PE cells, but that ectopic expression of Dab2 cannot compensate for Kdm3a knockdown; Dab2 is thus necessary, but insufficient on its own, to promote complete terminal differentiation. We conclude that Kdm3a plays a crucial role in progression through PE differentiation by regulating expression of a set of endoderm differentiation master genes. The emergence of Kdm3a as a key modulator of cell fate decision strengthens the view that histone demethylases are essential to cell differentiation.',
'date' => '2012-05-11',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22581778',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 52 => array(
'id' => '630',
'name' => 'Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.',
'authors' => 'Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B',
'description' => 'While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA hypomethylation in the cancer cell, primarily at partially methylated domains (PMDs) in normal breast cells. Unexpectedly, genes within these regions are largely silenced in cancer cells. The loss of DNA methylation in these regions is accompanied by formation of repressive chromatin, with a significant fraction displaying allelic DNA methylation where one allele is DNA methylated while the other allele is occupied by histone modifications H3K9me3 or H3K27me3. Our results show a mutually exclusive relationship between DNA methylation and H3K9me3 or H3K27me3. These results suggest that global DNA hypomethylation in breast cancer is tightly linked to the formation of repressive chromatin domains and gene silencing, thus identifying a potential epigenetic pathway for gene regulation in cancer cells.',
'date' => '2012-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22156296',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 53 => array(
'id' => '919',
'name' => 'Prepatterning of developmental gene expression by modified histones before zygotic genome activation.',
'authors' => 'Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Østrup O, Winata C, Mathavan S, Müller F, Aleström P, Collas P',
'description' => 'A hallmark of anamniote vertebrate development is a window of embryonic transcription-independent cell divisions before onset of zygotic genome activation (ZGA). Chromatin determinants of ZGA are unexplored; however, marking of developmental genes by modified histones in sperm suggests a predictive role of histone marks for ZGA. In zebrafish, pre-ZGA development for ten cell cycles provides an opportunity to examine whether genomic enrichment in modified histones is present before initiation of transcription. By profiling histone H3 trimethylation on all zebrafish promoters before and after ZGA, we demonstrate here an epigenetic prepatterning of developmental gene expression. This involves pre-ZGA marking of transcriptionally inactive genes involved in homeostatic and developmental regulation by permissive H3K4me3 with or without repressive H3K9me3 or H3K27me3. Our data suggest that histone modifications are instructive for the developmental gene expression program.',
'date' => '2011-12-13',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22137762',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 54 => array(
'id' => '637',
'name' => 'H3.5 is a novel hominid-specific histone H3 variant that is specifically expressed in the seminiferous tubules of human testes.',
'authors' => 'Schenk R, Jenke A, Zilbauer M, Wirth S, Postberg J',
'description' => 'The incorporation of histone variants into chromatin plays an important role for the establishment of particular chromatin states. Six human histone H3 variants are known to date, not counting CenH3 variants: H3.1, H3.2, H3.3 and the testis-specific H3.1t as well as the recently described variants H3.X and H3.Y. We report the discovery of H3.5, a novel non-CenH3 histone H3 variant. H3.5 is encoded on human chromosome 12p11.21 and probably evolved in a common ancestor of all recent great apes (Hominidae) as a consequence of H3F3B gene duplication by retrotransposition. H3.5 mRNA is specifically expressed in seminiferous tubules of human testis. Interestingly, H3.5 has two exact copies of ARKST motifs adjacent to lysine-9 or lysine-27, and lysine-79 is replaced by asparagine. In the Hek293 cell line, ectopically expressed H3.5 is assembled into chromatin and targeted by PTM. H3.5 preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes and can replace an essential function of RNAi-depleted H3.3 in cell growth.',
'date' => '2011-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21274551',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 55 => array(
'id' => '274',
'name' => 'Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability.',
'authors' => 'Cortázar D, Kunz C, Selfridge J, Lettieri T, Saito Y, MacDougall E, Wirz A, Schuermann D, Jacobs AL, Siegrist F, Steinacher R, Jiricny J, Bird A, Schär P',
'description' => 'Thymine DNA glycosylase (TDG) is a member of the uracil DNA glycosylase (UDG) superfamily of DNA repair enzymes. Owing to its ability to excise thymine when mispaired with guanine, it was proposed to act against the mutability of 5-methylcytosine (5-mC) deamination in mammalian DNA. However, TDG was also found to interact with transcription factors, histone acetyltransferases and de novo DNA methyltransferases, and it has been associated with DNA demethylation in gene promoters following activation of transcription, altogether implicating an engagement in gene regulation rather than DNA repair. Here we use a mouse genetic approach to determine the biological function of this multifaceted DNA repair enzyme. We find that, unlike other DNA glycosylases, TDG is essential for embryonic development, and that this phenotype is associated with epigenetic aberrations affecting the expression of developmental genes. Fibroblasts derived from Tdg null embryos (mouse embryonic fibroblasts, MEFs) show impaired gene regulation, coincident with imbalanced histone modification and CpG methylation at promoters of affected genes. TDG associates with the promoters of such genes both in fibroblasts and in embryonic stem cells (ESCs), but epigenetic aberrations only appear upon cell lineage commitment. We show that TDG contributes to the maintenance of active and bivalent chromatin throughout cell differentiation, facilitating a proper assembly of chromatin-modifying complexes and initiating base excision repair to counter aberrant de novo methylation. We thus conclude that TDG-dependent DNA repair has evolved to provide epigenetic stability in lineage committed cells.',
'date' => '2011-02-17',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21278727',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 56 => array(
'id' => '592',
'name' => 'Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.',
'authors' => 'Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ',
'description' => 'The H3K9me3 histone modification is often found at promoter regions, where it functions to repress transcription. However, we have previously shown that 3' exons of zinc finger genes (ZNFs) are marked by high levels of H3K9me3. We have now further investigated this unusual location for H3K9me3 in ZNF genes. Neither bioinformatic nor experimental approaches support the hypothesis that the 3' exons of ZNFs are promoters. We further characterized the histone modifications at the 3' ZNF exons and found that these regions also contain H3K36me3, a mark of transcriptional elongation. A genome-wide analysis of ChIP-seq data revealed that ZNFs constitute the majority of genes that have high levels of both H3K9me3 and H3K36me3. These results suggested the possibility that the ZNF genes may be imprinted, with one allele transcribed and one allele repressed. To test the hypothesis that the contradictory modifications are due to imprinting, we used a SNP analysis of RNA-seq data to demonstrate that both alleles of certain ZNF genes having H3K9me3 and H3K36me3 are transcribed. We next analyzed isolated ZNF 3' exons using stably integrated episomes. We found that although the H3K36me3 mark was lost when the 3' ZNF exon was removed from its natural genomic location, the isolated ZNF 3' exons retained the H3K9me3 mark. Thus, the H3K9me3 mark at ZNF 3' exons does not impede transcription and it is regulated independently of the H3K36me3 mark. Finally, we demonstrate a strong relationship between the number of tandemly repeated domains in the 3' exons and the H3K9me3 mark. We suggest that the H3K9me3 at ZNF 3' exons may function to protect the genome from inappropriate recombination rather than to regulate transcription.',
'date' => '2011-02-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21347206',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 57 => array(
'id' => '599',
'name' => 'ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes.',
'authors' => 'Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ',
'description' => 'Only a small percentage of human transcription factors (e.g. those associated with a specific differentiation program) are expressed in a given cell type. Thus, cell fate is mainly determined by cell type-specific silencing of transcription factors that drive different cellular lineages. Several histone modifications have been associated with gene silencing, including H3K27me3 and H3K9me3. We have previously shown that genes for the two largest classes of mammalian transcription factors are marked by distinct histone modifications; homeobox genes are marked by H3K27me3 and zinc finger genes are marked by H3K9me3. Several histone methyltransferases (e.g. G9a and SETDB1) may be involved in mediating the H3K9me3 silencing mark. We have used ChIP-chip and ChIP-seq to demonstrate that SETDB1, but not G9a, is associated with regions of the genome enriched for H3K9me3. One current model is that SETDB1 is recruited to specific genomic locations via interaction with the corepressor TRIM28 (KAP1), which is in turn recruited to the genome via interaction with zinc finger transcription factors that contain a Kruppel-associated box (KRAB) domain. However, specific KRAB-ZNFs that recruit TRIM28 (KAP1) and SETDB1 to the genome have not been identified. We now show that ZNF274 (a KRAB-ZNF that contains 5 C2H2 zinc finger domains), can interact with KAP1 both in vivo and in vitro and, using ChIP-seq, we show that ZNF274 binding sites co-localize with SETDB1, KAP1, and H3K9me3 at the 3' ends of zinc finger genes. Knockdown of ZNF274 with siRNAs reduced the levels of KAP1 and SETDB1 recruitment to the binding sites. These studies provide the first identification of a KRAB domain-containing ZNF that is involved in recruitment of the KAP1 and SETDB1 to specific regions of the human genome.',
'date' => '2010-12-08',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21170338',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 58 => array(
'id' => '74',
'name' => 'In vivo chromatin organization of mouse rod photoreceptors correlates with histone modifications.',
'authors' => 'Kizilyaprak C, Spehner D, Devys D, Schultz P',
'description' => 'BACKGROUND: The folding of genetic information into chromatin plays important regulatory roles in many nuclear processes and particularly in gene transcription. Post translational histone modifications are associated with specific chromatin condensation states and with distinct transcriptional activities. The peculiar chromatin organization of rod photoreceptor nuclei, with a large central domain of condensed chromatin surrounded by a thin border of extended chromatin was used as a model to correlate in vivo chromatin structure, histone modifications and transcriptional activity. METHODOLOGY: We investigated the functional relationships between chromatin compaction, distribution of histone modifications and location of RNA polymerase II in intact murine rod photoreceptors using cryo-preparation methods, electron tomography and immunogold labeling. Our results show that the characteristic central heterochromatin of rod nuclei is organized into concentric domains characterized by a progressive loosening of the chromatin architecture from inside towards outside and by specific combinations of silencing histone marks. The peripheral heterochromatin is formed by closely packed 30 nm fibers as revealed by a characteristic optical diffraction signal. Unexpectedly, the still highly condensed most external heterochromatin domain contains acetylated histones, which are usually associated with active transcription and decondensed chromatin. Histone acetylation is thus not sufficient in vivo for complete chromatin decondensation. The euchromatin domain contains several degrees of chromatin compaction and the histone tails are hyperacetylated, enriched in H3K4 monomethylation and hypo trimethylated on H3K9, H3K27 and H4K20. The transcriptionally active RNA polymerases II molecules are confined in the euchromatin domain and are preferentially located at the vicinity of the interface with heterochromatin. CONCLUSIONS: Our results show that transcription is located in the most decondensed and highly acetylated chromatin regions, but since acetylation is found associated with compact chromatin it is not sufficient to decondense chromatin in vivo. We also show that a combination of histone marks defines distinct concentric heterochromatin domains.',
'date' => '2010-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/20543957',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 59 => array(
'id' => '95',
'name' => 'MicroChIP--a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies.',
'authors' => 'Dahl JA, Collas P',
'description' => 'Chromatin immunoprecipitation (ChIP) is a powerful technique for studying protein-DNA interactions. Drawbacks of current ChIP assays however are a requirement for large cell numbers, which limits applicability of ChIP to rare cell samples, and/or lengthy procedures with limited applications. There are to date no protocols for fast and parallel ChIPs of post-translationally modified histones from small cell numbers or biopsies, and importantly, no protocol allowing for investigations of transcription factor binding in small cell numbers. We report here the development of a micro (micro) ChIP assay suitable for up to nine parallel quantitative ChIPs of modified histones or RNA polymerase II from a single batch of 1000 cells. MicroChIP can also be downscaled to monitor the association of one protein with multiple genomic sites in as few as 100 cells. MicroChIP is applicable to small fresh tissue biopsies, and a cross-link-while-thawing procedure makes the assay suitable for frozen biopsies. Using MicroChIP, we characterize transcriptionally permissive and repressive histone H3 modifications on developmentally regulated promoters in human embryonal carcinoma cells and in osteosarcoma biopsies. muChIP creates possibilities for multiple parallel and rapid transcription factor binding and epigenetic analyses of rare cell and tissue samples.',
'date' => '2008-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/18202078',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 60 => array(
'id' => '76',
'name' => 'A rapid micro chromatin immunoprecipitation assay (microChIP).',
'authors' => 'Dahl JA, Collas P',
'description' => 'Interactions of proteins with DNA mediate many critical nuclear functions. Chromatin immunoprecipitation (ChIP) is a robust technique for studying protein-DNA interactions. Current ChIP assays, however, either require large cell numbers, which prevent their application to rare cell samples or small-tissue biopsies, or involve lengthy procedures. We describe here a 1-day micro ChIP (microChIP) protocol suitable for up to eight parallel histone and/or transcription factor immunoprecipitations from a single batch of 1,000 cells. MicroChIP technique is also suitable for monitoring the association of one protein with multiple genomic sites in 100 cells. Alterations in cross-linking and chromatin preparation steps also make microChIP applicable to approximately 1-mm(3) fresh- or frozen-tissue biopsies. From cell fixation to PCR-ready DNA, the procedure takes approximately 8 h for 16 ChIPs.',
'date' => '2008-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/18536650',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 61 => array(
'id' => '75',
'name' => 'Fast genomic muChIP-chip from 1,000 cells',
'authors' => 'Dahl JA, Reiner AH, Collas P.',
'description' => 'Genome-wide location analysis of histone modifications and transcription factor binding relies on chromatin immunoprecipitation (ChIP) assays. These assays are, however, time-consuming and require large numbers of cells, hindering their application to the analysis of many interesting cell types. We report here a fast microChIP (μChIP) assay for 1,000 cells in combination with microarrays to produce genome-scale surveys of histone modifications. μChIP-chip reliably reproduces data obtained by large-scale assays: H3K9ac and H3K9m3 enrichment profiles are conserved and nucleosome-free regions are revealed.',
'date' => '0000-00-00',
'pmid' => '',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 62 => array(
'id' => '73',
'name' => 'Promoter DNA Methylation Patterns of Differentiated Cells Are Largely Programmed at the Progenitor Stage',
'authors' => 'Sørensen AL, Jacobsen BM, Reiner AH, Andersen IS, Collas P',
'description' => 'Mesenchymal stem cells (MSCs) isolated from various tissues share common phenotypic and functional properties. However, intrinsic molecular evidence supporting these observations has been lacking. Here, we unravel overlapping genome-wide promoter DNA methylation patterns between MSCs from adipose tissue, bone marrow, and skeletal muscle, whereas hematopoietic progenitors are more epigenetically distant from MSCs as a whole. Commonly hypermethylated genes are enriched in signaling, metabolic, and developmental functions, whereas genes hypermethylated only in MSCs are associated with early development functions. We find that most lineage-specification promoters are DNA hypomethylated and harbor a combination of trimethylated H3K4 and H3K27, whereas early developmental genes are DNA hypermethylated with or without H3K27 methylation. Promoter DNA methylation patterns of differentiated cells are largely established at the progenitor stage; yet, differentiation segregates a minor fraction of the commonly hypermethylated promoters, generating greater epigenetic divergence between differentiated cell types than between their undifferentiated counterparts. We also show an effect of promoter CpG content on methylation dynamics upon differentiation and distinct methylation profiles on transcriptionally active and inactive promoters. We infer that methylation state of lineage-specific promoters in MSCs is not a primary determinant of differentiation capacity. Our results support the view of a common origin of mesenchymal progenitors.',
'date' => '0000-00-00',
'pmid' => '',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 63 => array(
'id' => '72',
'name' => 'Chromatin Environment of Histone Variant H3.3 Revealed by Quantitative Imaging and Genome-scale Chromatin and DNA Immunoprecipitation',
'authors' => 'Delbarre E, Jacobsen BM, Reiner AH, Sørensen AL, Kuntziger T, Collas P',
'description' => 'In contrast to canonical histones, histone variant H3.3 is incorporated into chromatin in a replication-independent manner. Posttranslational modifications of H3.3 have been identified; however, the epigenetic environment of incorporated H3.3 is unclear. We have investigated the genomic distribution of epitope-tagged H3.3 in relation to histone modifications, DNA methylation, and transcription in mesenchymal stem cells. Quantitative imaging at the nucleus level shows that H3.3, relative to replicative H3.2 or canonical H2B, is enriched in chromatin domains marked by histone modifications of active or potentially active genes. Chromatin immunoprecipitation of epitope-tagged H3.3 and array hybridization identified 1649 H3.3-enriched promoters, a fraction of which is coenriched in H3K4me3 alone or together with H3K27me3, whereas H3K9me3 is excluded, corroborating nucleus-level imaging data. H3.3-enriched promoters are predominantly CpG-rich and preferentially DNA methylated, relative to the proportion of methylated RefSeq promoters in the genome. Most but not all H3.3-enriched promoters are transcriptionally active, and coenrichment of H3.3 with repressive H3K27me3 correlates with an enhanced proportion of expressed genes carrying this mark. H3.3-target genes are enriched in mesodermal differentiation and signaling functions. Our data suggest that in mesenchymal stem cells, H3.3 targets lineage-priming genes with a potential for activation facilitated by H3K4me3 in facultative association with H3K27me3.',
'date' => '0000-00-00',
'pmid' => '',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
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[maximum depth reached]
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<p><small> <strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022 ) on the SX-8G IP-Star automated system. A titration of the antibody consisting of 1, 2, 5, and 10 μg per ChIP experiment was analysed. IgG (2 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active c-fos and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><small> <strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 0.5 μg of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) on sheared chromatin from 1 million HeLa cells using the “iDeal ChIP-seq” kit (Cat. No. C01010051). The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoter regions of the active GAPDH and EIF4A2 genes, for the coding region of the ZNF510 gene and for the Sat2 satellite repeat (figure 2A). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the BWA algorithm. Figure 2B shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2C and D show the enrichment at ZNF510 and ZNF12 on chromosome 9 and 7, respectively. These results clearly show an enrichment of H3K9me3 at ZNF repeat genes. </small></p>
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<p><small> <strong>Figure 3. Determination of the antibody titer</strong><br /> To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (Cat. No. C15410056), crude serum and flow through in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:60,000. </small></p>
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<p><small> <strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<p><small> <strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot analysis was performed on histone extracts from HeLa cells (15 μg, lane 1) and on recombinant H3 (1 μg, lane2) using the Diagenode antibody against H3K9me3 (Cat. No. C15410056). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left. </small></p>
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<p><small> <strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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<p><small> <strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 0.5 μg of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) on sheared chromatin from 1 million HeLa cells using the “iDeal ChIP-seq” kit (Cat. No. C01010051). The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoter regions of the active GAPDH and EIF4A2 genes, for the coding region of the ZNF510 gene and for the Sat2 satellite repeat (figure 2A). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the BWA algorithm. Figure 2B shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2C and D show the enrichment at ZNF510 and ZNF12 on chromosome 9 and 7, respectively. These results clearly show an enrichment of H3K9me3 at ZNF repeat genes. </small></p>
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<p><small> <strong>Figure 3. Determination of the antibody titer</strong><br /> To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (Cat. No. C15410056), crude serum and flow through in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:60,000. </small></p>
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<p><small> <strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<p><small> <strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot analysis was performed on histone extracts from HeLa cells (15 μg, lane 1) and on recombinant H3 (1 μg, lane2) using the Diagenode antibody against H3K9me3 (Cat. No. C15410056). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left. </small></p>
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<p><small> <strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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'antibody_id' => '109',
'name' => 'H3K27ac Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the acetylated lysine 27</strong> (<strong>H3K27ac</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation Data',
'info1' => '<div class="row">
<div class="small-6 columns">A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1a.png" width="356" /><br /> B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1b.png" width="356" /></div>
<div class="small-6 columns">
<p><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>Figure 1A ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196) and optimized PCR primer pairs for qPCR. ChIP was performed with the “Auto Histone ChIP-seq” kit on the IP-Star automated system, using sheared chromatin from 1,000,000 cells. A titration consisting of 1, 2, 5 and 10 µg of antibody per ChIP experiment was analyzed. IgG (2 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active EIF4A2 and ACTB genes, used as positive controls, and for the inactive TSH2B and MYT1 genes, used as negative controls.</p>
<p>Figure 1B ChIP assays were performed using human K562 cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196)and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 100,000 cells. A titration consisting of 0.2, 0.5, 1 and 2 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active GAPDH and EIF4A2 genes, used as positive controls, and for the coding regions of the inactive MB and MYT1 genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis)</p>
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<div class="small-12 columns"><center>
<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2a.png" /></p>
</center><center>
<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2b.png" /></p>
</center><center>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2c.png" /></p>
</center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>ChIP was performed on sheared chromatin from 100,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) as described above. The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A shows the peak distribution along the complete human X-chromosome. Figure 2 B and C show the peak distribution in two regions surrounding the EIF4A2 and GAPDH positive control genes, respectively. The position of the PCR amplicon, used for validating the ChIP assay is indicated with an arrow.</p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-fig3.jpg" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (cat. No. C15410196) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions surrounding the EIF2S3 gene on the X-chromosome and the CCT5 gene on chromosome 5 (figure 3A and B, respectively).</p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-ELISA-Fig3.png" /></div>
<div class="small-6 columns">
<p><strong>Figure 4. Determination of the antibody titer</strong></p>
<p>To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:8,300.</p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-DB-Fig4.png" /></center></div>
<div class="small-8 columns">
<p><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27ac</strong><br />To test the cross reactivity of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>), a Dot Blot analysis was performed with peptides containing other histone modifications and the unmodified H3K27. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 5 shows a high specificity of the antibody for the modification of interest.</p>
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<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-WB-Fig5.png" /></center></div>
<div class="small-8 columns">
<p><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27ac</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27ac (Cat. No. C1541196). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The marker (in kDa) is shown on the left.</p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-IF-Fig6.png" /></div>
<div class="small-8 columns">
<p><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27ac</strong></p>
<p>HeLa cells were stained with the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/ TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K27ac antibody (top) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown at the bottom.</p>
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'info2' => '<p style="text-align: justify;">Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Acetylation of histone H3K27 is associated with active promoters and enhancers.</p>',
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'name' => 'H3K9me3 Antibody (sample size)',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 9 (H3K9me3)</strong>, using a KLH-conjugated synthetic peptide.</span></p>',
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_ChIP.jpg" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="278" height="189" /></p>
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<div class="small-8 columns">
<p><small> <strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022 ) on the SX-8G IP-Star automated system. A titration of the antibody consisting of 1, 2, 5, and 10 μg per ChIP experiment was analysed. IgG (2 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active c-fos and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq assay" caption="false" width="400" height="358" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " caption="false" width="432" height="214" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="432" height="61" /> <img src="https://www.diagenode.com/img/product/antibodies/C15410056-FigD.jpg" alt="H3K9me3 Antibody validated in ChIP-seq " caption="false" width="700" height="112" /></p>
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<div class="small-6 columns">
<p><small> <strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 0.5 μg of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) on sheared chromatin from 1 million HeLa cells using the “iDeal ChIP-seq” kit (Cat. No. C01010051). The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoter regions of the active GAPDH and EIF4A2 genes, for the coding region of the ZNF510 gene and for the Sat2 satellite repeat (figure 2A). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the BWA algorithm. Figure 2B shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2C and D show the enrichment at ZNF510 and ZNF12 on chromosome 9 and 7, respectively. These results clearly show an enrichment of H3K9me3 at ZNF repeat genes. </small></p>
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<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" caption="false" width="278" height="212" /></p>
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<div class="small-8 columns">
<p><small> <strong>Figure 3. Determination of the antibody titer</strong><br /> To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (Cat. No. C15410056), crude serum and flow through in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:60,000. </small></p>
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<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" caption="false" width="400" height="304" /></p>
</div>
<div class="small-8 columns">
<p><small> <strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western Blot" caption="false" width="200" height="213" /></p>
</div>
<div class="small-8 columns">
<p><small> <strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot analysis was performed on histone extracts from HeLa cells (15 μg, lane 1) and on recombinant H3 (1 μg, lane2) using the Diagenode antibody against H3K9me3 (Cat. No. C15410056). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left. </small></p>
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<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-IF.jpg" alt="H3K9me3 Antibody validated in Immunofluorescence " caption="false" width="354" height="117" /></p>
</div>
<div class="small-7 columns">
<p><small> <strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
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'name' => 'Chromatin Environment of Histone Variant H3.3 Revealed by Quantitative Imaging and Genome-scale Chromatin and DNA Immunoprecipitation',
'authors' => 'Delbarre E, Jacobsen BM, Reiner AH, Sørensen AL, Kuntziger T, Collas P',
'description' => 'In contrast to canonical histones, histone variant H3.3 is incorporated into chromatin in a replication-independent manner. Posttranslational modifications of H3.3 have been identified; however, the epigenetic environment of incorporated H3.3 is unclear. We have investigated the genomic distribution of epitope-tagged H3.3 in relation to histone modifications, DNA methylation, and transcription in mesenchymal stem cells. Quantitative imaging at the nucleus level shows that H3.3, relative to replicative H3.2 or canonical H2B, is enriched in chromatin domains marked by histone modifications of active or potentially active genes. Chromatin immunoprecipitation of epitope-tagged H3.3 and array hybridization identified 1649 H3.3-enriched promoters, a fraction of which is coenriched in H3K4me3 alone or together with H3K27me3, whereas H3K9me3 is excluded, corroborating nucleus-level imaging data. H3.3-enriched promoters are predominantly CpG-rich and preferentially DNA methylated, relative to the proportion of methylated RefSeq promoters in the genome. Most but not all H3.3-enriched promoters are transcriptionally active, and coenrichment of H3.3 with repressive H3K27me3 correlates with an enhanced proportion of expressed genes carrying this mark. H3.3-target genes are enriched in mesodermal differentiation and signaling functions. Our data suggest that in mesenchymal stem cells, H3.3 targets lineage-priming genes with a potential for activation facilitated by H3K4me3 in facultative association with H3K27me3.',
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'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, ELISA, DB, WB and IF. Batch specific data available on the website.',
'meta_title' => 'H3K9me3 Antibody - ChIP-seq Grade (C15410056) | Diagenode',
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'id' => '2216',
'antibody_id' => '120',
'name' => 'H3K9me3 Antibody - ChIP-seq Grade',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone H3 containing the trimethylated lysine 9 (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation data',
'info1' => '<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_ChIP.jpg" alt="H3K9me3 Antibody ChIP Grade" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1 and 2 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control.<br /> <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for the ZNF510 gene and the Sat2 satellite repeat, used as positive controls, and for the EIF4A2 and GAPDH promoters, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).<br /> <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K9me1, H3K9me2, H3K9me3, H3K4me3, H3K27me3, H3K36me3, H4K20me3 modifications and the unmodified H3K9 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K9me3 modification when using 0.5 or 1 µg. With 2 µg of antibody, some recovery of the H3K27me3 nucleosome is observed.</small></p>
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<div class="row">
<div class="small-12 columns">
<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq Grade" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " /></p>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" /></p>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq4000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoom-in to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B and 2C show the enrichment along the ZNF510 positive control target and at the KCNQ1 imprinted gene.</small></p>
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<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" /></p>
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<div class="small-6 columns">
<p><strong></strong></p>
<p><strong></strong></p>
<p><small><strong>Figure 3. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410056) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:198,000.</small></p>
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<p></p>
<p></p>
<p></p>
<p></p>
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" /></p>
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<div class="small-8 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410056) with peptides containing other modifications of histone H3 and H4 and the unmodified sequence of histone H3. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 4 shows a high specificity of the antibody for the modification of interest.</small></p>
<p></p>
<p></p>
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western blot" /></p>
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<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot was performed on 40 µg whole cell extracts from HeLa cells (lane 1) and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K9me3 (cat. No. C15410056). The antibody was diluted 1:2,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right, the marker (in kDa) is shown on the left.</small></p>
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'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, ELISA, DB, WB and IF. Batch specific data available on the website.',
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'Antibody' => array(
'host' => '*****',
'id' => '120',
'name' => 'H3K9me3 polyclonal antibody',
'description' => 'Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Trimethylation of histone H3K9 is associated with satellite repeat regions and ZNF repeat genes.',
'clonality' => '',
'isotype' => '',
'lot' => 'A2810P',
'concentration' => '1.85 µg/µl',
'reactivity' => 'Human, mouse, zebrafish, trout, Daphnia, Arabidopsis, Drosophila, silena latifolia: positive. Other species: not tested.',
'type' => 'Polyclonal ChIP grade, ChIP-seq grade',
'purity' => 'Affinity purified polyclonal antibody.',
'classification' => 'Classic',
'application_table' => '<table>
<thead>
<tr>
<th>Applications</th>
<th>Suggested dilution</th>
<th>References</th>
</tr>
</thead>
<tbody>
<tr>
<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>0.5 - 1 µg per ChIP</td>
<td>Fig 1, 2</td>
</tr>
<tr>
<td>ELISA</td>
<td>1:1,000 - 1:10,000</td>
<td>Fig 3</td>
</tr>
<tr>
<td>Dot Blotting</td>
<td>1:2,000</td>
<td>Fig 4</td>
</tr>
<tr>
<td>Western Blotting</td>
<td>1:2,000</td>
<td>Fig 5</td>
</tr>
</tbody>
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'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone H3 containing the trimethylated lysine 9 (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_ChIP.jpg" alt="H3K9me3 Antibody ChIP Grade" /></p>
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1 and 2 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control.<br /> <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for the ZNF510 gene and the Sat2 satellite repeat, used as positive controls, and for the EIF4A2 and GAPDH promoters, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).<br /> <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K9me1, H3K9me2, H3K9me3, H3K4me3, H3K27me3, H3K36me3, H4K20me3 modifications and the unmodified H3K9 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K9me3 modification when using 0.5 or 1 µg. With 2 µg of antibody, some recovery of the H3K27me3 nucleosome is observed.</small></p>
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<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " /></p>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" /></p>
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<div class="row">
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<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq4000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoom-in to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B and 2C show the enrichment along the ZNF510 positive control target and at the KCNQ1 imprinted gene.</small></p>
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<p><strong></strong></p>
<p><strong></strong></p>
<p><small><strong>Figure 3. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410056) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:198,000.</small></p>
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<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410056) with peptides containing other modifications of histone H3 and H4 and the unmodified sequence of histone H3. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 4 shows a high specificity of the antibody for the modification of interest.</small></p>
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<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot was performed on 40 µg whole cell extracts from HeLa cells (lane 1) and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K9me3 (cat. No. C15410056). The antibody was diluted 1:2,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right, the marker (in kDa) is shown on the left.</small></p>
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'description' => 'Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Trimethylation of histone H3K9 is associated with satellite repeat regions and ZNF repeat genes.',
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'concentration' => '1.85 µg/µl',
'reactivity' => 'Human, mouse, zebrafish, trout, Daphnia, Arabidopsis, Drosophila, silena latifolia: positive. Other species: not tested.',
'type' => 'Polyclonal ChIP grade, ChIP-seq grade',
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<th>Suggested dilution</th>
<th>References</th>
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<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>0.5 - 1 µg per ChIP</td>
<td>Fig 1, 2</td>
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<td>ELISA</td>
<td>1:1,000 - 1:10,000</td>
<td>Fig 3</td>
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<td>Dot Blotting</td>
<td>1:2,000</td>
<td>Fig 4</td>
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<td>Western Blotting</td>
<td>1:2,000</td>
<td>Fig 5</td>
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<p><small><sup>*</sup> Please note that the optimal antibody amount per IP should be determined by the end-user. We recommend testing 0.5-5 µg per IP.</small></p>',
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1 and 2 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control.<br /> <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for the ZNF510 gene and the Sat2 satellite repeat, used as positive controls, and for the EIF4A2 and GAPDH promoters, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).<br /> <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K9me1, H3K9me2, H3K9me3, H3K4me3, H3K27me3, H3K36me3, H4K20me3 modifications and the unmodified H3K9 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K9me3 modification when using 0.5 or 1 µg. With 2 µg of antibody, some recovery of the H3K27me3 nucleosome is observed.</small></p>
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<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq Grade" /></p>
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<div class="row">
<div class="small-12 columns">
<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " /></p>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" /></p>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq4000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoom-in to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B and 2C show the enrichment along the ZNF510 positive control target and at the KCNQ1 imprinted gene.</small></p>
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<div class="extra-spaced"></div>
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<p><strong></strong></p>
<p><strong></strong></p>
<p><small><strong>Figure 3. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410056) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:198,000.</small></p>
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<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" /></p>
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<div class="small-8 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410056) with peptides containing other modifications of histone H3 and H4 and the unmodified sequence of histone H3. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 4 shows a high specificity of the antibody for the modification of interest.</small></p>
<p></p>
<p></p>
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<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot was performed on 40 µg whole cell extracts from HeLa cells (lane 1) and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K9me3 (cat. No. C15410056). The antibody was diluted 1:2,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right, the marker (in kDa) is shown on the left.</small></p>
</div>
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'format' => '50 µg',
'catalog_number' => 'C15410056',
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'sf_code' => 'C15410056-D001-000581',
'type' => 'FRE',
'search_order' => '03-Antibody',
'price_EUR' => '380',
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'slug' => 'h3k9me3-polyclonal-antibody-classic-50-ug',
'meta_title' => 'H3K9me3 Antibody - ChIP-seq Grade (C15410056) | Diagenode',
'meta_keywords' => '',
'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, ELISA, DB, WB and IF. Batch specific data available on the website.',
'modified' => '2021-10-20 09:33:57',
'created' => '2015-06-29 14:08:20'
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(int) 0 => array(
'id' => '1836',
'antibody_id' => null,
'name' => 'iDeal ChIP-seq kit for Histones',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/ideal-chipseq-for-histones-complete-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>Don’t risk wasting your precious sequencing samples. Diagenode’s validated <strong>iDeal ChIP-seq kit for Histones</strong> has everything you need for a successful start-to-finish <strong>ChIP of histones prior to Next-Generation Sequencing</strong>. The complete kit contains all buffers and reagents for cell lysis, chromatin shearing, immunoprecipitation and DNA purification. In addition, unlike competing solutions, the kit contains positive and negative control antibodies (H3K4me3 and IgG, respectively) as well as positive and negative control PCR primers pairs (GAPDH TSS and Myoglobin exon 2, respectively) for your convenience and a guarantee of optimal results. The kit has been validated on multiple histone marks.</p>
<p> The iDeal ChIP-seq kit for Histones<strong> </strong>is perfect for <strong>cells</strong> (<strong>100,000 cells</strong> to <strong>1,000,000 cells</strong> per IP) and has been validated for <strong>tissues</strong> (<strong>1.5 mg</strong> to <strong>5 mg</strong> of tissue per IP).</p>
<p> The iDeal ChIP-seq kit is the only kit on the market validated for the major sequencing systems. Our expertise in ChIP-seq tools allows reproducible and efficient results every time.</p>
<p></p>
<p> <strong></strong></p>
<p></p>',
'label1' => 'Characteristics',
'info1' => '<ul style="list-style-type: disc;">
<li>Highly <strong>optimized</strong> protocol for ChIP-seq from cells and tissues</li>
<li><strong>Validated</strong> for ChIP-seq with multiple histones marks</li>
<li>Most <strong>complete</strong> kit available (covers all steps, including the control antibodies and primers)</li>
<li>Optimized chromatin preparation in combination with the Bioruptor ensuring the best <strong>epitope integrity</strong></li>
<li>Magnetic beads make ChIP easy, fast and more <strong>reproducible</strong></li>
<li>Combination with Diagenode ChIP-seq antibodies provides high yields with excellent <strong>specificity</strong> and <strong>sensitivity</strong></li>
<li>Purified DNA suitable for any downstream application</li>
<li>Easy-to-follow protocol</li>
</ul>
<p>Note: to obtain optimal results, this kit should be used in combination with the DiaMag1.5 - magnetic rack.</p>
<h3>ChIP-seq on cells</h3>
<p><img src="https://www.diagenode.com/img/product/kits/iDeal-kit-C01010053-figure-1.jpg" alt="Figure 1A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 1A. The high consistency of the iDeal ChIP-seq kit on the Ion Torrent™ PGM™ (Life Technologies) and GAIIx (Illumina<sup>®</sup>)</strong><br /> ChIP was performed on sheared chromatin from 1 million HelaS3 cells using the iDeal ChIP-seq kit and 1 µg of H3K4me3 positive control antibody. Two different biological samples have been analyzed using two different sequencers - GAIIx (Illumina<sup>®</sup>) and PGM™ (Ion Torrent™). The expected ChIP-seq profile for H3K4me3 on the GAPDH promoter region has been obtained.<br /> Image A shows a several hundred bp along chr12 with high similarity of read distribution despite the radically different sequencers. Image B is a close capture focusing on the GAPDH that shows that even the peak structure is similar.</p>
<p class="text-center"><strong>Perfect match between ChIP-seq data obtained with the iDeal ChIP-seq workflow and reference dataset</strong></p>
<p><img src="https://www.diagenode.com/img/product/kits/perfect-match-between-chipseq-data.png" alt="Figure 1B" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 1B.</strong> The ChIP-seq dataset from this experiment has been compared with a reference dataset from the Broad Institute. We observed a perfect match between the top 40% of Diagenode peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>
<p><img src="https://www.diagenode.com/img/product/kits/iDeal-kit-C01010053-figure-2.jpg" alt="Figure 2" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 2. Efficient and easy chromatin shearing using the Bioruptor<sup>®</sup> and Shearing buffer iS1 from the iDeal ChIP-seq kit</strong><br /> Chromatin from 1 million of Hela cells was sheared using the Bioruptor<sup>®</sup> combined with the Bioruptor<sup>®</sup> Water cooler (Cat No. BioAcc-cool) during 3 rounds of 10 cycles of 30 seconds “ON” / 30 seconds “OFF” at HIGH power setting (position H). Diagenode 1.5 ml TPX tubes (Cat No. M-50001) were used for chromatin shearing. Samples were gently vortexed before and after performing each sonication round (rounds of 10 cycles), followed by a short centrifugation at 4°C to recover the sample volume at the bottom of the tube. The sheared chromatin was then decross-linked as described in the kit manual and analyzed by agarose gel electrophoresis.</p>
<p><img src="https://www.diagenode.com/img/product/kits/iDeal-kit-C01010053-figure-3.jpg" alt="Figure 3" style="display: block; margin-left: auto; margin-right: auto;" width="264" height="320" /></p>
<p><strong>Figure 3. Validation of ChIP by qPCR: reliable results using Diagenode’s ChIP-seq grade H3K4me3 antibody, isotype control and sets of validated primers</strong><br /> Specific enrichment on positive loci (GAPDH, EIF4A2, c-fos promoter regions) comparing to no enrichment on negative loci (TSH2B promoter region and Myoglobin exon 2) was detected by qPCR. Samples were prepared using the Diagenode iDeal ChIP-seq kit. Diagenode ChIP-seq grade antibody against H3K4me3 and the corresponding isotype control IgG were used for immunoprecipitation. qPCR amplification was performed with sets of validated primers.</p>
<h3>ChIP-seq on tissue</h3>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-figure-h3k4me3.jpg" alt="Figure 4A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 4A.</strong> Chromatin Immunoprecipitation has been performed using chromatin from mouse liver tissue, the iDeal ChIP-seq kit for Histones and the Diagenode ChIP-seq-grade H3K4me3 (Cat. No. C15410003) antibody. The IP'd DNA was subsequently analysed on an Illumina® HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. This figure shows the peak distribution in a region surrounding the GAPDH positive control gene.</p>
<p><img src="https://www.diagenode.com/img/product/kits/match-of-the-top40-peaks-2.png" alt="Figure 4B" caption="false" style="display: block; margin-left: auto; margin-right: auto;" width="700" height="280" /></p>
<p><strong>Figure 4B.</strong> The ChIP-seq dataset from this experiment has been compared with a reference dataset from the Broad Institute. We observed a perfect match between the top 40% of Diagenode peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>',
'label2' => 'Species, cell lines, tissues tested',
'info2' => '<p>The iDeal ChIP-seq Kit for Histones is compatible with a broad variety of cell lines, tissues and species - some examples are shown below. Other species / cell lines / tissues can be used with this kit.</p>
<p><u>Cell lines:</u></p>
<p>Human: A549, A673, CD8+ T, Blood vascular endothelial cells, Lymphatic endothelial cells, fibroblasts, K562, MDA-MB231</p>
<p>Pig: Alveolar macrophages</p>
<p>Mouse: C2C12, primary HSPC, synovial fibroblasts, HeLa-S3, FACS sorted cells from embryonic kidneys, macrophages, mesodermal cells, myoblasts, NPC, salivary glands, spermatids, spermatocytes, skeletal muscle stem cells, stem cells, Th2</p>
<p>Hamster: CHO</p>
<p>Other cell lines / species: compatible, not tested</p>
<p><u>Tissues</u></p>
<p>Bee – brain</p>
<p>Daphnia – whole animal</p>
<p>Horse – brain, heart, lamina, liver, lung, skeletal muscles, ovary</p>
<p>Human – Erwing sarcoma tumor samples</p>
<p>Other tissues: compatible, not tested</p>
<p>Did you use the iDeal ChIP-seq for Histones Kit on other cell line / tissue / species? <a href="mailto:agnieszka.zelisko@diagenode.com?subject=Species, cell lines, tissues tested with the iDeal ChIP-seq Kit for TF&body=Dear Customer,%0D%0A%0D%0APlease, leave below your feedback about the iDeal ChIP-seq for Transcription Factors (cell / tissue type, species, other information...).%0D%0A%0D%0AThank you for sharing with us your experience !%0D%0A%0D%0ABest regards,%0D%0A%0D%0AAgnieszka Zelisko-Schmidt, PhD">Let us know!</a></p>',
'label3' => ' Additional solutions compatible with iDeal ChIP-seq Kit for Histones',
'info3' => '<p><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin EasyShear Kit - Ultra Low SDS </a>optimizes chromatin shearing, a critical step for ChIP.</p>
<p> The <a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq">MicroPlex Library Preparation Kit </a>provides easy and optimal library preparation of ChIPed samples.</p>
<p><a href="../categories/chip-seq-grade-antibodies">ChIP-seq grade anti-histone antibodies</a> provide high yields with excellent specificity and sensitivity.</p>
<p> Plus, for our IP-Star Automation users for automated ChIP, check out our <a href="../p/auto-ideal-chip-seq-kit-for-histones-x24-24-rxns">automated</a> version of this kit.</p>',
'format' => '4 chrom. prep./24 IPs',
'catalog_number' => 'C01010051',
'old_catalog_number' => 'AB-001-0024',
'sf_code' => 'C01010051-',
'type' => 'RFR',
'search_order' => '04-undefined',
'price_EUR' => '915',
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'slug' => 'ideal-chip-seq-kit-x24-24-rxns',
'meta_title' => 'iDeal ChIP-seq kit x24',
'meta_keywords' => '',
'meta_description' => 'iDeal ChIP-seq kit x24',
'modified' => '2023-04-20 16:00:20',
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(int) 1 => array(
'id' => '1856',
'antibody_id' => null,
'name' => 'True MicroChIP-seq Kit',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/truemicrochipseq-kit-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>The <b>True </b><b>MicroChIP-seq</b><b> kit </b>provides a robust ChIP protocol suitable for the investigation of histone modifications within chromatin from as few as <b>10 000 cells</b>, including <b>FACS sorted cells</b>. The kit can be used for chromatin preparation for downstream ChIP-qPCR or ChIP-seq analysis. The <b>complete kit</b> contains everything you need for start-to-finish ChIP including all validated buffers and reagents for chromatin shearing, immunoprecipitation and DNA purification for exceptional <strong>ChIP-qPCR</strong> or <strong>ChIP-seq</strong> results. In addition, positive control antibodies and negative control PCR primers are included for your convenience and assurance of result sensitivity and specificity.</p>
<p>The True MicroChIP-seq kit offers unique benefits:</p>
<ul>
<li>An <b>optimized chromatin preparation </b>protocol compatible with low number of cells (<b>10.000</b>) in combination with the Bioruptor™ shearing device</li>
<li>Most <b>complete kit </b>available (covers all steps and includes control antibodies and primers)</li>
<li><b>Magnetic beads </b>make ChIP easy, fast, and more reproducible</li>
<li>MicroChIP DiaPure columns (included in the kit) enable the <b>maximum recovery </b>of immunoprecipitation DNA suitable for any downstream application</li>
<li><b>Excellent </b><b>ChIP</b><b>-seq </b>result when combined with <a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq">MicroPlex</a><a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq"> Library Preparation kit </a>adapted for low input</li>
</ul>
<p>For fast ChIP-seq on low input – check out Diagenode’s <a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns">µ</a><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns">ChIPmentation</a><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns"> for histones</a>.</p>
<p><sub>The True MicroChIP-seq kit, Cat. No. C01010132 is an upgraded version of the kit True MicroChIP, Cat. No. C01010130, with the new validated protocols (e.g. FACS sorted cells) and MicroChIP DiaPure columns included in the kit.</sub></p>',
'label1' => 'Characteristics',
'info1' => '<ul>
<li><b>Revolutionary:</b> Only 10,000 cells needed for complete ChIP-seq procedure</li>
<li><b>Validated on</b> studies for histone marks</li>
<li><b>Automated protocol </b>for the IP-Star<sup>®</sup> Compact Automated Platform available</li>
</ul>
<p></p>
<p>The True MicroChIP-seq kit protocol has been optimized for the use of 10,000 - 100,000 cells per immunoprecipitation reaction. Regarding chromatin immunoprecipitation, three protocol variants have been optimized:<br />starting with a batch, starting with an individual sample and starting with the FACS-sorted cells.</p>
<div><button id="readmorebtn" style="background-color: #b02736; color: white; border-radius: 5px; border: none; padding: 5px;">Show Workflow</button></div>
<p><br /> <img src="https://www.diagenode.com/img/product/kits/workflow-microchip.png" id="workflowchip" class="hidden" width="600px" /></p>
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<div class="carrousel" style="background-position: center;">
<div class="container">
<div class="row" style="background: rgba(255,255,255,0.1);">
<div class="large-12 columns truemicro-slider" id="truemicro-slider">
<div>
<h3>High efficiency ChIP on 10,000 cells</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-histone-results.png" width="800px" /></div>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center>
<p><small><strong>Figure 1. </strong>ChIP efficiency on 10,000 cells. ChIP was performed on human Hela cells using the Diagenode antibodies <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (Cat. No. C15410003), <a href="https://www.diagenode.com/en/p/h3k27ac-polyclonal-antibody-classic-50-mg-42-ml">H3K27ac</a> (C15410174), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-classic-50-ug">H3K9me3</a> (C15410056) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-classic-50-mg-34-ml">H3K27me3</a> (C15410069). Sheared chromatin from 10,000 cells and 0.1 µg (H3K27ac), 0.25 µg (H3K4me3 and H3K27me3) or 0.5 µg (H3K9me3) of the antibody were used per IP. Corresponding amount of IgG was used as control. Quantitative PCR was performed with primers for corresponding positive and negative loci. Figure shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
</center></div>
</div>
<div>
<h3>True MicroChIP-seq protocol in a combination with MicroPlex library preparation kit results in reliable and accurate sequencing data</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><img src="https://www.diagenode.com/img/product/kits/fig2-truemicro.jpg" alt="True MicroChip results" width="800px" /></div>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center>
<p><small><strong>Figure 2.</strong> Integrative genomics viewer (IGV) visualization of ChIP-seq experiments using 50.000 of K562 cells. ChIP has been performed accordingly to True MicroChIP protocol followed by the library preparation using MicroPlex Library Preparation Kit (C05010001). The above figure shows the peaks from ChIP-seq experiments using the following antibodies: H3K4me1 (C15410194), H3K9/14ac (C15410200), H3K27ac (C15410196) and H3K36me3 (C15410192).</small></p>
</center></div>
</div>
<div>
<h3>Successful chromatin profiling from 10.000 of FACS-sorted cells</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><img src="https://www.diagenode.com/img/product/kits/fig3ab-truemicro.jpg" alt="small non coding RNA" width="800px" /></div>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center>
<p><small><strong>Figure 3.</strong> (A) Integrative genomics viewer (IGV) visualization of ChIP-seq experiments and heatmap 3kb upstream and downstream of the TSS (B) for H3K4me3. ChIP has been performed using 10.000 of FACS-sorted cells (K562) and H3K4me3 antibody (C15410003) accordingly to True MicroChIP protocol followed by the library preparation using MicroPlex Library Preparation Kit (C05010001). Data were compared to ENCODE standards.</small></p>
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'label2' => 'Additional solutions compatible with the True MicroChIP-seq Kit',
'info2' => '<p><span style="font-weight: 400;">The <a href="https://www.diagenode.com/en/p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin EasyShear Kit – High SDS</a></span><span style="font-weight: 400;"> Recommended for the optimizing chromatin shearing.</span></p>
<p><a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies"><span style="font-weight: 400;">ChIP-seq grade antibodies</span></a><span style="font-weight: 400;"> for high yields, specificity, and sensitivity.</span></p>
<p><span style="font-weight: 400;">Check the list of available </span><a href="https://www.diagenode.com/en/categories/primer-pairs"><span style="font-weight: 400;">primer pairs</span></a><span style="font-weight: 400;"> designed for high specificity to specific genomic regions.</span></p>
<p><span style="font-weight: 400;">For library preparation of immunoprecipitated samples we recommend to use the </span><b> </b><a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq"><span style="font-weight: 400;">MicroPlex Library Preparation Kit</span></a><span style="font-weight: 400;"> - validated for library preparation from picogram inputs.</span></p>
<p><span style="font-weight: 400;">For IP-Star Automation users, check out the </span><a href="https://www.diagenode.com/en/p/auto-true-microchip-kit-16-rxns"><span style="font-weight: 400;">automated version</span></a><span style="font-weight: 400;"> of this kit.</span></p>
<p><span style="font-weight: 400;">Application note: </span><a href="https://www.diagenode.com/files/application_notes/Diagenode_AATI_Joint.pdf"><span style="font-weight: 400;">Best Workflow Practices for ChIP-seq Analysis with Small Samples</span></a></p>
<p></p>',
'label3' => 'Species, cell lines, tissues tested',
'info3' => '<p>The True MicroChIP-seq kit is compatible with a broad variety of cell lines, tissues and species - some examples are shown below. Other species / cell lines / tissues can be used with this kit.</p>
<p><strong>Cell lines:</strong></p>
<p>Bovine: blastocysts,<br />Drosophila: embryos, salivary glands<br />Human: EndoC-ẞH1 cells, HeLa cells, PBMC, urothelial cells<br />Mouse: adipocytes, B cells, blastocysts, pre-B cells, BMDM cells, chondrocytes, embryonic stem cells, KH2 cells, LSK cells, macrophages, MEP cells, microglia, NK cells, oocytes, pancreatic cells, P19Cl6 cells, RPE cells,</p>
<p>Other cell lines / species: compatible, not tested</p>
<p><strong>Tissues:</strong></p>
<p>Horse: adipose tissue</p>
<p>Mice: intestine tissue</p>
<p>Other tissues: not tested</p>',
'format' => '20 rxns',
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'meta_title' => 'True MicroChIP-seq Kit | Diagenode C01010132',
'meta_keywords' => '',
'meta_description' => 'True MicroChIP-seq Kit provides a robust ChIP protocol suitable for the investigation of histone modifications within chromatin from as few as 10 000 cells, including FACS sorted cells. Compatible with ChIP-qPCR as well as ChIP-seq.',
'modified' => '2023-04-20 16:06:10',
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'id' => '1927',
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'name' => 'MicroPlex Library Preparation Kit v2 (12 indexes)',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/MicroPlex-Libary-Prep-Kit-v2-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p><span><strong>Specifically optimized for ChIP-seq</strong></span><br /><br /><span>The MicroPlex Library Preparation™ kit is the only kit on the market which is validated for ChIP-seq and which allows the preparation of indexed libraries from just picogram inputs. In combination with the </span><a href="./true-microchip-kit-x16-16-rxns">True MicroChIP kit</a><span>, it allows for performing ChIP-seq on as few as 10,000 cells. Less input, fewer steps, fewer supplies, faster time to results! </span></p>
<p>The MicroPlex v2 kit (Cat. No. C05010012) contains all necessary reagents including single indexes for multiplexing up to 12 samples using single barcoding. For higher multiplexing (using dual indexes) check <a href="https://www.diagenode.com/en/p/microplex-lib-prep-kit-v3-48-rxns">MicroPlex Library Preparation Kits v3</a>.</p>',
'label1' => 'Characteristics',
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<li><strong>1 tube, 2 hours, 3 steps</strong> protocol</li>
<li><strong>Input: </strong>50 pg – 50 ng</li>
<li><strong>Reduce potential bias</strong> - few PCR amplification cycles needed</li>
<li><strong>High sensitivity ChIP-seq</strong> - low PCR duplication rate</li>
<li><strong>Great multiplexing flexibility</strong> with 12 barcodes (8 nt) included</li>
<li><strong>Validated with the <a href="https://www.diagenode.com/p/sx-8g-ip-star-compact-automated-system-1-unit" title="IP-Star Automated System">IP-Star<sup>®</sup> Automated Platform</a></strong></li>
</ul>
<h3>How it works</h3>
<center><img src="https://www.diagenode.com/img/product/kits/microplex-method-overview-v2.png" /></center>
<p style="margin-bottom: 0;"><small><strong>Microplex workflow - protocol with single indexes</strong><br />An input of 50 pg to 50 ng of fragmented dsDNA is converted into sequencing-ready libraries for Illumina® NGS platforms using a fast and simple 3-step protocol</small></p>
<ul class="accordion" data-accordion="" id="readmore" style="margin-left: 0;">
<li class="accordion-navigation"><a href="#first" style="background: #ffffff; padding: 0rem; margin: 0rem; color: #13b2a2;"><small>Read more about MicroPlex workflow</small></a>
<div id="first" class="content">
<p><small><strong>Step 1. Template Preparation</strong> provides efficient repair of the fragmented double-stranded DNA input.</small></p>
<p><small>In this step, the DNA is repaired and yields molecules with blunt ends.</small></p>
<p><small><strong>Step 2. Library Synthesis.</strong> enables ligation of MicroPlex patented stem- loop adapters.</small></p>
<p><small>In the next step, stem-loop adaptors with blocked 5’ ends are ligated with high efficiency to the 5’ end of the genomic DNA, leaving a nick at the 3’ end. The adaptors cannot ligate to each other and do not have single- strand tails, both of which contribute to non-specific background found with many other NGS preparations.</small></p>
<p><small><strong>Step 3. Library Amplification</strong> enables extension of the template, cleavage of the stem-loop adaptors, and amplification of the library. Illumina- compatible indexes are also introduced using a high-fidelity, highly- processive, low-bias DNA polymerase.</small></p>
<p><small>In the final step, the 3’ ends of the genomic DNA are extended to complete library synthesis and Illumina-compatible indexes are added through a high-fidelity amplification. Any remaining free adaptors are destroyed. Hands-on time and the risk of contamination are minimized by using a single tube and eliminating intermediate purifications.</small></p>
<p><small>Obtained libraries are purified, quantified and sized. The libraries pooling can be performed as well before sequencing.</small></p>
</div>
</li>
</ul>
<p></p>
<h3>Reliable detection of enrichments in ChIP-seq</h3>
<p><img src="https://www.diagenode.com/img/product/kits/microplex-library-prep-kit-figure-a.png" alt="Reliable detection of enrichments in ChIP-seq figure 1" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure A.</strong> ChIP has been peformed with H3K4me3 antibody, amplification of 17 pg of DNA ChIP'd from 10.000 cells and amplification of 35 pg of DNA ChIP'd from 100.000 cells (control experiment). The IP'd DNA was amplified and transformed into a sequencing-ready preparation for the Illumina plateform with the MicroPlex Library Preparation kit. The library was then analysed on an Illumina<sup>®</sup> Genome Analyzer. Cluster generation and sequencing were performed according to the manufacturer's instructions.</p>
<p><img src="https://www.diagenode.com/img/product/kits/microplex-library-prep-kit-figure-b.png" alt="Reliable detection of enrichments in ChIP-seq figure 2" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure B.</strong> We observed a perfect match between the top 40% of True MicroChIP peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>',
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'name' => 'H3K9me3 Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone<strong> H3 containing the trimethylated lysine 9</strong> (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig1.png" /></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (cat. No. C15410193) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). A titration of the antibody consisting of 0.5, 1, 2, and 5 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
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<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2a.png" width="700" /></center><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2b.png" width="700" /></center><center>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2c.png" width="700" /></center><center>D.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2d.png" width="700" /></center></div>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with 0.5 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410193) on sheared chromatin from 1,000,000 HeLa cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq 2000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B, 2C and 2D show the enrichment along the ZNF510 positive control target and at the H19 and KCNQ1 imprinted genes.</small></p>
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<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-CT-Fig3a.png" width="700" /></center><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-CT-Fig3b.png" width="700" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K9me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410193) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in a genomic regions on chromosome 1 containing several ZNF repeat genes and in a genomic region surrounding the KCNQ1 imprinting control gene on chromosome 11 (figure 3A and B, respectively).</small></p>
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<div class="row">
<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-Elisa-Fig4.png" /></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410193) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:87,000.</small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-DB-Fig5.png" /></center></div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410193) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 5 shows a high specificity of the antibody for the modification of interest.</small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-WB-Fig6.png" /></center></div>
<div class="small-8 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K9me3 (cat. No. C15410193). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-IF-Fig7.png" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br />HeLa cells were stained with the Diagenode antibody against H3K9me3 (cat. No. C15410193) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (middle) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The left panel shows staining of the nuclei with DAPI. A merge of both stainings is shown on the right.</small></p>
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'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 4</strong> (<strong>H3K4me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me3</strong><br />ChIP assays were performed using human K562 cells, the Diagenode antibody against H3K4me3 (cat. No. C15410003) and optimized PCR primer pairs for qPCR. ChIP was performed with the iDeal ChIP-seq kit (cat. No. C01010051), using sheared chromatin from 500,000 cells. A titration consisting of 0.5, 1, 2 and 5 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers specific for the promoter of the active genes GAPDH and EIF4A2, used as positive controls, and for the inactive MYOD1 gene and the Sat2 satellite repeat, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p></p>
<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2a-ChIP-seq.jpg" width="800" /></center><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2b-ChIP-seq.jpg" width="800" /></center><center>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2c-ChIP-seq.jpg" width="800" /></center><center>D.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2d-ChIP-seq.jpg" width="800" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me3</strong><br />ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using 1 µg of the Diagenode antibody against H3K4me3 (cat. No. C15410003) as described above. The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2 shows the peak distribution along the complete sequence and a 600 kb region of the X-chromosome (figure 2A and B) and in two regions surrounding the GAPDH and EIF4A2 positive control genes, respectively (figure 2C and D). These results clearly show an enrichment of the H3K4 trimethylation at the promoters of active genes.</small></p>
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<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-cuttag-a.png" width="800" /></center></div>
<div class="small-12 columns"><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-cuttag-b.png" width="800" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K4me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 0.5 µg of the Diagenode antibody against H3K4me3 (cat. No. C15410003) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions surrounding the FOS gene on chromosome 14 and the ACTB gene on chromosome 7 (figure 3A and B, respectively).</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig3-ELISA.jpg" width="350" /></center><center></center><center></center><center></center><center></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody against H3K4me3 (cat. No. C15410003). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:11,000.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig4-DB.jpg" /></div>
<div class="small-6 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K4me3</strong><br />To test the cross reactivity of the Diagenode antibody against H3K4me3 (cat. No. C15410003), a Dot Blot analysis was performed with peptides containing other histone modifications and the unmodified H3K4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 5A shows a high specificity of the antibody for the modification of interest.</small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig5-WB.jpg" /></div>
<div class="small-8 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K4me3</strong><br />Western blot was performed on whole cell extracts (40 µg, lane 1) from HeLa cells, and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K4me3 (cat. No. C15410003). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig6-if.jpg" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K4me3</strong><br />HeLa cells were stained with the Diagenode antibody against H3K4me3 (cat. No. C15410003) and with DAPI. Cells were fixed with 4% formaldehyde for 20’ and blocked with PBS/TX-100 containing 5% normal goat serum. The cells were immunofluorescently labelled with the H3K4me3 antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa568 or with DAPI (middle), which specifically labels DNA. The right picture shows a merge of both stainings.</small></p>
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'name' => 'H3K27me3 Antibody',
'description' => '<p>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 27</strong> (<strong>H3K27me3</strong>), using a KLH-conjugated synthetic peptide.</p>',
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<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig1.png" alt="H3K27me3 Antibody ChIP Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2.png" alt="H3K27me3 Antibody for ChIP" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 1 million cells. The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation. A titration consisting of 0.5, 1, 2 and 5 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control.</small></p>
<p><small><strong>Figure 1A.</strong> Quantitative PCR was performed with primers specific for the promoter of the active GAPDH and EIF4A2 genes, used as negative controls, and for the inactive TSH2B and MYT1 genes, used as positive controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
<p><small><strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K27me1, H3K27me2, H3K27me3, H3K4me3, H3K9me3 and H3K36me3 modifications and the unmodified H3K27 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K27me3 modification.</small></p>
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<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2a.png" alt="H3K27me3 Antibody ChIP-seq Grade" /></p>
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<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2b.png" alt="H3K27me3 Antibody for ChIP-seq" /></p>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2c.png" alt="H3K27me3 Antibody for ChIP-seq assay" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2d.png" alt="H3K27me3 Antibody validated in ChIP-seq" /></p>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP was performed on sheared chromatin from 1 million HeLa cells using 1 µg of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2 shows the enrichment in genomic regions of chromosome 6 and 20, surrounding the TSH2B and MYT1 positive control genes (fig 2A and 2B, respectively), and in two genomic regions of chromosome 1 and X (figure 2C and D).</small></p>
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<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3A.png" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3B.png" /></p>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27me3 (cat. No. C15410195) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions on chromosome and 13 and 20 (figure 3A and B, respectively).</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-ELISA-Fig4.png" alt="H3K27me3 Antibody ELISA Validation " /></p>
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<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K27me3 (Cat. No. C15410195). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:3,000.</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-DB-Fig5a.png" alt="H3K27me3 Antibody Dot Blot Validation " /></p>
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<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) with peptides containing other modifications of histone H3 and H4 and the unmodified H3K27 sequence. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:5,000. Figure 5 shows a high specificity of the antibody for the modification of interest. Please note that the antibody also recognizes the modification if S28 is phosphorylated.</small></p>
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<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-WB-Fig6.png" alt="H3K27me3 Antibody validated in Western Blot" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27me3</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27me3 (cat. No. C15410195) diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-IF-Fig7.png" alt="H3K27me3 Antibody validated for Immunofluorescence" /></p>
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<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27me3</strong><br />Human HeLa cells were stained with the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K27me3 antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.</small></p>
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<div class="small-6 columns">A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1a.png" width="356" /><br /> B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1b.png" width="356" /></div>
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<p><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>Figure 1A ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196) and optimized PCR primer pairs for qPCR. ChIP was performed with the “Auto Histone ChIP-seq” kit on the IP-Star automated system, using sheared chromatin from 1,000,000 cells. A titration consisting of 1, 2, 5 and 10 µg of antibody per ChIP experiment was analyzed. IgG (2 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active EIF4A2 and ACTB genes, used as positive controls, and for the inactive TSH2B and MYT1 genes, used as negative controls.</p>
<p>Figure 1B ChIP assays were performed using human K562 cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196)and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 100,000 cells. A titration consisting of 0.2, 0.5, 1 and 2 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active GAPDH and EIF4A2 genes, used as positive controls, and for the coding regions of the inactive MB and MYT1 genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis)</p>
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<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2a.png" /></p>
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<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2b.png" /></p>
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<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2c.png" /></p>
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<div class="small-12 columns">
<p><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>ChIP was performed on sheared chromatin from 100,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) as described above. The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A shows the peak distribution along the complete human X-chromosome. Figure 2 B and C show the peak distribution in two regions surrounding the EIF4A2 and GAPDH positive control genes, respectively. The position of the PCR amplicon, used for validating the ChIP assay is indicated with an arrow.</p>
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<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-fig3.jpg" /></center></div>
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<div class="small-12 columns">
<p><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (cat. No. C15410196) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions surrounding the EIF2S3 gene on the X-chromosome and the CCT5 gene on chromosome 5 (figure 3A and B, respectively).</p>
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<div class="small-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-ELISA-Fig3.png" /></div>
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<p><strong>Figure 4. Determination of the antibody titer</strong></p>
<p>To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:8,300.</p>
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<p><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27ac</strong><br />To test the cross reactivity of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>), a Dot Blot analysis was performed with peptides containing other histone modifications and the unmodified H3K27. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 5 shows a high specificity of the antibody for the modification of interest.</p>
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<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-WB-Fig5.png" /></center></div>
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<p><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27ac</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27ac (Cat. No. C1541196). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The marker (in kDa) is shown on the left.</p>
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<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-IF-Fig6.png" /></div>
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<p><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27ac</strong></p>
<p>HeLa cells were stained with the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/ TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K27ac antibody (top) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown at the bottom.</p>
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'description' => '<p>Histones are the main protein components of chromatin involved in the compaction of DNA into nucleosomes, the basic units of chromatin. A <strong>nucleosome</strong> consists of one pair of each of the core histones (<strong>H2A</strong>, <strong>H2B</strong>, <strong>H3</strong> and <strong>H4</strong>) forming an octameric structure wrapped by 146 base pairs of DNA. The different nucleosomes are linked by the linker histone<strong> H1, </strong>allowing for further condensation of chromatin.</p>
<p>The core histones have a globular structure with large unstructured N-terminal tails protruding from the nucleosome. They can undergo to multiple post-translational modifications (PTM), mainly at the N-terminal tails. These <strong>post-translational modifications </strong>include methylation, acetylation, phosphorylation, ubiquitinylation, citrullination, sumoylation, deamination and crotonylation. The most well characterized PTMs are <strong>methylation,</strong> <strong>acetylation and phosphorylation</strong>. Histone methylation occurs mainly on lysine (K) residues, which can be mono-, di- or tri-methylated, and on arginines (R), which can be mono-methylated and symmetrically or asymmetrically di-methylated. Histone acetylation occurs on lysines and histone phosphorylation mainly on serines (S), threonines (T) and tyrosines (Y).</p>
<p>The PTMs of the different residues are involved in numerous processes such as DNA repair, DNA replication and chromosome condensation. They influence the chromatin organization and can be positively or negatively associated with gene expression. Trimethylation of H3K4, H3K36 and H3K79, and lysine acetylation generally result in an open chromatin configuration (figure below) and are therefore associated with <strong>euchromatin</strong> and gene activation. Trimethylation of H3K9, K3K27 and H4K20, on the other hand, is enriched in <strong>heterochromatin </strong>and associated with gene silencing. The combination of different histone modifications is called the "<strong>histone code</strong>”, analogous to the genetic code.</p>
<p><img src="https://www.diagenode.com/img/categories/antibodies/histone-marks-illustration.png" /></p>
<p>Diagenode is proud to offer a large range of antibodies against histones and histone modifications. Our antibodies are highly specific and have been validated in many applications, including <strong>ChIP</strong> and <strong>ChIP-seq</strong>.</p>
<p>Diagenode’s collection includes antibodies recognizing:</p>
<ul>
<li><strong>Histone H1 variants</strong></li>
<li><strong>Histone H2A, H2A variants and histone H2A</strong> <strong>modifications</strong> (serine phosphorylation, lysine acetylation, lysine ubiquitinylation)</li>
<li><strong>Histone H2B and H2B</strong> <strong>modifications </strong>(serine phosphorylation, lysine acetylation)</li>
<li><strong>Histone H3 and H3 modifications </strong>(lysine methylation (mono-, di- and tri-methylated), lysine acetylation, serine phosphorylation, threonine phosphorylation, arginine methylation (mono-methylated, symmetrically and asymmetrically di-methylated))</li>
<li><strong>Histone H4 and H4 modifications (</strong>lysine methylation (mono-, di- and tri-methylated), lysine acetylation, arginine methylation (mono-methylated and symmetrically di-methylated), serine phosphorylation )</li>
</ul>
<p><span style="font-weight: 400;"><strong>HDAC's HAT's, HMT's and other</strong> <strong>enzymes</strong> which modify histones can be found in the category <a href="../categories/chromatin-modifying-proteins-histone-transferase">Histone modifying enzymes</a><br /></span></p>
<p><span style="font-weight: 400;"> Diagenode’s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> Expert technical support</span></li>
<li><span style="font-weight: 400;"> Sample sizes available</span></li>
<li><span style="font-weight: 400;"> 100% satisfaction guarantee</span></li>
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'meta_description' => 'Polyclonal and Monoclonal Antibodies against Histones and their modifications validated for many applications, including Chromatin Immunoprecipitation (ChIP) and ChIP-Sequencing (ChIP-seq)',
'meta_title' => 'Histone and Modified Histone Antibodies | Diagenode',
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'description' => '<p><span style="font-weight: 400;">All Diagenode’s antibodies are listed below. Please, use our Quick search field to find the antibody of interest by target name, application, purity.</span></p>
<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
</ul>',
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'meta_description' => 'Diagenode Offers Strict quality standards with Rigorous QC and validated Antibodies. Classified based on level of validation for flexibility of Application. Comprehensive selection of histone and non-histone Antibodies',
'meta_title' => 'Diagenode's selection of Antibodies is exclusively dedicated for Epigenetic Research | Diagenode',
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'name' => 'ChIP-grade antibodies',
'description' => '<div class="row">
<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
<p></p>
</div>
</div>
<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
<div class="row">
<div class="small-12 medium-6 large-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" alt="" width="400" height="315" /> </div>
<div class="small-12 medium-6 large-6 columns">
<p></p>
<p></p>
<p></p>
</div>
</div>
<p></p>
<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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'meta_description' => 'Diagenode Offers Extensively Validated ChIP-Grade Antibodies, Confirmed for their Specificity, and high level of Performance in Chromatin Immunoprecipitation ChIP',
'meta_title' => 'Chromatin immunoprecipitation ChIP-grade antibodies | Diagenode',
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'name' => 'Datasheet H3K9me3 C15410056',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone H3 containing the trimethylated lysine 9 (H3K9me3), using a KLH-conjugated synthetic peptide.</span></p>',
'image_id' => null,
'type' => 'Datasheet',
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'id' => '38',
'name' => 'Epigenetic Antibodies Brochure',
'description' => '<p>More than in any other immuoprecipitation assays, quality antibodies are critical tools in many epigenetics experiments. Since 10 years, Diagenode has developed the most stringent quality production available on the market for antibodies exclusively focused on epigenetic uses. All our antibodies have been qualified to work in epigenetic applications.</p>',
'image_id' => null,
'type' => 'Brochure',
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'name' => 'Antibodies you can trust',
'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
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'Publication' => array(
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'id' => '4844',
'name' => 'SMYD3 represses tumor-intrinsic interferon response in HPV-negativesquamous cell carcinoma of the head and neck.',
'authors' => 'Nigam N. et al.',
'description' => '<p>Cancers often display immune escape, but the mechanisms are incompletely understood. Herein, we identify SMYD3 as a mediator of immune escape in human papilloma virus (HPV)-negative head and neck squamous cell carcinoma (HNSCC), an aggressive disease with poor response to immunotherapy with pembrolizumab. SMYD3 depletion induces upregulation of multiple type I interferon (IFN) response and antigen presentation machinery genes in HNSCC cells. Mechanistically, SMYD3 binds to and regulates the transcription of UHRF1, encoding for a reader of H3K9me3, which binds to H3K9me3-enriched promoters of key immune-related genes, recruits DNMT1, and silences their expression. SMYD3 further maintains the repression of immune-related genes through intragenic deposition of H4K20me3. In vivo, Smyd3 depletion induces influx of CD8 T cells and increases sensitivity to anti-programmed death 1 (PD-1) therapy. SMYD3 overexpression is associated with decreased CD8 T cell infiltration and poor response to neoadjuvant pembrolizumab. These data support combining SMYD3 depletion strategies with checkpoint blockade to overcome anti-PD-1 resistance in HPV-negative HNSCC.</p>',
'date' => '2023-07-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37463106',
'doi' => '10.1016/j.celrep.2023.112823',
'modified' => '2023-08-01 14:15:28',
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'name' => 'RUNX1 colludes with NOTCH1 to reprogram chromatin in T-cell acutelymphoblastic leukemia',
'authors' => 'Islam R. et al.',
'description' => '<p><span>Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including </span><em>MYC, DTX1, HES4, IL7R,</em><span><span> </span>and<span> </span></span><em>NOTCH3</em><span>. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.</span></p>',
'date' => '2023-05-01',
'pmid' => 'https://doi.org/10.1016%2Fj.isci.2023.106795',
'doi' => '10.1016/j.isci.2023.106795',
'modified' => '2023-06-19 10:14:27',
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'id' => '4605',
'name' => 'Gene Regulatory Interactions at Lamina-Associated Domains',
'authors' => 'Madsen-Østerbye J. et al.',
'description' => '<p>The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are inactive, over ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to interact with regulatory elements remain unclear. Here, we integrate publicly available enhancer-capture Hi-C data with our own chromatin state and transcriptomic datasets to show that inferred enhancers of active genes in LADs are able to form connections with other enhancers within LADs and outside LADs. Fluorescence in situ hybridization analyses show proximity changes between differentially expressed genes in LADs and distant enhancers upon the induction of adipogenic differentiation. We also provide evidence of involvement of lamin A/C, but not lamin B1, in repressing genes at the border of an in-LAD active region within a topological domain. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with gene expression in this dynamic nuclear compartment.</p>',
'date' => '2023-01-01',
'pmid' => 'https://doi.org/10.3390%2Fgenes14020334',
'doi' => '10.3390/genes14020334',
'modified' => '2023-04-04 08:57:32',
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'id' => '4566',
'name' => 'Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing.',
'authors' => 'O'Geen H.et al.',
'description' => '<p>Precision epigenome editing has gained significant attention as a method to modulate gene expression without altering genetic information. However, a major limiting factor has been that the gene expression changes are often transient, unlike the life-long epigenetic changes that occur frequently in nature. Here, we systematically interrogate the ability of CRISPR/dCas9-based epigenome editors (Epi-dCas9) to engineer persistent epigenetic silencing. We elucidated cis regulatory features that contribute to the differential stability of epigenetic reprogramming, such as the active transcription histone marks H3K36me3 and H3K27ac strongly correlating with resistance to short-term repression and resistance to long-term silencing, respectively. H3K27ac inversely correlates with increased DNA methylation. Interestingly, the dependance on H3K27ac was only observed when a combination of KRAB-dCas9 and targetable DNA methyltransferases (DNMT3A-dCas9 + DNMT3L) was used, but not when KRAB was replaced with the targetable H3K27 histone methyltransferase Ezh2. In addition, programmable Ezh2/DNMT3A + L treatment demonstrated enhanced engineering of localized DNA methylation and was not sensitive to a divergent chromatin state. Our results highlight the importance of local chromatin features for heritability of programmable silencing and the differential response to KRAB- and Ezh2-based epigenetic editing platforms. The information gained in this study provides fundamental insights into understanding contextual cues to more predictably engineer persistent silencing.</p>',
'date' => '2022-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35234927',
'doi' => '10.1093/nar/gkac123',
'modified' => '2022-11-24 09:26:11',
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'id' => '4292',
'name' => 'The prolyl-isomerase PIN1 is essential for nuclear Lamin-Bstructure and function and protects heterochromatin under mechanicalstress.',
'authors' => 'Napoletano Francesco et al.',
'description' => '<p>Chromatin organization plays a crucial role in tissue homeostasis. Heterochromatin relaxation and consequent unscheduled mobilization of transposable elements (TEs) are emerging as key contributors of aging and aging-related pathologies, including Alzheimer's disease (AD) and cancer. However, the mechanisms governing heterochromatin maintenance or its relaxation in pathological conditions remain poorly understood. Here we show that PIN1, the only phosphorylation-specific cis/trans prolyl isomerase, whose loss is associated with premature aging and AD, is essential to preserve heterochromatin. We demonstrate that this PIN1 function is conserved from Drosophila to humans and prevents TE mobilization-dependent neurodegeneration and cognitive defects. Mechanistically, PIN1 maintains nuclear type-B Lamin structure and anchoring function for heterochromatin protein 1α (HP1α). This mechanism prevents nuclear envelope alterations and heterochromatin relaxation under mechanical stress, which is a key contributor to aging-related pathologies.</p>',
'date' => '2021-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34525372',
'doi' => '10.1016/j.celrep.2021.109694',
'modified' => '2022-05-24 09:18:40',
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(int) 5 => array(
'id' => '4174',
'name' => 'Dynamic association of the H3K64 trimethylation mark with genes encodingexported proteins in Plasmodium falciparum.',
'authors' => 'Jabeena, C A et al.',
'description' => '<p>Epigenetic modifications have emerged as critical regulators of virulence genes and stage-specific gene expression in Plasmodium falciparum. However, the specific roles of histone core epigenetic modifications in regulating the stage-specific gene expression are not well understood. In this study, we report an unconventional trimethylation at lysine 64 on histone 3 (H3K64me3) and characterize its functional relevance in P. falciparum. We show that PfSET4 and PfSET5 proteins of P. falciparum methylate H3K64 and that they prefer the nucleosome as a substrate over free histone 3 proteins. Structural analysis of PfSET5 revealed that it interacts with the nucleosome as a dimer. The H3K64me3 mark is dynamic, being enriched in the ring and trophozoite stages and drastically reduced in schizont stages. Stage-specific global ChIP-sequencing analysis of the H3K64me3 mark revealed the selective enrichment of this methyl mark on the genes of exported family proteins in the ring and trophozoite stages, and a significant reduction of the same in the schizont stages. Collectively, our data identify a novel epigenetic mark that are associated with the subset of genes encoding for exported proteins which may regulate their expression in different stages of P. falciparum.</p>',
'date' => '2021-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33839154',
'doi' => '10.1016/j.jbc.2021.100614',
'modified' => '2021-12-21 16:07:05',
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(int) 6 => array(
'id' => '4149',
'name' => 'Restricted nucleation and piRNA-mediated establishment of heterochromatinduring embryogenesis in Drosophila miranda',
'authors' => 'Wei, K. et al.',
'description' => '<p>Heterochromatin is a key architectural feature of eukaryotic genomes, crucial for silencing of repetitive elements and maintaining genome stability. Heterochromatin shows stereotypical enrichment patterns around centromeres and repetitive sequences, but the molecular details of how heterochromatin is established during embryogenesis are poorly understood. Here, we map the genome-wide distribution of H3K9me3-dependent heterochromatin in individual embryos of D. miranda at precisely staged developmental time points. We find that canonical H3K9me3 enrichment patterns are established early on before cellularization, and mature into stable and broad heterochromatin domains through development. Intriguingly, initial nucleation sites of H3K9me3 enrichment appear as early as embryonic stage3 (nuclear cycle 9) over transposable elements (TE) and progressively broaden, consistent with spreading to neighboring nucleosomes. The earliest nucleation sites are limited to specific regions of a small number of TE families and often appear over promoter regions, while late nucleation develops broadly across most TEs. Early nucleating TEs are highly targeted by maternal piRNAs and show early zygotic transcription, consistent with a model of co-transcriptional silencing of TEs by small RNAs. Interestingly, truncated TE insertions lacking nucleation sites show significantly reduced enrichment across development, suggesting that the underlying sequences play an important role in recruiting histone methyltransferases for heterochromatin</p>',
'date' => '2021-02-01',
'pmid' => 'https://doi.org/10.1101%2F2021.02.16.431328',
'doi' => '10.1101/2021.02.16.431328',
'modified' => '2021-12-14 09:28:27',
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(int) 7 => array(
'id' => '3995',
'name' => 'Epigenetic, transcriptional and phenotypic responses in Daphnia magna exposed to low-level ionizing radiation',
'authors' => 'Thaulow Jens, Song You, Lindeman Leif C., Kamstra Jorke H., Lee YeonKyeong, Xie Li, Aleström Peter, Salbu Brit, Tollefsen Knut Erik',
'description' => '<p>Ionizing radiation is known to induce oxidative stress and DNA damage as well as epigenetic effects in aquatic organisms. Epigenetic changes can be part of the adaptive responses to protect organisms from radiation-induced damage, or act as drivers of toxicity pathways leading to adverse effects. To investigate the potential roles of epigenetic mechanisms in low-dose ionizing radiation-induced stress responses, an ecologically relevant crustacean, adult Daphnia magna were chronically exposed to low and medium level external 60Co gamma radiation ranging from 0.4, 1, 4, 10, and 40 mGy/h for seven days. Biological effects at the molecular (global DNA methylation, histone modification, gene expression), cellular (reactive oxygen species formation), tissue/organ (ovary, gut and epidermal histology) and organismal (fecundity) levels were investigated using a suite of effect assessment tools. The results showed an increase in global DNA methylation associated with loci-specific alterations of histone H3K9 methylation and acetylation, and downregulation of genes involved in DNA methylation, one-carbon metabolism, antioxidant defense, DNA repair, apoptosis, calcium signaling and endocrine regulation of development and reproduction. Temporal changes of reactive oxygen species (ROS) formation were also observed with an apparent transition from ROS suppression to induction from 2-7 days after gamma exposure. The cumulative fecundity, however, was not significantly changed by the gamma exposure. On the basis of the new experimental evidence and existing knowledge, a hypothetical model was proposed to provide in-depth mechanistic understanding of the roles of epigenetic mechanisms in low dose ionizing radiation induced stress responses in D. magna.</p>',
'date' => '2020-07-18',
'pmid' => 'https://www.sciencedirect.com/science/article/pii/S0013935120308252',
'doi' => '10.1016/j.envres.2020.109930',
'modified' => '2020-09-01 14:51:16',
'created' => '2020-08-21 16:41:39',
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(int) 8 => array(
'id' => '3964',
'name' => 'The 20S proteasome activator PA28γ controls the compaction of chromatin',
'authors' => 'Didier Fesquet, David Llères, Cristina Viganò, Francisca Méchali, Séverine Boulon, Robert Feil, Olivier Coux, Catherine Bonne-Andrea, Véronique Baldin',
'description' => '<p>The nuclear PA28γ is known to activate the 20S proteasome, but its precise cellular functions remains unclear. Here, we identify PA28γ as a key factor that structures heterochromatin. We find that in human cells, a fraction of PA28γ-20S proteasome complexes localizes within HP1-linked heterochromatin foci. Our biochemical studies show that PA28γ interacts with HP1 proteins, particularly HP1β, which recruits the PA28γ-20S proteasome complexes to heterochromatin. Loss of PA28γ does not modify the localization of HP1β, its mobility within nuclear foci, or the level of H3K9 tri-methylation, but reduces H4K20 mono- and tri-methylation, modifications involved in heterochromatin establishment. Concordantly, using a quantitative FRET-based microscopy assay to monitor nanometer-scale proximity between nucleosomes in living cells, we find that PA28γ regulates nucleosome proximity within heterochromatin, and thereby controls its compaction. This function of PA28γ is independent of the 20S proteasome. Importantly, HP1β on its own is unable to drive heterochromatin compaction without PA28γ. Combined, our data reveal an unexpected chromatin structural role of PA28γ, and provide new insights into the mechanism that controls HP1β-mediated heterochromatin compaction.</p>',
'date' => '2020-05-28',
'pmid' => 'https://www.biorxiv.org/content/10.1101/716332v1.article-info',
'doi' => 'https://doi.org/10.1101/716332',
'modified' => '2020-08-12 09:44:09',
'created' => '2020-08-10 12:12:25',
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(int) 9 => array(
'id' => '3965',
'name' => 'Histone post-translational modifications in Silene latifolia X and Y chromosomes suggest a mammal-like dosage compensation system',
'authors' => 'Luis Rodríguez Lorenzo José, Hubinský Marcel, Vyskot Boris, Hobza Roman',
'description' => '<p>Silene latifolia is a model organism to study evolutionary young heteromorphic sex chromosome evolution in plants. Previous research indicates a Y-allele gene degeneration and a dosage compensation system already operating. Here, we propose an epigenetic approach based on analysis of several histone post-translational modifications (PTMs) to find the first epigenetic hints of the X:Y sex chromosome system regulation in S. latifolia. Through chromatin immunoprecipitation we interrogated six genes from X and Y alleles. Several histone PTMS linked to DNA methylation and transcriptional repression (H3K27me3, H3K23me, H3K9me2 and H3K9me3) and to transcriptional activation (H3K4me3 and H4K5, 8, 12, 16ac) were used. DNA enrichment (Immunoprecipitated DNA/input DNA) was analyzed and showed three main results: i) promoters of the Y allele are associated with heterochromatin marks, ii) promoters of the X allele in males are associated with activation of transcription marks and finally, iii) promoters of X alleles in females are associated with active and repressive marks. Our finding indicates a transcription activation of X allele and transcription repression of Y allele in males. In females we found a possible differential regulation (up X1, down X2) of each female X allele. These results agree with the mammal-like epigenetic dosage compensation regulation.</p>',
'date' => '2020-05-24',
'pmid' => 'https://www.sciencedirect.com/science/article/abs/pii/S0168945220301333',
'doi' => '10.1016/j.plantsci.2020.110528',
'modified' => '2020-08-12 09:42:21',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 10 => array(
'id' => '3943',
'name' => 'SETDB2 promoted breast cancer stem cell maintenance by interaction with and stabilization of ΔNp63α protein',
'authors' => 'Ying Liu, Fei Xie, Jialun Li, Jianpeng Xiao, Jie Wang, Zhaolin Mei, Hongjia Fan, Huan Fang, Sha Li, Qiuju Wu, Lin Yuan, Cuicui Liu, You Peng, Weiwei Zhao, Lulu Wang, Jiemin Wong, Jing Li, Jing Feng',
'description' => '<p>The histone H3K9 methyltransferase SETDB2 is involved in cell cycle dysregulation in acute leukemia and has oncogenic roles in gastric cancer. In our study, we found that SETDB2 plays essential roles in breast cancer stem cell maintenance. Depleted SETDB2 significantly decreased the breast cancer stem cell population and mammosphere formation in vitro and also inhibited breast tumor initiation and growth in vivo. Restoring SETDB2 expression rescued the defect in breast cancer stem cell maintenance. A mechanistic analysis showed that SETDB2 upregulated the transcription of the ΔNp63α downstream Hedgehog pathway gene. SETDB2 also interacted with and methylated ΔNp63α, and stabilized ΔNp63α protein. Restoring ΔNp63α expression rescued the breast cancer stem cell maintenance defect which mediated by SETDB2 knockdown. In conclusion, our study reveals a novel function of SETDB2 in cancer stem cell maintenance in breast cancer.</p>',
'date' => '2020-04-28',
'pmid' => 'https://www.ijbs.com/v16p2180',
'doi' => '10.7150/ijbs.43611',
'modified' => '2020-08-17 10:17:33',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 11 => array(
'id' => '3762',
'name' => 'Transit amplifying cells coordinate mouse incisor mesenchymal stem cell activation.',
'authors' => 'Walker JV, Zhuang H, Singer D, Illsley CS, Kok WL, Sivaraj KK, Gao Y, Bolton C, Liu Y, Zhao M, Grayson PRC, Wang S, Karbanová J, Lee T, Ardu S, Lai Q, Liu J, Kassem M, Chen S, Yang K, Bai Y, Tredwin C, Zambon AC, Corbeil D, Adams R, Abdallah BM, Hu B',
'description' => '<p>Stem cells (SCs) receive inductive cues from the surrounding microenvironment and cells. Limited molecular evidence has connected tissue-specific mesenchymal stem cells (MSCs) with mesenchymal transit amplifying cells (MTACs). Using mouse incisor as the model, we discover a population of MSCs neibouring to the MTACs and epithelial SCs. With Notch signaling as the key regulator, we disclose molecular proof and lineage tracing evidence showing the distinct MSCs contribute to incisor MTACs and the other mesenchymal cell lineages. MTACs can feedback and regulate the homeostasis and activation of CL-MSCs through Delta-like 1 homolog (Dlk1), which balances MSCs-MTACs number and the lineage differentiation. Dlk1's function on SCs priming and self-renewal depends on its biological forms and its gene expression is under dynamic epigenetic control. Our findings can be validated in clinical samples and applied to accelerate tooth wound healing, providing an intriguing insight of how to direct SCs towards tissue regeneration.</p>',
'date' => '2019-08-09',
'pmid' => 'http://www.pubmed.gov/31399601',
'doi' => '10.1038/s41467-019-11611-0',
'modified' => '2019-10-03 10:03:31',
'created' => '2019-10-02 16:16:55',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 12 => array(
'id' => '3715',
'name' => 'Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner.',
'authors' => 'O'Geen H, Bates SL, Carter SS, Nisson KA, Halmai J, Fink KD, Rhie SK, Farnham PJ, Segal DJ',
'description' => '<p>BACKGROUND: Rewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve in a predictable manner using targeted systems. RESULTS: Here, we report that persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). We demonstrate that the histone methyltransferase requirement can be locus specific. Co-targeting Ezh2-dCas9, but not KRAB-dCas9, with DNMT3A-dCas9 and DNMT3L induced long-term HER2 repression over at least 50 days (approximately 57 cell divisions) and triggered an epigenetic switch to a heterochromatic environment. An increase in H3K27 trimethylation and DNA methylation was stably maintained and accompanied by a sustained loss of H3K27 acetylation. Interestingly, substitution of Ezh2-dCas9 with KRAB-dCas9 enabled long-term repression at some target genes (e.g., SNURF) but not at HER2, at which H3K9me3 and DNA methylation were transiently acquired and subsequently lost. Off-target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the off-target loci tested. Conversely, robust hypermethylation was observed at HER2. We further demonstrated that Ezh2-dCas9 required full-length DNMT3L for maximal activity and that co-targeting DNMT3L was sufficient for persistent repression by Ezh2-dCas9 or KRAB-dCas9. CONCLUSIONS: These data demonstrate that targeting different combinations of histone and DNA methyltransferases is required to achieve maximal repression at different loci. Fine-tuning of targeting tools is a necessity to engineer epigenetic memory at any given locus in any given cell type.</p>',
'date' => '2019-05-03',
'pmid' => 'http://www.pubmed.gov/31053162',
'doi' => '10.1186/s13072-019-0275-8',
'modified' => '2019-07-05 13:15:49',
'created' => '2019-07-04 10:42:34',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 13 => array(
'id' => '3709',
'name' => 'Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation.',
'authors' => 'Paulsen J, Liyakat Ali TM, Nekrasov M, Delbarre E, Baudement MO, Kurscheid S, Tremethick D, Collas P',
'description' => '<p>Genomic information is selectively used to direct spatial and temporal gene expression during differentiation. Interactions between topologically associating domains (TADs) and between chromatin and the nuclear lamina organize and position chromosomes in the nucleus. However, how these genomic organizers together shape genome architecture is unclear. Here, using a dual-lineage differentiation system, we report long-range TAD-TAD interactions that form constitutive and variable TAD cliques. A differentiation-coupled relationship between TAD cliques and lamina-associated domains suggests that TAD cliques stabilize heterochromatin at the nuclear periphery. We also provide evidence of dynamic TAD cliques during mouse embryonic stem-cell differentiation and somatic cell reprogramming and of inter-TAD associations in single-cell high-resolution chromosome conformation capture (Hi-C) data. TAD cliques represent a level of four-dimensional genome conformation that reinforces the silencing of repressed developmental genes.</p>',
'date' => '2019-05-01',
'pmid' => 'http://www.pubmed.gov/31011212',
'doi' => '10.1038/s41588-019-0392-0',
'modified' => '2019-07-05 14:33:38',
'created' => '2019-07-04 10:42:34',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 14 => array(
'id' => '3692',
'name' => 'PML modulates H3.3 targeting to telomeric and centromeric repeats in mouse fibroblasts.',
'authors' => 'Spirkoski J, Shah A, Reiner AH, Collas P, Delbarre E',
'description' => '<p>Targeted deposition of histone variant H3.3 into chromatin is paramount for proper regulation of chromatin integrity, particularly in heterochromatic regions including repeats. We have recently shown that the promyelocytic leukemia (PML) protein prevents H3.3 from being deposited in large heterochromatic PML-associated domains (PADs). However, to what extent PML modulates H3.3 loading on chromatin in other areas of the genome remains unexplored. Here, we examined the impact of PML on targeting of H3.3 to genes and repeat regions that reside outside PADs. We show that loss of PML increases H3.3 deposition in subtelomeric, telomeric, pericentric and centromeric repeats in mouse embryonic fibroblasts, while other repeat classes are not affected. Expression of major satellite, minor satellite and telomeric non-coding transcripts is altered in Pml-null cells. In particular, telomeric Terra transcripts are strongly upregulated, in concordance with a marked reduction in H4K20me3 at these sites. Lastly, for most genes H3.3 enrichment or gene expression outcomes are independent of PML. Our data argue towards the importance of a PML-H3.3 axis in preserving a heterochromatin state at centromeres and telomeres.</p>',
'date' => '2019-04-16',
'pmid' => 'http://www.pubmed.gov/30850162',
'doi' => '10.1016/j.bbrc.2019.02.087',
'modified' => '2019-06-28 13:50:40',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 15 => array(
'id' => '3644',
'name' => 'Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs.',
'authors' => 'Pontis J, Planet E, Offner S, Turelli P, Duc J, Coudray A, Theunissen TW, Jaenisch R, Trono D',
'description' => '<p>Expansion of transposable elements (TEs) coincides with evolutionary shifts in gene expression. TEs frequently harbor binding sites for transcriptional regulators, thus enabling coordinated genome-wide activation of species- and context-specific gene expression programs, but such regulation must be balanced against their genotoxic potential. Here, we show that Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) control the timely and pleiotropic activation of TE-derived transcriptional cis regulators during early embryogenesis. Evolutionarily recent SVA, HERVK, and HERVH TE subgroups contribute significantly to chromatin opening during human embryonic genome activation and are KLF-stimulated enhancers in naive human embryonic stem cells (hESCs). KZFPs of corresponding evolutionary ages are simultaneously induced and repress the transcriptional activity of these TEs. Finally, the same KZFP-controlled TE-based enhancers later serve as developmental and tissue-specific enhancers. Thus, by controlling the transcriptional impact of TEs during embryogenesis, KZFPs facilitate their genome-wide incorporation into transcriptional networks, thereby contributing to human genome regulation.</p>',
'date' => '2019-03-27',
'pmid' => 'http://www.pubmed.gov/31006620',
'doi' => '10.1016/j.stem.2019.03.012',
'modified' => '2019-06-07 10:16:36',
'created' => '2019-06-06 12:11:18',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 16 => array(
'id' => '3686',
'name' => 'Gamma radiation induces locus specific changes to histone modification enrichment in zebrafish and Atlantic salmon.',
'authors' => 'Lindeman LC, Kamstra JH, Ballangby J, Hurem S, Martín LM, Brede DA, Teien HC, Oughton DH, Salbu B, Lyche JL, Aleström P',
'description' => '<p>Ionizing radiation is a recognized genotoxic agent, however, little is known about the role of the functional form of DNA in these processes. Post translational modifications on histone proteins control the organization of chromatin and hence control transcriptional responses that ultimately affect the phenotype. The purpose of this study was to investigate effects on chromatin caused by ionizing radiation in fish. Direct exposure of zebrafish (Danio rerio) embryos to gamma radiation (10.9 mGy/h for 3h) induced hyper-enrichment of H3K4me3 at the genes hnf4a, gmnn and vegfab. A similar relative hyper-enrichment was seen at the hnf4a loci of irradiated Atlantic salmon (Salmo salar) embryos (30 mGy/h for 10 days). At the selected genes in ovaries of adult zebrafish irradiated during gametogenesis (8.7 and 53 mGy/h for 27 days), a reduced enrichment of H3K4me3 was observed, which was correlated with reduced levels of histone H3 was observed. F1 embryos of the exposed parents showed hyper-methylation of H3K4me3, H3K9me3 and H3K27me3 on the same three loci, while these differences were almost negligible in F2 embryos. Our results from three selected loci suggest that ionizing radiation can affect chromatin structure and organization, and that these changes can be detected in F1 offspring, but not in subsequent generations.</p>',
'date' => '2019-01-01',
'pmid' => 'http://www.pubmed.gov/30759148',
'doi' => '10.1371/journal.pone.0212123',
'modified' => '2019-06-28 13:57:39',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 17 => array(
'id' => '3635',
'name' => 'TIP60: an actor in acetylation of H3K4 and tumor development in breast cancer.',
'authors' => 'Judes G, Dubois L, Rifaï K, Idrissou M, Mishellany F, Pajon A, Besse S, Daures M, Degoul F, Bignon YJ, Penault-Llorca F, Bernard-Gallon D',
'description' => '<p>AIM: The acetyltransferase TIP60 is reported to be downregulated in several cancers, in particular breast cancer, but the molecular mechanisms resulting from its alteration are still unclear. MATERIALS & METHODS: In breast tumors, H3K4ac enrichment and its link with TIP60 were evaluated by chromatin immunoprecipitation-qPCR and re-chromatin immunoprecipitation techniques. To assess the biological roles of TIP60 in breast cancer, two cell lines of breast cancer, MDA-MB-231 (ER-) and MCF-7 (ER+) were transfected with shRNA specifically targeting TIP60 and injected to athymic Balb-c mice. RESULTS: We identified a potential target of TIP60, H3K4. We show that an underexpression of TIP60 could contribute to a reduction of H3K4 acetylation in breast cancer. An increase in tumor development was noted in sh-TIP60 MDA-MB-231 xenografts and a slowdown of tumor growth in sh-TIP60 MCF-7 xenografts. CONCLUSION: This is evidence that the underexpression of TIP60 observed in breast cancer can promote the tumorigenesis of ER-negative tumors.</p>',
'date' => '2018-11-01',
'pmid' => 'http://www.pubmed.gov/30324811',
'doi' => '10.2217/epi-2018-0004',
'modified' => '2019-06-07 10:29:04',
'created' => '2019-06-06 12:11:18',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 18 => array(
'id' => '3556',
'name' => 'PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex.',
'authors' => 'Link S, Spitzer RMM, Sana M, Torrado M, Völker-Albert MC, Keilhauer EC, Burgold T, Pünzeler S, Low JKK, Lindström I, Nist A, Regnard C, Stiewe T, Hendrich B, Imhof A, Mann M, Mackay JP, Bartkuhn M, Hake SB',
'description' => '<p>Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified that PWWP2A tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial-facial development. Here, using in vitro assays, we show that distinct domains of PWWP2A mediate binding to free linker DNA as well as H3K36me3 nucleosomes. In vivo, PWWP2A strongly recognizes H2A.Z-containing regulatory regions and weakly binds H3K36me3-containing gene bodies. Further, PWWP2A binds to an MTA1-specific subcomplex of the NuRD complex (M1HR), which consists solely of MTA1, HDAC1, and RBBP4/7, and excludes CHD, GATAD2 and MBD proteins. Depletion of PWWP2A leads to an increase of acetylation levels on H3K27 as well as H2A.Z, presumably by impaired chromatin recruitment of M1HR. Thus, this study identifies PWWP2A as a complex chromatin-binding protein that serves to direct the deacetylase complex M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels.</p>',
'date' => '2018-10-16',
'pmid' => 'http://www.pubmed.gov/30327463',
'doi' => '10.1038/s41467-018-06665-5',
'modified' => '2019-07-22 09:17:39',
'created' => '2019-03-21 14:12:08',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 19 => array(
'id' => '3551',
'name' => 'HIV-2/SIV viral protein X counteracts HUSH repressor complex.',
'authors' => 'Ghina Chougui, Soundasse Munir-Matloob, Roy Matkovic, Michaël M Martin, Marina Morel, Hichem Lahouassa, Marjorie Leduc, Bertha Cecilia Ramirez, Lucie Etienne and Florence Margottin-Goguet',
'description' => '<p>To evade host immune defences, human immunodeficiency viruses 1 and 2 (HIV-1 and HIV-2) have evolved auxiliary proteins that target cell restriction factors. Viral protein X (Vpx) from the HIV-2/SIVsmm lineage enhances viral infection by antagonizing SAMHD1 (refs ), but this antagonism is not sufficient to explain all Vpx phenotypes. Here, through a proteomic screen, we identified another Vpx target-HUSH (TASOR, MPP8 and periphilin)-a complex involved in position-effect variegation. HUSH downregulation by Vpx is observed in primary cells and HIV-2-infected cells. Vpx binds HUSH and induces its proteasomal degradation through the recruitment of the DCAF1 ubiquitin ligase adaptor, independently from SAMHD1 antagonism. As a consequence, Vpx is able to reactivate HIV latent proviruses, unlike Vpx mutants, which are unable to induce HUSH degradation. Although antagonism of human HUSH is not conserved among all lentiviral lineages including HIV-1, it is a feature of viral protein R (Vpr) from simian immunodeficiency viruses (SIVs) of African green monkeys and from the divergent SIV of l'Hoest's monkey, arguing in favour of an ancient lentiviral species-specific vpx/vpr gene function. Altogether, our results suggest the HUSH complex as a restriction factor, active in primary CD4 T cells and counteracted by Vpx, therefore providing a molecular link between intrinsic immunity and epigenetic control.</p>',
'date' => '2018-08-01',
'pmid' => 'http://www.pubmed.gov/29891865',
'doi' => '10.1038/s41564-018-0179-6',
'modified' => '2019-02-28 10:20:23',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 20 => array(
'id' => '3470',
'name' => 'Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes.',
'authors' => 'Lomberk G, Blum Y, Nicolle R, Nair A, Gaonkar KS, Marisa L, Mathison A, Sun Z, Yan H, Elarouci N, Armenoult L, Ayadi M, Ordog T, Lee JH, Oliver G, Klee E, Moutardier V, Gayet O, Bian B, Duconseil P, Gilabert M, Bigonnet M, Garcia S, Turrini O, Delpero JR,',
'description' => '<p>Recent studies have offered ample insight into genome-wide expression patterns to define pancreatic ductal adenocarcinoma (PDAC) subtypes, although there remains a lack of knowledge regarding the underlying epigenomics of PDAC. Here we perform multi-parametric integrative analyses of chromatin immunoprecipitation-sequencing (ChIP-seq) on multiple histone modifications, RNA-sequencing (RNA-seq), and DNA methylation to define epigenomic landscapes for PDAC subtypes, which can predict their relative aggressiveness and survival. Moreover, we describe the state of promoters, enhancers, super-enhancers, euchromatic, and heterochromatic regions for each subtype. Further analyses indicate that the distinct epigenomic landscapes are regulated by different membrane-to-nucleus pathways. Inactivation of a basal-specific super-enhancer associated pathway reveals the existence of plasticity between subtypes. Thus, our study provides new insight into the epigenetic landscapes associated with the heterogeneity of PDAC, thereby increasing our mechanistic understanding of this disease, as well as offering potential new markers and therapeutic targets.</p>',
'date' => '2018-05-17',
'pmid' => 'http://www.pubmed.gov/29773832',
'doi' => '10.1038/s41467-018-04383-6',
'modified' => '2019-02-15 21:08:07',
'created' => '2019-02-14 15:01:22',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 21 => array(
'id' => '3536',
'name' => 'PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites.',
'authors' => 'Diagouraga B, Clément JAJ, Duret L, Kadlec J, de Massy B, Baudat F',
'description' => '<p>The programmed formation of hundreds of DNA double-strand breaks (DSBs) is essential for proper meiosis and fertility. In mice and humans, the location of these breaks is determined by the meiosis-specific protein PRDM9, through the DNA-binding specificity of its zinc-finger domain. PRDM9 also has methyltransferase activity. Here, we show that this activity is required for H3K4me3 and H3K36me3 deposition and for DSB formation at PRDM9-binding sites. By analyzing mice that express two PRDM9 variants with distinct DNA-binding specificities, we show that each variant generates its own set of H3K4me3 marks independently from the other variant. Altogether, we reveal several basic principles of PRDM9-dependent DSB site determination, in which an excess of sites are designated through PRDM9 binding and subsequent histone methylation, from which a subset is selected for DSB formation.</p>',
'date' => '2018-03-01',
'pmid' => 'http://www.pubmed.gov/29478809',
'doi' => '10.1016/j.molcel.2018.01.033',
'modified' => '2019-02-28 10:51:44',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 22 => array(
'id' => '3276',
'name' => 'DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease',
'authors' => 'Jeziorska D.M. et al.',
'description' => '<p>The human genome contains ∼30,000 CpG islands (CGIs). While CGIs associated with promoters nearly always remain unmethylated, many of the ∼9,000 CGIs lying within gene bodies become methylated during development and differentiation. Both promoter and intragenic CGIs may also become abnormally methylated as a result of genome rearrangements and in malignancy. The epigenetic mechanisms by which some CGIs become methylated but others, in the same cell, remain unmethylated in these situations are poorly understood. Analyzing specific loci and using a genome-wide analysis, we show that transcription running across CGIs, associated with specific chromatin modifications, is required for DNA methyltransferase 3B (DNMT3B)-mediated DNA methylation of many naturally occurring intragenic CGIs. Importantly, we also show that a subgroup of intragenic CGIs is not sensitive to this process of transcription-mediated methylation and that this correlates with their individual intrinsic capacity to initiate transcription in vivo. We propose a general model of how transcription could act as a primary determinant of the patterns of CGI methylation in normal development and differentiation, and in human disease.</p>',
'date' => '2017-09-05',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28827334',
'doi' => '',
'modified' => '2017-10-16 10:16:06',
'created' => '2017-10-16 10:16:06',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 23 => array(
'id' => '3240',
'name' => 'Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation',
'authors' => 'Pünzeler S. et al.',
'description' => '<p>Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA-based processes via poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel H2A.Z-nucleosome binder. PWWP2A is a functionally uncharacterized, vertebrate-specific protein that binds very tightly to chromatin through a concerted multivalent binding mode. Two internal protein regions mediate H2A.Z-specificity and nucleosome interaction, whereas the PWWP domain exhibits direct DNA binding. Genome-wide mapping reveals that PWWP2A binds selectively to H2A.Z-containing nucleosomes with strong preference for promoters of highly transcribed genes. In human cells, its depletion affects gene expression and impairs proliferation via a mitotic delay. While PWWP2A does not influence H2A.Z occupancy, the C-terminal tail of H2A.Z is one important mediator to recruit PWWP2A to chromatin. Knockdown of PWWP2A in <i>Xenopus</i> results in severe cranial facial defects, arising from neural crest cell differentiation and migration problems. Thus, PWWP2A is a novel H2A.Z-specific multivalent chromatin binder providing a surprising link between H2A.Z, chromosome segregation, and organ development.</p>',
'date' => '2017-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28645917',
'doi' => '',
'modified' => '2017-08-29 09:45:44',
'created' => '2017-08-29 09:45:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 24 => array(
'id' => '3216',
'name' => 'Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b',
'authors' => 'Kevin T. Ebata, Kathryn Mesh, Shichong Liu, Misha Bilenky, Alexander Fekete, Michael G. Acker, Martin Hirst, Benjamin A. Garcia and Miguel Ramalho-Santos',
'description' => '<section xmlns="" xmlns:fn="http://www.w3.org/2005/xpath-functions" xmlns:meta="http://www.springer.com/app/meta" class="Abstract" id="Abs1" lang="en">
<div class="js-CollapseSection">
<div xmlns:func="http://oscar.fig.bmc.com" xmlns="http://www.w3.org/1999/xhtml" class="AbstractSection" id="ASec1">
<h3 xmlns="" class="Heading">Background</h3>
<p id="Par1" class="Para">Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that vitamin C enhances the activity of Tet enzymes in embryonic stem (ES) cells, leading to DNA demethylation and activation of germline genes.</p>
</div>
<div xmlns:func="http://oscar.fig.bmc.com" xmlns="http://www.w3.org/1999/xhtml" class="AbstractSection" id="ASec2">
<h3 xmlns="" class="Heading">Results</h3>
<p id="Par2" class="Para">We report here that vitamin C induces a remarkably specific demethylation of histone H3 lysine 9 dimethylation (H3K9me2) in naïve ES cells. Vitamin C treatment reduces global levels of H3K9me2, but not other histone methylation marks analyzed, as measured by western blot, immunofluorescence and mass spectrometry. Vitamin C leads to widespread loss of H3K9me2 at large chromosomal domains as well as gene promoters and repeat elements. Vitamin C-induced loss of H3K9me2 occurs rapidly within 24 h and is reversible. Importantly, we found that the histone demethylases Kdm3a and Kdm3b are required for vitamin C-induced demethylation of H3K9me2. Moreover, we show that vitamin C-induced Kdm3a/b-mediated H3K9me2 demethylation and Tet-mediated DNA demethylation are independent processes at specific loci. Lastly, we document Kdm3a/b are partially required for the upregulation of germline genes by vitamin C.</p>
</div>
<div xmlns:func="http://oscar.fig.bmc.com" xmlns="http://www.w3.org/1999/xhtml" class="AbstractSection" id="ASec3">
<h3 xmlns="" class="Heading">Conclusions</h3>
<p id="Par3" class="Para">These results reveal a specific role for vitamin C in histone demethylation in ES cells and document that DNA methylation and H3K9me2 cooperate to silence germline genes in pluripotent cells.</p>
</div>
</div>
</section>',
'date' => '2017-07-12',
'pmid' => 'https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-017-0143-3',
'doi' => 'https://doi.org/10.1186/s13072-017-0143-3',
'modified' => '2017-08-23 14:47:51',
'created' => '2017-07-29 08:04:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 25 => array(
'id' => '3177',
'name' => 'Microinjection of Antibodies Targeting the Lamin A/C Histone-Binding Site Blocks Mitotic Entry and Reveals Separate Chromatin Interactions with HP1, CenpB and PML.',
'authors' => 'Dixon C.R. et al.',
'description' => '<p>Lamins form a scaffold lining the nucleus that binds chromatin and contributes to spatial genome organization; however, due to the many other functions of lamins, studies knocking out or altering the lamin polymer cannot clearly distinguish between direct and indirect effects. To overcome this obstacle, we specifically targeted the mapped histone-binding site of A/C lamins by microinjecting antibodies specific to this region predicting that this would make the genome more mobile. No increase in chromatin mobility was observed; however, interestingly, injected cells failed to go through mitosis, while control antibody-injected cells did. This effect was not due to crosslinking of the lamin polymer, as Fab fragments also blocked mitosis. The lack of genome mobility suggested other lamin-chromatin interactions. To determine what these might be, mini-lamin A constructs were expressed with or without the histone-binding site that assembled into independent intranuclear structures. HP1, CenpB and PML proteins accumulated at these structures for both constructs, indicating that other sites supporting chromatin interactions exist on lamin A. Together, these results indicate that lamin A-chromatin interactions are highly redundant and more diverse than generally acknowledged and highlight the importance of trying to experimentally separate their individual functions.</p>',
'date' => '2017-03-25',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28346356',
'doi' => '',
'modified' => '2017-05-17 10:39:58',
'created' => '2017-05-17 10:39:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 26 => array(
'id' => '3172',
'name' => 'Decoupling of DNA methylation and activity of intergenic LINE-1 promoters in colorectal cancer',
'authors' => 'Vafadar-Isfahani N. et al.',
'description' => '<p>Hypomethylation of LINE-1 repeats in cancer has been proposed as the main mechanism behind their activation; this assumption, however, was based on findings from early studies that were biased toward young and transpositionally active elements. Here, we investigate the relationship between methylation of 2 intergenic, transpositionally inactive LINE-1 elements and expression of the LINE-1 chimeric transcript (LCT) 13 and LCT14 driven by their antisense promoters (L1-ASP). Our data from DNA modification, expression, and 5'RACE analyses suggest that colorectal cancer methylation in the regions analyzed is not always associated with LCT repression. Consistent with this, in HCT116 colorectal cancer cells lacking DNA methyltransferases DNMT1 or DNMT3B, LCT13 expression decreases, while cells lacking both DNMTs or treated with the DNMT inhibitor 5-azacytidine (5-aza) show no change in LCT13 expression. Interestingly, levels of the H4K20me3 histone modification are inversely associated with LCT13 and LCT14 expression. Moreover, at these LINE-1s, H4K20me3 levels rather than DNA methylation seem to be good predictor of their sensitivity to 5-aza treatment. Therefore, by studying individual LINE-1 promoters we have shown that in some cases these promoters can be active without losing methylation; in addition, we provide evidence that other factors (e.g., H4K20me3 levels) play prominent roles in their regulation.</p>',
'date' => '2017-03-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28300471',
'doi' => '',
'modified' => '2017-05-10 16:26:24',
'created' => '2017-05-10 16:26:24',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 27 => array(
'id' => '3152',
'name' => 'H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements',
'authors' => 'Zink L.M. et al.',
'description' => '<p>Histone chaperones prevent promiscuous histone interactions before chromatin assembly. They guarantee faithful deposition of canonical histones and functionally specialized histone variants into chromatin in a spatial- and temporally-restricted manner. Here, we identify the binding partners of the primate-specific and H3.3-related histone variant H3.Y using several quantitative mass spectrometry approaches, and biochemical and cell biological assays. We find the HIRA, but not the DAXX/ATRX, complex to recognize H3.Y, explaining its presence in transcriptionally active euchromatic regions. Accordingly, H3.Y nucleosomes are enriched in the transcription-promoting FACT complex and depleted of repressive post-translational histone modifications. H3.Y mutational gain-of-function screens reveal an unexpected combinatorial amino acid sequence requirement for histone H3.3 interaction with DAXX but not HIRA, and for H3.3 recruitment to PML nuclear bodies. We demonstrate the importance and necessity of specific H3.3 core and C-terminal amino acids in discriminating between distinct chaperone complexes. Further, chromatin immunoprecipitation sequencing experiments reveal that in contrast to euchromatic HIRA-dependent deposition sites, human DAXX/ATRX-dependent regions of histone H3 variant incorporation are enriched in heterochromatic H3K9me3 and simple repeat sequences. These data demonstrate that H3.Y's unique amino acids allow a functional distinction between HIRA and DAXX binding and its consequent deposition into open chromatin.</p>',
'date' => '2017-02-21',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28334823',
'doi' => '',
'modified' => '2017-03-31 14:13:36',
'created' => '2017-03-31 14:13:36',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 28 => array(
'id' => '3100',
'name' => 'Muscle catabolic capacities and global hepatic epigenome are modified in juvenile rainbow trout fed different vitamin levels at first feeding',
'authors' => 'Panserat S. et al.',
'description' => '<p>Based on the concept of nutritional programming in mammals, we tested whether a short term hyper or hypo vitamin stimulus during first-feeding could induce long-lasting changes in nutrient metabolism in rainbow trout. Trout alevins received during the 4 first weeks of exogenous feeding a diet either without supplemental vitamins (NOSUP), a diet supplemented with a vitamin premix to satisfy the minimal requirement in all the vitamins (NRC) or a diet with a vitamin premix corresponding to an optimal vitamin nutrition (OVN). Following a common rearing period on the control diet, all three groups were then evaluated in terms of metabolic marker gene expressions at the end of the feeding period (day 119). Whereas no gene modifications for proteins involved in energy and lipid metabolism were observed in whole alevins (short-term effect), some of these genes showed a long-term molecular adaptation in the muscle of juveniles (long-term effect). Indeed, muscle of juveniles subjected at an early feeding of the OVN diet displayed up-regulated expression of markers of lipid catabolism (3-hydroxyacyl-CoA dehydrogenase – HOAD - enzyme) and mitochondrial energy metabolism (Citrate synthase - <em>cs</em>, Ubiquitinol cytochrome <em>c</em> reductase core protein 2 - QCR2, cytochrome oxidase 4 - COX4, ATP synthase form 5 - ATP5A) compared to fish fed the NOSUP diet. Moreover, some key enzymes involved in glucose catabolism (Muscle Pyruvate kinase - PKM) and amino acid catabolism (Glutamate dehydrogenase - GDH3) were also up regulated in muscle of juvenile fish fed with the OVN diet at first-feeding compared to fish fed the NOSUP diet. We researched if these permanently modified gene expressions could be related to global modifications of epigenetic marks (global DNA methylation and global histone acetylation and methylation). There was no variation of the epigenetic marks in muscle. However, we found changes in hepatic DNA methylation, global H3 acetylation and H3K4 methylation, dependent on the vitamin intake at early life. In summary, our data show, for the first time in fish, that a short-term vitamin-stimulus during early life may durably influence muscle energy and lipid metabolism as well as some hepatic epigenetic marks in rainbow trout.</p>',
'date' => '2017-02-01',
'pmid' => 'http://www.sciencedirect.com/science/article/pii/S0044848616309693',
'doi' => '',
'modified' => '2017-01-03 15:01:50',
'created' => '2017-01-03 15:01:50',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 29 => array(
'id' => '2825',
'name' => 'Oestrogen receptor β regulates epigenetic patterns at specific genomic loci through interaction with thymine DNA glycosylase.',
'authors' => 'Liu Y, Duong W, Krawczyk C, Bretschneider N, Borbély G, Varshney M, Zinser C, Schär P, Rüegg J.',
'description' => '<div class="">
<h4>BACKGROUND:</h4>
<p><abstracttext label="BACKGROUND" nlmcategory="BACKGROUND">DNA methylation is one way to encode epigenetic information and plays a crucial role in regulating gene expression during embryonic development. DNA methylation marks are established by the DNA methyltransferases and, recently, a mechanism for active DNA demethylation has emerged involving the ten-eleven translocator proteins and thymine DNA glycosylase (TDG). However, so far it is not clear how these enzymes are recruited to, and regulate DNA methylation at, specific genomic loci. A number of studies imply that sequence-specific transcription factors are involved in targeting DNA methylation and demethylation processes. Oestrogen receptor beta (ERβ) is a ligand-inducible transcription factor regulating gene expression in response to the female sex hormone oestrogen. Previously, we found that ERβ deficiency results in changes in DNA methylation patterns at two gene promoters, implicating an involvement of ERβ in DNA methylation. In this study, we set out to explore this involvement on a genome-wide level, and to investigate the underlying mechanisms of this function.</abstracttext></p>
<h4>RESULTS:</h4>
<p><abstracttext label="RESULTS" nlmcategory="RESULTS">Using reduced representation bisulfite sequencing, we compared genome-wide DNA methylation in mouse embryonic fibroblasts derived from wildtype and ERβ knock-out mice, and identified around 8000 differentially methylated positions (DMPs). Validation and further characterisation of selected DMPs showed that differences in methylation correlated with changes in expression of the nearest gene. Additionally, re-introduction of ERβ into the knock-out cells could reverse hypermethylation and reactivate expression of some of the genes. We also show that ERβ is recruited to regions around hypermethylated DMPs. Finally, we demonstrate here that ERβ interacts with TDG and that TDG binds ERβ-dependently to hypermethylated DMPs.</abstracttext></p>
<h4>CONCLUSION:</h4>
<p><abstracttext label="CONCLUSION" nlmcategory="CONCLUSIONS">We provide evidence that ERβ plays a role in regulating DNA methylation at specific genomic loci, likely as the result of its interaction with TDG at these regions. Our findings imply a novel function of ERβ, beyond direct transcriptional control, in regulating DNA methylation at target genes. Further, they shed light on the question how DNA methylation is regulated at specific genomic loci by supporting a concept in which sequence-specific transcription factors can target factors that regulate DNA methylation patterns.</abstracttext></p>
</div>',
'date' => '2016-02-16',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/26889208',
'doi' => '10.1186/s13072-016-0055-7.',
'modified' => '2016-02-22 10:05:14',
'created' => '2016-02-22 10:05:14',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 30 => array(
'id' => '2909',
'name' => 'Epigenetic priming of inflammatory response genes by high glucose in adipose progenitor cells',
'authors' => 'Rønningen T, Shah A, Reiner AH, Collas P, Moskaug JØ',
'description' => '<p>Cellular metabolism confers wide-spread epigenetic modifications required for regulation of transcriptional networks that determine cellular states. Mesenchymal stromal cells are responsive to metabolic cues including circulating glucose levels and modulate inflammatory responses. We show here that long term exposure of undifferentiated human adipose tissue stromal cells (ASCs) to high glucose upregulates a subset of inflammation response (IR) genes and alters their promoter histone methylation patterns in a manner consistent with transcriptional de-repression. Modeling of chromatin states from combinations of histone modifications in nearly 500 IR genes unveil three overarching chromatin configurations reflecting repressive, active, and potentially active states in promoter and enhancer elements. Accordingly, we show that adipogenic differentiation in high glucose predominantly upregulates IR genes. Our results indicate that elevated extracellular glucose levels sensitize in ASCs an IR gene expression program which is exacerbated during adipocyte differentiation. We propose that high glucose exposure conveys an epigenetic 'priming' of IR genes, favoring a transcriptional inflammatory response upon adipogenic stimulation. Chromatin alterations at IR genes by high glucose exposure may play a role in the etiology of metabolic diseases.</p>',
'date' => '2015-11-27',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/26462465',
'doi' => '10.1016/j.bbrc.2015.10.030',
'modified' => '2016-05-09 22:54:48',
'created' => '2016-05-09 22:54:48',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 31 => array(
'id' => '2874',
'name' => 'Polycomb RING1A- and RING1B-dependent histone H2A monoubiquitylation at pericentromeric regions promotes S-phase progression',
'authors' => 'Bravo M, Nicolini F, Starowicz K, Barroso S, Calés C, Aguilera A, Vidal M',
'description' => '<p>The functions of polycomb products extend beyond their well-known activity as transcriptional regulators to include genome duplication processes. Polycomb activities during DNA replication and DNA damage repair are unclear, particularly without induced replicative stress. We have used a cellular model of conditionally inactive polycomb E3 ligases (RING1A and RING1B), which monoubiquitylate lysine 119 of histone H2A (H2AK119Ub), to examine DNA replication in unperturbed cells. We identify slow elongation and fork stalling during DNA replication that is associated with the accumulation of mid and late S-phase cells. Signs of replicative stress and colocalisation of double-strand breaks with chromocenters, the sites of coalesced pericentromeric heterocromatic (PCH) domains, were enriched in cells at mid S-phase, the stage at which PCH is replicated. Altered replication was rescued by targeted monoubiquitylation of PCH through methyl-CpG binding domain protein 1. The acute senescence associated with the depletion of RING1 proteins, which is mediated by p21 (also known as CDKN1A) upregulation, could be uncoupled from a response to DNA damage. These findings link cell proliferation and the polycomb proteins RING1A and RING1B to S-phase progression through a specific function in PCH replication.</p>',
'date' => '2015-08-13',
'pmid' => 'http://jcs.biologists.org/content/128/19/3660',
'doi' => '10.1242/jcs.173021 ',
'modified' => '2016-03-29 16:29:38',
'created' => '2016-03-29 16:29:38',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 32 => array(
'id' => '2725',
'name' => 'Erosion of X Chromosome Inactivation in Human Pluripotent Cells Initiates with XACT Coating and Depends on a Specific Heterochromatin Landscape.',
'authors' => 'Vallot C, Ouimette JF, Makhlouf M, Féraud O, Pontis J, Côme J, Martinat C, Bennaceur-Griscelli A, Lalande M, Rougeulle C',
'description' => 'Human pluripotent stem cells (hPSCs) display extensive epigenetic instability, particularly on the X chromosome. In this study, we show that, in hPSCs, the inactive X chromosome has a specific heterochromatin landscape that predisposes it to erosion of X chromosome inactivation (XCI), a process that occurs spontaneously in hPSCs. Heterochromatin remodeling and gene reactivation occur in a non-random fashion and are confined to specific H3K27me3-enriched domains, leaving H3K9me3-marked regions unaffected. Using single-cell monitoring of XCI erosion, we show that this instability only occurs in pluripotent cells. We also provide evidence that loss of XIST expression is not the primary cause of XCI instability and that gene reactivation from the inactive X (Xi) precedes loss of XIST coating. Notably, expression and coating by the long non-coding RNA XACT are early events in XCI erosion and, therefore, may play a role in mediating this process.',
'date' => '2015-05-07',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25921272',
'doi' => '',
'modified' => '2015-07-24 15:39:05',
'created' => '2015-07-24 15:39:05',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 33 => array(
'id' => '2575',
'name' => 'Embryonic stem cell differentiation requires full length Chd1.',
'authors' => 'Piatti P, Lim CY, Nat R, Villunger A, Geley S, Shue YT, Soratroi C, Moser M, Lusser A',
'description' => 'The modulation of chromatin dynamics by ATP-dependent chromatin remodeling factors has been recognized as an important mechanism to regulate the balancing of self-renewal and pluripotency in embryonic stem cells (ESCs). Here we have studied the effects of a partial deletion of the gene encoding the chromatin remodeling factor Chd1 that generates an N-terminally truncated version of Chd1 in mouse ESCs in vitro as well as in vivo. We found that a previously uncharacterized serine-rich region (SRR) at the N-terminus is not required for chromatin assembly activity of Chd1 but that it is subject to phosphorylation. Expression of Chd1 lacking this region in ESCs resulted in aberrant differentiation properties of these cells. The self-renewal capacity and ESC chromatin structure, however, were not affected. Notably, we found that newly established ESCs derived from Chd1(Δ2/Δ2) mutant mice exhibited similar differentiation defects as in vitro generated mutant ESCs, even though the N-terminal truncation of Chd1 was fully compatible with embryogenesis and post-natal life in the mouse. These results underscore the importance of Chd1 for the regulation of pluripotency in ESCs and provide evidence for a hitherto unrecognized critical role of the phosphorylated N-terminal SRR for full functionality of Chd1.',
'date' => '2015-01-26',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25620209',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 34 => array(
'id' => '2513',
'name' => 'The histone demethylase enzyme KDM3A is a key estrogen receptor regulator in breast cancer.',
'authors' => 'Wade MA, Jones D, Wilson L, Stockley J, Coffey K, Robson CN, Gaughan L',
'description' => '<p>Endocrine therapy has successfully been used to treat estrogen receptor (ER)-positive breast cancer, but this invariably fails with cancers becoming refractory to treatment. Emerging evidence has suggested that fluctuations in ER co-regulatory protein expression may facilitate resistance to therapy and be involved in breast cancer progression. To date, a small number of enzymes that control methylation status of histones have been identified as co-regulators of ER signalling. We have identified the histone H3 lysine 9 mono- and di-methyl demethylase enzyme KDM3A as a positive regulator of ER activity. Here, we demonstrate that depletion of KDM3A by RNAi abrogates the recruitment of the ER to cis-regulatory elements within target gene promoters, thereby inhibiting estrogen-induced gene expression changes. Global gene expression analysis of KDM3A-depleted cells identified gene clusters associated with cell growth. Consistent with this, we show that knockdown of KDM3A reduces ER-positive cell proliferation and demonstrate that KDM3A is required for growth in a model of endocrine therapy-resistant disease. Crucially, we show that KDM3A catalytic activity is required for both ER-target gene expression and cell growth, demonstrating that developing compounds which target demethylase enzymatic activity may be efficacious in treating both ER-positive and endocrine therapy-resistant disease.</p>',
'date' => '2015-01-09',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25488809',
'doi' => '',
'modified' => '2016-05-03 11:59:18',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 35 => array(
'id' => '2502',
'name' => 'TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells.',
'authors' => 'Fasching L, Kapopoulou A, Sachdeva R, Petri R, Jönsson ME, Männe C, Turelli P, Jern P, Cammas F, Trono D, Jakobsson J',
'description' => '<p>TRIM28 is a corepressor that mediates transcriptional silencing by establishing local heterochromatin. Here, we show that deletion of TRIM28 in neural progenitor cells (NPCs) results in high-level expression of two groups of endogenous retroviruses (ERVs): IAP1 and MMERVK10C. We find that NPCs use TRIM28-mediated histone modifications to dynamically regulate transcription and silencing of ERVs, which is in contrast to other somatic cell types using DNA methylation. We also show that derepression of ERVs influences transcriptional dynamics in NPCs through the activation of nearby genes and the expression of long noncoding RNAs. These findings demonstrate a unique dynamic transcriptional regulation of ERVs in NPCs. Our results warrant future studies on the role of ERVs in the healthy and diseased brain.</p>',
'date' => '2015-01-06',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25543143',
'doi' => '',
'modified' => '2017-06-22 13:34:19',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 36 => array(
'id' => '2492',
'name' => 'Cryosectioning the intestinal crypt-villus axis: an ex vivo method to study the dynamics of epigenetic modifications from stem cells to differentiated cells',
'authors' => 'Vincent A, Kazmierczak C, Duchêne B, Jonckheere N, Leteurtre E, Van Seuningen I',
'description' => 'The intestinal epithelium is a particularly attractive biological adult model to study epigenetic mechanisms driving adult stem cell renewal and cell differentiation. Since epigenetic modifications are dynamic, we have developed an original ex vivo approach to study the expression and epigenetic profiles of key genes associated with either intestinal cell pluripotency or differentiation by isolating cryosections of the intestinal crypt-villus axis. Gene expression, DNA methylation and histone modifications were studied by qRT-PCR, Methylation Specific-PCR and micro-Chromatin Immunoprecipitation, respectively. Using this approach, it was possible to identify segment-specific methylation and chromatin profiles. We show that (i) expression of intestinal stem cell markers (Lgr5, Ascl2) exclusively in the crypt is associated with active histone marks, (ii) promoters of all pluripotency genes studied and transcription factors involved in intestinal cell fate (Cdx2) harbour a bivalent chromatin pattern in the crypts, (iii) expression of differentiation markers (Muc2, Sox9) along the crypt-villus axis is associated with DNA methylation. Hence, using an original model of cryosectioning along the crypt-villus axis that allows in situ detection of dynamic epigenetic modifications, we demonstrate that regulation of pluripotency and differentiation markers in healthy intestinal mucosa involves different and specific epigenetic mechanisms.',
'date' => '2014-12-27',
'pmid' => 'http://www.sciencedirect.com/science/article/pii/S1873506114001585',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 37 => array(
'id' => '2215',
'name' => 'Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation.',
'authors' => 'Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ',
'description' => 'Artificial transcription factors (ATFs) and genomic nucleases based on a DNA binding platform consisting of multiple zinc finger domains are currently being developed for clinical applications. However, no genome-wide investigations into their binding specificity have been performed. We have created six-finger ATFs to target two different 18 nt regions of the human SOX2 promoter; each ATF is constructed such that it contains or lacks a super KRAB domain (SKD) that interacts with a complex containing repressive histone methyltransferases. ChIP-seq analysis of the effector-free ATFs in MCF7 breast cancer cells identified thousands of binding sites, mostly in promoter regions; the addition of an SKD domain increased the number of binding sites ∼5-fold, with a majority of the new sites located outside of promoters. De novo motif analyses suggest that the lack of binding specificity is due to subsets of the finger domains being used for genomic interactions. Although the ATFs display widespread binding, few genes showed expression differences; genes repressed by the ATF-SKD have stronger binding sites and are more enriched for a 12 nt motif. Interestingly, epigenetic analyses indicate that the transcriptional repression caused by the ATF-SKD is not due to changes in active histone modifications.',
'date' => '2014-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25122745',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 38 => array(
'id' => '2664',
'name' => 'The PML-associated protein DEK regulates the balance of H3.3 loading on chromatin and is important for telomere integrity.',
'authors' => 'Ivanauskiene K, Delbarre E, McGhie JD, Küntziger T, Wong LH, Collas P',
'description' => 'Histone variant H3.3 is deposited in chromatin at active sites, telomeres, and pericentric heterochromatin by distinct chaperones, but the mechanisms of regulation and coordination of chaperone-mediated H3.3 loading remain largely unknown. We show here that the chromatin-associated oncoprotein DEK regulates differential HIRA- and DAAX/ATRX-dependent distribution of H3.3 on chromosomes in somatic cells and embryonic stem cells. Live cell imaging studies show that nonnucleosomal H3.3 normally destined to PML nuclear bodies is re-routed to chromatin after depletion of DEK. This results in HIRA-dependent widespread chromatin deposition of H3.3 and H3.3 incorporation in the foci of heterochromatin in a process requiring the DAXX/ATRX complex. In embryonic stem cells, loss of DEK leads to displacement of PML bodies and ATRX from telomeres, redistribution of H3.3 from telomeres to chromosome arms and pericentric heterochromatin, induction of a fragile telomere phenotype, and telomere dysfunction. Our results indicate that DEK is required for proper loading of ATRX and H3.3 on telomeres and for telomeric chromatin architecture. We propose that DEK acts as a "gatekeeper" of chromatin, controlling chromatin integrity by restricting broad access to H3.3 by dedicated chaperones. Our results also suggest that telomere stability relies on mechanisms ensuring proper histone supply and routing.',
'date' => '2014-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25049225',
'doi' => '',
'modified' => '2015-07-24 15:39:05',
'created' => '2015-07-24 15:39:05',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 39 => array(
'id' => '2338',
'name' => 'The specific alteration of histone methylation profiles by DZNep during early zebrafish development.',
'authors' => 'Ostrup O, Reiner AH, Aleström P, Collas P',
'description' => '<p>Early embryo development constitutes a unique opportunity to study acquisition of epigenetic marks, including histone methylation. This study investigates the in vivo function and specificity of 3-deazaneplanocin A (DZNep), a promising anti-cancer drug that targets polycomb complex genes. One- to two-cell stage embryos were cultured with DZNep, and subsequently evaluated at the post-mid blastula transition stage for H3K27me3, H3K4me3 and H3K9me3 occupancy and enrichment at promoters using ChIP-chip microarrays. DZNep affected promoter enrichment of H3K27me3 and H3K9me3, whereas H3K4me3 remained stable. Interestingly, DZNep induced a loss of H3K27me3 and H3K9me3 from a substantial number of promoters but did not prevent de novo acquisition of these marks on others, indicating gene-specific targeting of its action. Loss/gain of H3K27me3 on promoters did not result in changes in gene expression levels until 24h post-fertilization. In contrast, genes gaining H3K9me3 displayed strong and constant down-regulation upon DZNep treatment. H3K9me3 enrichment on these gene promoters was observed not only in the proximal area as expected, but also over the transcription start site. Altered H3K9me3 profiles were associated with severe neuronal and cranial phenotypes at day 4-5 post-fertilization. Thus, DZNep was shown to affect enrichment patterns of H3K27me3 and H3K9me3 at promoters in a gene-specific manner.</p>',
'date' => '2014-09-28',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25260724',
'doi' => '',
'modified' => '2016-04-08 09:43:32',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 40 => array(
'id' => '2226',
'name' => 'KMTase Set7/9 is a critical regulator of E2F1 activity upon genotoxic stress.',
'authors' => 'Lezina L, Aksenova V, Ivanova T, Purmessur N, Antonov AV, Tentler D, Fedorova O, Garabadgiu AV, Talianidis I, Melino G, Barlev NA',
'description' => 'During the recent years lysine methyltransferase Set7/9 ((Su(var)-3-9, Enhancer-of-Zeste, Trithorax) domain containing protein 7/9) has emerged as an important regulator of different transcription factors. In this study, we report a novel function for Set7/9 as a critical co-activator of E2 promoter-binding factor 1 (E2F1)-dependent transcription in response to DNA damage. By means of various biochemical, cell biology, and bioinformatics approaches, we uncovered that cell-cycle progression through the G1/S checkpoint of tumour cells upon DNA damage is defined by the threshold of expression of both E2F1 and Set7/9. The latter affects the activity of E2F1 by indirectly modulating histone modifications in the promoters of E2F1-dependent genes. Moreover, Set7/9 differentially affects E2F1 transcription targets: it promotes cell proliferation via expression of the CCNE1 gene and represses apoptosis by inhibiting the TP73 gene. Our biochemical screening of the panel of lung tumour cell lines suggests that these two factors are critically important for transcriptional upregulation of the CCNE1 gene product and hence successful progression through cell cycle. These findings identify Set7/9 as a potential biomarker in tumour cells with overexpressed E2F1 activity.Cell Death and Differentiation advance online publication, 15 August 2014; doi:10.1038/cdd.2014.108.',
'date' => '2014-08-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25124555',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 41 => array(
'id' => '2206',
'name' => 'The histone variant composition of centromeres is controlled by the pericentric heterochromatin state during the cell cycle.',
'authors' => 'Boyarchuk E, Filipescu D, Vassias I, Cantaloube S, Almouzni G',
'description' => 'Correct chromosome segregation requires a unique chromatin environment at centromeres and in their vicinity. Here, we address how the deposition of canonical H2A and H2A.Z histone variants is controlled at pericentric heterochromatin (PHC). Whereas in euchromatin newly synthesized H2A and H2A.Z are deposited throughout the cell cycle, we reveal two discrete waves of deposition at PHC - during mid to late S phase in a replication-dependent manner for H2A and during G1 phase for H2A.Z. This G1 cell cycle restriction is lost when heterochromatin features are altered, leading to the accumulation of H2A.Z at the domain. Interestingly, compromising PHC integrity also impacts upon neighboring centric chromatin, increasing the amount of centromeric CENP-A without changing the timing of its deposition. We conclude that the higher-order chromatin structure at the pericentric domain influences dynamics at the nucleosomal level within centromeric chromatin. The two different modes of rearrangement of the PHC during the cell cycle provide distinct opportunities to replenish one or the other H2A variant, highlighting PHC integrity as a potential signal to regulate the deposition timing and stoichiometry of histone variants at the centromere.',
'date' => '2014-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24906798',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 42 => array(
'id' => '2081',
'name' => 'RNAi-Mediated Gene silencing in Zebrafish Triggered by Convergent Transcription.',
'authors' => 'Andrews OE, Cha DJ, Wei C, Patton JG',
'description' => 'RNAi based strategies to induce gene silencing are commonly employed in numerous model organisms but have not been extensively used in zebrafish. We found that introduction of transgenes containing convergent transcription units in zebrafish embryos induced stable transcriptional gene silencing (TGS) in cis and trans for reporter (mCherry) and endogenous (One-Eyed Pinhead (OEP) and miR-27a/b) genes. Convergent transcription enabled detection of both sense and antisense transcripts and silencing was suppressed upon Dicer knockdown, indicating processing of double stranded RNA. By ChIP analyses, increased silencing was accompanied by enrichment of the heterochromatin mark H3K9me3 in the two convergently arranged promoters and in the intervening reading frame. Our work demonstrates that convergent transcription can induce gene silencing in zebrafish providing another tool to create specific temporal and spatial control of gene expression.',
'date' => '2014-06-09',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24909225',
'doi' => '',
'modified' => '2015-07-24 15:39:02',
'created' => '2015-07-24 15:39:02',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 43 => array(
'id' => '1888',
'name' => 'Transcriptional Derepression of the ERVWE1 Locus following Influenza A Virus Infection.',
'authors' => 'Li F, Nellåker C, Sabunciyan S, Yolken RH, Jones-Brando L, Johansson AS, Owe-Larsson B, Karlsson H',
'description' => 'UNLABELLED: Syncytin-1, a fusogenic protein encoded by a human endogenous retrovirus of the W family (HERV-W) element (ERVWE1), is expressed in the syncytiotrophoblast layer of the placenta. This locus is transcriptionally repressed in adult tissues through promoter CpG methylation and suppressive histone modifications. Whereas syncytin-1 appears to be crucial for the development and functioning of the human placenta, its ectopic expression has been associated with pathological conditions, such as multiple sclerosis and schizophrenia. We previously reported on the transactivation of HERV-W elements, including ERVWE1, during influenza A/WSN/33 virus infection in a range of human cell lines. Here we report the results of quantitative PCR analyses of transcripts encoding syncytin-1 in both cell lines and primary fibroblast cells. We observed that spliced ERVWE1 transcripts and those encoding the transcription factor glial cells missing 1 (GCM1), acting as an enhancer element upstream of ERVWE1, are prominently upregulated in response to influenza A/WSN/33 virus infection in nonplacental cells. Knockdown of GCM1 by small interfering RNA followed by infection suppressed the transactivation of ERVWE1. While the infection had no influence on CpG methylation in the ERVWE1 promoter, chromatin immunoprecipitation assays detected decreased H3K9 trimethylation (H3K9me3) and histone methyltransferase SETDB1 levels along with influenza virus proteins associated with ERVWE1 and other HERV-W loci in infected CCF-STTG1 cells. The present findings suggest that an exogenous influenza virus infection can transactivate ERVWE1 by increasing transcription of GCM1 and reducing H3K9me3 in this region and in other regions harboring HERV-W elements. IMPORTANCE: Syncytin-1, a protein encoded by the env gene in the HERV-W locus ERVWE1, appears to be crucial for the development and functioning of the human placenta and is transcriptionally repressed in nonplacental tissues. Nevertheless, its ectopic expression has been associated with pathological conditions, such as multiple sclerosis and schizophrenia. In the present paper, we report findings suggesting that an exogenous influenza A virus infection can transactivate ERVWE1 by increasing the transcription of GCM1 and reducing the repressive histone mark H3K9me3 in this region and in other regions harboring HERV-W elements. These observations have implications of potential relevance for viral pathogenesis and for conditions associated with the aberrant transcription of HERV-W loci.',
'date' => '2014-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24478419',
'doi' => '',
'modified' => '2015-07-24 15:39:02',
'created' => '2015-07-24 15:39:02',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 44 => array(
'id' => '1723',
'name' => 'HDAC inhibitor confers radiosensitivity to prostate stem-like cells.',
'authors' => 'Frame FM, Pellacani D, Collins AT, Simms MS, Mann VM, Jones G, Meuth M, Bristow RG, Maitland NJ',
'description' => 'Background:Radiotherapy can be an effective treatment for prostate cancer, but radiorecurrent tumours do develop. Considering prostate cancer heterogeneity, we hypothesised that primitive stem-like cells may constitute the radiation-resistant fraction.Methods:Primary cultures were derived from patients undergoing resection for prostate cancer or benign prostatic hyperplasia. After short-term culture, three populations of cells were sorted, reflecting the prostate epithelial hierarchy, namely stem-like cells (SCs, α2β1integrin(hi)/CD133(+)), transit-amplifying (TA, α2β1integrin(hi)/CD133(-)) and committed basal (CB, α2β1integrin(lo)) cells. Radiosensitivity was measured by colony-forming efficiency (CFE) and DNA damage by comet assay and DNA damage foci quantification. Immunofluorescence and flow cytometry were used to measure heterochromatin. The HDAC (histone deacetylase) inhibitor Trichostatin A was used as a radiosensitiser.Results:Stem-like cells had increased CFE post irradiation compared with the more differentiated cells (TA and CB). The SC population sustained fewer lethal double-strand breaks than either TA or CB cells, which correlated with SCs being less proliferative and having increased levels of heterochromatin. Finally, treatment with an HDAC inhibitor sensitised the SCs to radiation.Interpretation:Prostate SCs are more radioresistant than more differentiated cell populations. We suggest that the primitive cells survive radiation therapy and that pre-treatment with HDAC inhibitors may sensitise this resistant fraction.',
'date' => '2013-12-10',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24220693',
'doi' => '',
'modified' => '2015-07-24 15:39:01',
'created' => '2015-07-24 15:39:01',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 45 => array(
'id' => '1516',
'name' => 'Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes.',
'authors' => 'Lund E, Oldenburg AR, Delbarre E, Freberg CT, Duband-Goulet I, Eskeland R, Buendia B, Collas P',
'description' => 'The nuclear lamina is implicated in the organization of the eukaryotic nucleus. Association of nuclear lamins with the genome occurs through large chromatin domains including mostly, but not exclusively, repressed genes. How lamin interactions with regulatory elements modulate gene expression in different cellular contexts is unknown. We show here that in human adipose tissue stem cells, lamin A/C interacts with distinct spatially restricted subpromoter regions, both within and outside peripheral and intra-nuclear lamin-rich domains. These localized interactions are associated with distinct transcriptional outcomes in a manner dependent on local chromatin modifications. Down-regulation of lamin A/C leads to dissociation of lamin A/C from promoters and remodels repressive and permissive histone modifications by enhancing transcriptional permissiveness, but is not sufficient to elicit gene activation. Adipogenic differentiation resets a large number of lamin-genome associations globally and at subpromoter levels and redefines associated transcription outputs. We propose that lamin A/C acts as a modulator of local gene expression outcome through interaction with adjustable sites on promoters, and that these position-dependent transcriptional readouts may be reset upon differentiation.',
'date' => '2013-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23861385',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 46 => array(
'id' => '1595',
'name' => 'Long range epigenetic silencing is a trans-species mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells.',
'authors' => 'Forn M, Muñoz M, Tauriello DV, Merlos-Suárez A, Rodilla V, Bigas A, Batlle E, Jordà M, Peinado MA',
'description' => 'DNA methylation and chromatin remodeling are frequently implicated in the silencing of genes involved in carcinogenesis. Long Range Epigenetic Silencing (LRES) is a mechanism of gene inactivation that affects multiple contiguous CpG islands and has been described in different human cancer types. However, it is unknown whether there is a coordinated regulation of the genes embedded in these regions in normal cells and in early stages of tumor progression. To better characterize the molecular events associated with the regulation and remodeling of these regions we analyzed two regions undergoing LRES in human colon cancer in the mouse model. We demonstrate that LRES also occurs in murine cancer in vivo and mimics the molecular features of the human phenomenon, namely, downregulation of gene expression, acquisition of inactive histone marks, and DNA hypermethylation of specific CpG islands. The genes embedded in these regions showed a dynamic and autonomous regulation during mouse intestinal cell differentiation, indicating that, in the framework considered here, the coordinated regulation in LRES is restricted to cancer. Unexpectedly, benign adenomas in Apc(Min/+) mice showed overexpression of most of the genes affected by LRES in cancer, which suggests that the repressive remodeling of the region is a late event. Chromatin immunoprecipitation analysis of the transcriptional insulator CTCF in mouse colon cancer cells revealed disrupted chromatin domain boundaries as compared with normal cells. Malignant regression of cancer cells by in vitro differentiation resulted in partial reversion of LRES and gain of CTCF binding. We conclude that genes in LRES regions are plastically regulated in cell differentiation and hyperproliferation, but are constrained to a coordinated repression by abolishing boundaries and the autonomous regulation of chromatin domains in cancer cells.',
'date' => '2013-08-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24035705',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 47 => array(
'id' => '1486',
'name' => 'Transgene- and locus-dependent imprinting reveals allele-specific chromosome conformations.',
'authors' => 'Lonfat N, Montavon T, Jebb D, Tschopp P, Nguyen Huynh TH, Zakany J, Duboule D',
'description' => 'When positioned into the integrin α-6 gene, an Hoxd9lacZ reporter transgene displayed parental imprinting in mouse embryos. While the expression from the paternal allele was comparable with patterns seen for the same transgene when present at the neighboring HoxD locus, almost no signal was scored at this integration site when the transgene was inherited from the mother, although the Itga6 locus itself is not imprinted. The transgene exhibited maternal allele-specific DNA hypermethylation acquired during oogenesis, and its expression silencing was reversible on passage through the male germ line. Histone modifications also corresponded to profiles described at known imprinted loci. Chromosome conformation analyses revealed distinct chromatin microarchitectures, with a more compact structure characterizing the maternally inherited repressed allele. Such genetic analyses of well-characterized transgene insertions associated with a de novo-induced parental imprint may help us understand the molecular determinants of imprinting.',
'date' => '2013-07-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23818637',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 48 => array(
'id' => '1425',
'name' => 'Expression of a large LINE-1-driven antisense RNA is linked to epigenetic silencing of the metastasis suppressor gene TFPI-2 in cancer.',
'authors' => 'Cruickshanks HA, Vafadar-Isfahani N, Dunican DS, Lee A, Sproul D, Lund JN, Meehan RR, Tufarelli C',
'description' => 'LINE-1 retrotransposons are abundant repetitive elements of viral origin, which in normal cells are kept quiescent through epigenetic mechanisms. Activation of LINE-1 occurs frequently in cancer and can enable LINE-1 mobilization but also has retrotransposition-independent consequences. We previously reported that in cancer, aberrantly active LINE-1 promoters can drive transcription of flanking unique sequences giving rise to LINE-1 chimeric transcripts (LCTs). Here, we show that one such LCT, LCT13, is a large transcript (>300 kb) running antisense to the metastasis-suppressor gene TFPI-2. We have modelled antisense RNA expression at TFPI-2 in transgenic mouse embryonic stem (ES) cells and demonstrate that antisense RNA induces silencing and deposition of repressive histone modifications implying a causal link. Consistent with this, LCT13 expression in breast and colon cancer cell lines is associated with silencing and repressive chromatin at TFPI-2. Furthermore, we detected LCT13 transcripts in 56% of colorectal tumours exhibiting reduced TFPI-2 expression. Our findings implicate activation of LINE-1 elements in subsequent epigenetic remodelling of surrounding genes, thus hinting a novel retrotransposition-independent role for LINE-1 elements in malignancy.',
'date' => '2013-05-23',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23703216',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 49 => array(
'id' => '1497',
'name' => 'Histone lysine trimethylation or acetylation can be modulated by phytoestrogen, estrogen or anti-HDAC in breast cancer cell lines.',
'authors' => 'Dagdemir A, Durif J, Ngollo M, Bignon YJ, Bernard-Gallon D',
'description' => '<p>AIM: The isoflavones genistein, daidzein and equol (daidzein metabolite) have been reported to interact with epigenetic modifications, specifically hypermethylation of tumor suppressor genes. The objective of this study was to analyze and understand the mechanisms by which phytoestrogens act on chromatin in breast cancer cell lines. MATERIALS & METHODS: Two breast cancer cell lines, MCF-7 and MDA-MB 231, were treated with genistein (18.5 µM), daidzein (78.5 µM), equol (12.8 µM), 17β-estradiol (10 nM) and suberoylanilide hydroxamic acid (1 µM) for 48 h. A control with untreated cells was performed. 17β-estradiol and an anti-HDAC were used to compare their actions with phytoestrogens. The chromatin immunoprecipitation coupled with quantitative PCR was used to follow soy phytoestrogen effects on H3 and H4 histones on H3K27me3, H3K9me3, H3K4me3, H4K8ac and H3K4ac marks, and we selected six genes (EZH2, BRCA1, ERα, ERβ, SRC3 and P300) for analysis. RESULTS: Soy phytoestrogens induced a decrease in trimethylated marks and an increase in acetylating marks studied at six selected genes. CONCLUSION: We demonstrated that soy phytoestrogens tend to modify transcription through the demethylation and acetylation of histones in breast cancer cell lines.</p>',
'date' => '2013-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23414320',
'doi' => '',
'modified' => '2016-05-03 12:17:35',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 50 => array(
'id' => '1179',
'name' => 'Epigenetic Regulation of Nestin Expression During Neurogenic Differentiation of Adipose Tissue Stem Cells.',
'authors' => 'Boulland JL, Mastrangelopoulou M, Boquest AC, Jakobsen R, Noer A, Glover JC, Collas P.',
'description' => 'Adipose-tissue-derived stem cells (ASCs) have received considerable attention due to their easy access, expansion potential, and differentiation capacity. ASCs are believed to have the potential to differentiate into neurons. However, the mechanisms by which this may occur remain largely unknown. Here, we show that culturing ASCs under active proliferation conditions greatly improves their propensity to differentiate toward osteogenic, adipogenic, and neurogenic lineages. Neurogenic-induced ASCs express early neurogenic genes as well as markers of mature neurons, including voltage-gated ion channels. Nestin, highly expressed in neural progenitors, is upregulated by mitogenic stimulation of ASCs, and as in neural progenitors, then repressed during neurogenic differentiation. Nestin gene (NES) expression under these conditions appears to be regulated by epigenetic mechanisms. The neural-specific, but not muscle-specific, enhancer regions of NES are DNA demethylated by mitogenic stimulation, and remethylated upon neurogenic differentiation. We observe dynamic changes in histone H3K4, H3K9, and H3K27 methylation on the NES locus before and during neurogenic differentiation that are consistent with epigenetic processes involved in the regulation of NES expression. We suggest that ASCs are epigenetically prepatterned to differentiate toward a neural lineage and that this prepatterning is enhanced by demethylation of critical NES enhancer elements upon mitogenic stimulation preceding neurogenic differentiation. Our findings provide molecular evidence that the differentiation repertoire of ASCs may extend beyond mesodermal lineages.',
'date' => '2012-12-21',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/23140086',
'doi' => '',
'modified' => '2015-07-24 15:38:59',
'created' => '2015-07-24 15:38:59',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 51 => array(
'id' => '752',
'name' => 'The histone demethylase Kdm3a is essential to progression through differentiation.',
'authors' => 'Herzog M, Josseaux E, Dedeurwaerder S, Calonne E, Volkmar M, Fuks F',
'description' => 'Histone demethylation has important roles in regulating gene expression and forms part of the epigenetic memory system that regulates cell fate and identity by still poorly understood mechanisms. Here, we examined the role of histone demethylase Kdm3a during cell differentiation, showing that Kdm3a is essential for differentiation into parietal endoderm-like (PE) cells in the F9 mouse embryonal carcinoma model. We identified a number of target genes regulated by Kdm3a during endoderm differentiation; among the most dysregulated were the three developmental master regulators Dab2, Pdlim4 and FoxQ1. We show that dysregulation of the expression of these genes correlates with Kdm3a H3K9me2 demethylase activity. We further demonstrate that either Dab2 depletion or Kdm3a depletion prevents F9 cells from fully differentiating into PE cells, but that ectopic expression of Dab2 cannot compensate for Kdm3a knockdown; Dab2 is thus necessary, but insufficient on its own, to promote complete terminal differentiation. We conclude that Kdm3a plays a crucial role in progression through PE differentiation by regulating expression of a set of endoderm differentiation master genes. The emergence of Kdm3a as a key modulator of cell fate decision strengthens the view that histone demethylases are essential to cell differentiation.',
'date' => '2012-05-11',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22581778',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 52 => array(
'id' => '630',
'name' => 'Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.',
'authors' => 'Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B',
'description' => 'While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA hypomethylation in the cancer cell, primarily at partially methylated domains (PMDs) in normal breast cells. Unexpectedly, genes within these regions are largely silenced in cancer cells. The loss of DNA methylation in these regions is accompanied by formation of repressive chromatin, with a significant fraction displaying allelic DNA methylation where one allele is DNA methylated while the other allele is occupied by histone modifications H3K9me3 or H3K27me3. Our results show a mutually exclusive relationship between DNA methylation and H3K9me3 or H3K27me3. These results suggest that global DNA hypomethylation in breast cancer is tightly linked to the formation of repressive chromatin domains and gene silencing, thus identifying a potential epigenetic pathway for gene regulation in cancer cells.',
'date' => '2012-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22156296',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 53 => array(
'id' => '919',
'name' => 'Prepatterning of developmental gene expression by modified histones before zygotic genome activation.',
'authors' => 'Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Østrup O, Winata C, Mathavan S, Müller F, Aleström P, Collas P',
'description' => 'A hallmark of anamniote vertebrate development is a window of embryonic transcription-independent cell divisions before onset of zygotic genome activation (ZGA). Chromatin determinants of ZGA are unexplored; however, marking of developmental genes by modified histones in sperm suggests a predictive role of histone marks for ZGA. In zebrafish, pre-ZGA development for ten cell cycles provides an opportunity to examine whether genomic enrichment in modified histones is present before initiation of transcription. By profiling histone H3 trimethylation on all zebrafish promoters before and after ZGA, we demonstrate here an epigenetic prepatterning of developmental gene expression. This involves pre-ZGA marking of transcriptionally inactive genes involved in homeostatic and developmental regulation by permissive H3K4me3 with or without repressive H3K9me3 or H3K27me3. Our data suggest that histone modifications are instructive for the developmental gene expression program.',
'date' => '2011-12-13',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22137762',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 54 => array(
'id' => '637',
'name' => 'H3.5 is a novel hominid-specific histone H3 variant that is specifically expressed in the seminiferous tubules of human testes.',
'authors' => 'Schenk R, Jenke A, Zilbauer M, Wirth S, Postberg J',
'description' => 'The incorporation of histone variants into chromatin plays an important role for the establishment of particular chromatin states. Six human histone H3 variants are known to date, not counting CenH3 variants: H3.1, H3.2, H3.3 and the testis-specific H3.1t as well as the recently described variants H3.X and H3.Y. We report the discovery of H3.5, a novel non-CenH3 histone H3 variant. H3.5 is encoded on human chromosome 12p11.21 and probably evolved in a common ancestor of all recent great apes (Hominidae) as a consequence of H3F3B gene duplication by retrotransposition. H3.5 mRNA is specifically expressed in seminiferous tubules of human testis. Interestingly, H3.5 has two exact copies of ARKST motifs adjacent to lysine-9 or lysine-27, and lysine-79 is replaced by asparagine. In the Hek293 cell line, ectopically expressed H3.5 is assembled into chromatin and targeted by PTM. H3.5 preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes and can replace an essential function of RNAi-depleted H3.3 in cell growth.',
'date' => '2011-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21274551',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 55 => array(
'id' => '274',
'name' => 'Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability.',
'authors' => 'Cortázar D, Kunz C, Selfridge J, Lettieri T, Saito Y, MacDougall E, Wirz A, Schuermann D, Jacobs AL, Siegrist F, Steinacher R, Jiricny J, Bird A, Schär P',
'description' => 'Thymine DNA glycosylase (TDG) is a member of the uracil DNA glycosylase (UDG) superfamily of DNA repair enzymes. Owing to its ability to excise thymine when mispaired with guanine, it was proposed to act against the mutability of 5-methylcytosine (5-mC) deamination in mammalian DNA. However, TDG was also found to interact with transcription factors, histone acetyltransferases and de novo DNA methyltransferases, and it has been associated with DNA demethylation in gene promoters following activation of transcription, altogether implicating an engagement in gene regulation rather than DNA repair. Here we use a mouse genetic approach to determine the biological function of this multifaceted DNA repair enzyme. We find that, unlike other DNA glycosylases, TDG is essential for embryonic development, and that this phenotype is associated with epigenetic aberrations affecting the expression of developmental genes. Fibroblasts derived from Tdg null embryos (mouse embryonic fibroblasts, MEFs) show impaired gene regulation, coincident with imbalanced histone modification and CpG methylation at promoters of affected genes. TDG associates with the promoters of such genes both in fibroblasts and in embryonic stem cells (ESCs), but epigenetic aberrations only appear upon cell lineage commitment. We show that TDG contributes to the maintenance of active and bivalent chromatin throughout cell differentiation, facilitating a proper assembly of chromatin-modifying complexes and initiating base excision repair to counter aberrant de novo methylation. We thus conclude that TDG-dependent DNA repair has evolved to provide epigenetic stability in lineage committed cells.',
'date' => '2011-02-17',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21278727',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 56 => array(
'id' => '592',
'name' => 'Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.',
'authors' => 'Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ',
'description' => 'The H3K9me3 histone modification is often found at promoter regions, where it functions to repress transcription. However, we have previously shown that 3' exons of zinc finger genes (ZNFs) are marked by high levels of H3K9me3. We have now further investigated this unusual location for H3K9me3 in ZNF genes. Neither bioinformatic nor experimental approaches support the hypothesis that the 3' exons of ZNFs are promoters. We further characterized the histone modifications at the 3' ZNF exons and found that these regions also contain H3K36me3, a mark of transcriptional elongation. A genome-wide analysis of ChIP-seq data revealed that ZNFs constitute the majority of genes that have high levels of both H3K9me3 and H3K36me3. These results suggested the possibility that the ZNF genes may be imprinted, with one allele transcribed and one allele repressed. To test the hypothesis that the contradictory modifications are due to imprinting, we used a SNP analysis of RNA-seq data to demonstrate that both alleles of certain ZNF genes having H3K9me3 and H3K36me3 are transcribed. We next analyzed isolated ZNF 3' exons using stably integrated episomes. We found that although the H3K36me3 mark was lost when the 3' ZNF exon was removed from its natural genomic location, the isolated ZNF 3' exons retained the H3K9me3 mark. Thus, the H3K9me3 mark at ZNF 3' exons does not impede transcription and it is regulated independently of the H3K36me3 mark. Finally, we demonstrate a strong relationship between the number of tandemly repeated domains in the 3' exons and the H3K9me3 mark. We suggest that the H3K9me3 at ZNF 3' exons may function to protect the genome from inappropriate recombination rather than to regulate transcription.',
'date' => '2011-02-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21347206',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
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(int) 57 => array(
'id' => '599',
'name' => 'ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes.',
'authors' => 'Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ',
'description' => 'Only a small percentage of human transcription factors (e.g. those associated with a specific differentiation program) are expressed in a given cell type. Thus, cell fate is mainly determined by cell type-specific silencing of transcription factors that drive different cellular lineages. Several histone modifications have been associated with gene silencing, including H3K27me3 and H3K9me3. We have previously shown that genes for the two largest classes of mammalian transcription factors are marked by distinct histone modifications; homeobox genes are marked by H3K27me3 and zinc finger genes are marked by H3K9me3. Several histone methyltransferases (e.g. G9a and SETDB1) may be involved in mediating the H3K9me3 silencing mark. We have used ChIP-chip and ChIP-seq to demonstrate that SETDB1, but not G9a, is associated with regions of the genome enriched for H3K9me3. One current model is that SETDB1 is recruited to specific genomic locations via interaction with the corepressor TRIM28 (KAP1), which is in turn recruited to the genome via interaction with zinc finger transcription factors that contain a Kruppel-associated box (KRAB) domain. However, specific KRAB-ZNFs that recruit TRIM28 (KAP1) and SETDB1 to the genome have not been identified. We now show that ZNF274 (a KRAB-ZNF that contains 5 C2H2 zinc finger domains), can interact with KAP1 both in vivo and in vitro and, using ChIP-seq, we show that ZNF274 binding sites co-localize with SETDB1, KAP1, and H3K9me3 at the 3' ends of zinc finger genes. Knockdown of ZNF274 with siRNAs reduced the levels of KAP1 and SETDB1 recruitment to the binding sites. These studies provide the first identification of a KRAB domain-containing ZNF that is involved in recruitment of the KAP1 and SETDB1 to specific regions of the human genome.',
'date' => '2010-12-08',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21170338',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
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(int) 58 => array(
'id' => '74',
'name' => 'In vivo chromatin organization of mouse rod photoreceptors correlates with histone modifications.',
'authors' => 'Kizilyaprak C, Spehner D, Devys D, Schultz P',
'description' => 'BACKGROUND: The folding of genetic information into chromatin plays important regulatory roles in many nuclear processes and particularly in gene transcription. Post translational histone modifications are associated with specific chromatin condensation states and with distinct transcriptional activities. The peculiar chromatin organization of rod photoreceptor nuclei, with a large central domain of condensed chromatin surrounded by a thin border of extended chromatin was used as a model to correlate in vivo chromatin structure, histone modifications and transcriptional activity. METHODOLOGY: We investigated the functional relationships between chromatin compaction, distribution of histone modifications and location of RNA polymerase II in intact murine rod photoreceptors using cryo-preparation methods, electron tomography and immunogold labeling. Our results show that the characteristic central heterochromatin of rod nuclei is organized into concentric domains characterized by a progressive loosening of the chromatin architecture from inside towards outside and by specific combinations of silencing histone marks. The peripheral heterochromatin is formed by closely packed 30 nm fibers as revealed by a characteristic optical diffraction signal. Unexpectedly, the still highly condensed most external heterochromatin domain contains acetylated histones, which are usually associated with active transcription and decondensed chromatin. Histone acetylation is thus not sufficient in vivo for complete chromatin decondensation. The euchromatin domain contains several degrees of chromatin compaction and the histone tails are hyperacetylated, enriched in H3K4 monomethylation and hypo trimethylated on H3K9, H3K27 and H4K20. The transcriptionally active RNA polymerases II molecules are confined in the euchromatin domain and are preferentially located at the vicinity of the interface with heterochromatin. CONCLUSIONS: Our results show that transcription is located in the most decondensed and highly acetylated chromatin regions, but since acetylation is found associated with compact chromatin it is not sufficient to decondense chromatin in vivo. We also show that a combination of histone marks defines distinct concentric heterochromatin domains.',
'date' => '2010-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/20543957',
'doi' => '',
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(int) 59 => array(
'id' => '95',
'name' => 'MicroChIP--a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies.',
'authors' => 'Dahl JA, Collas P',
'description' => 'Chromatin immunoprecipitation (ChIP) is a powerful technique for studying protein-DNA interactions. Drawbacks of current ChIP assays however are a requirement for large cell numbers, which limits applicability of ChIP to rare cell samples, and/or lengthy procedures with limited applications. There are to date no protocols for fast and parallel ChIPs of post-translationally modified histones from small cell numbers or biopsies, and importantly, no protocol allowing for investigations of transcription factor binding in small cell numbers. We report here the development of a micro (micro) ChIP assay suitable for up to nine parallel quantitative ChIPs of modified histones or RNA polymerase II from a single batch of 1000 cells. MicroChIP can also be downscaled to monitor the association of one protein with multiple genomic sites in as few as 100 cells. MicroChIP is applicable to small fresh tissue biopsies, and a cross-link-while-thawing procedure makes the assay suitable for frozen biopsies. Using MicroChIP, we characterize transcriptionally permissive and repressive histone H3 modifications on developmentally regulated promoters in human embryonal carcinoma cells and in osteosarcoma biopsies. muChIP creates possibilities for multiple parallel and rapid transcription factor binding and epigenetic analyses of rare cell and tissue samples.',
'date' => '2008-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/18202078',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
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(int) 60 => array(
'id' => '76',
'name' => 'A rapid micro chromatin immunoprecipitation assay (microChIP).',
'authors' => 'Dahl JA, Collas P',
'description' => 'Interactions of proteins with DNA mediate many critical nuclear functions. Chromatin immunoprecipitation (ChIP) is a robust technique for studying protein-DNA interactions. Current ChIP assays, however, either require large cell numbers, which prevent their application to rare cell samples or small-tissue biopsies, or involve lengthy procedures. We describe here a 1-day micro ChIP (microChIP) protocol suitable for up to eight parallel histone and/or transcription factor immunoprecipitations from a single batch of 1,000 cells. MicroChIP technique is also suitable for monitoring the association of one protein with multiple genomic sites in 100 cells. Alterations in cross-linking and chromatin preparation steps also make microChIP applicable to approximately 1-mm(3) fresh- or frozen-tissue biopsies. From cell fixation to PCR-ready DNA, the procedure takes approximately 8 h for 16 ChIPs.',
'date' => '2008-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/18536650',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
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(int) 61 => array(
'id' => '75',
'name' => 'Fast genomic muChIP-chip from 1,000 cells',
'authors' => 'Dahl JA, Reiner AH, Collas P.',
'description' => 'Genome-wide location analysis of histone modifications and transcription factor binding relies on chromatin immunoprecipitation (ChIP) assays. These assays are, however, time-consuming and require large numbers of cells, hindering their application to the analysis of many interesting cell types. We report here a fast microChIP (μChIP) assay for 1,000 cells in combination with microarrays to produce genome-scale surveys of histone modifications. μChIP-chip reliably reproduces data obtained by large-scale assays: H3K9ac and H3K9m3 enrichment profiles are conserved and nucleosome-free regions are revealed.',
'date' => '0000-00-00',
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'modified' => '2015-07-24 15:38:56',
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'name' => 'Promoter DNA Methylation Patterns of Differentiated Cells Are Largely Programmed at the Progenitor Stage',
'authors' => 'Sørensen AL, Jacobsen BM, Reiner AH, Andersen IS, Collas P',
'description' => 'Mesenchymal stem cells (MSCs) isolated from various tissues share common phenotypic and functional properties. However, intrinsic molecular evidence supporting these observations has been lacking. Here, we unravel overlapping genome-wide promoter DNA methylation patterns between MSCs from adipose tissue, bone marrow, and skeletal muscle, whereas hematopoietic progenitors are more epigenetically distant from MSCs as a whole. Commonly hypermethylated genes are enriched in signaling, metabolic, and developmental functions, whereas genes hypermethylated only in MSCs are associated with early development functions. We find that most lineage-specification promoters are DNA hypomethylated and harbor a combination of trimethylated H3K4 and H3K27, whereas early developmental genes are DNA hypermethylated with or without H3K27 methylation. Promoter DNA methylation patterns of differentiated cells are largely established at the progenitor stage; yet, differentiation segregates a minor fraction of the commonly hypermethylated promoters, generating greater epigenetic divergence between differentiated cell types than between their undifferentiated counterparts. We also show an effect of promoter CpG content on methylation dynamics upon differentiation and distinct methylation profiles on transcriptionally active and inactive promoters. We infer that methylation state of lineage-specific promoters in MSCs is not a primary determinant of differentiation capacity. Our results support the view of a common origin of mesenchymal progenitors.',
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'name' => 'Chromatin Environment of Histone Variant H3.3 Revealed by Quantitative Imaging and Genome-scale Chromatin and DNA Immunoprecipitation',
'authors' => 'Delbarre E, Jacobsen BM, Reiner AH, Sørensen AL, Kuntziger T, Collas P',
'description' => 'In contrast to canonical histones, histone variant H3.3 is incorporated into chromatin in a replication-independent manner. Posttranslational modifications of H3.3 have been identified; however, the epigenetic environment of incorporated H3.3 is unclear. We have investigated the genomic distribution of epitope-tagged H3.3 in relation to histone modifications, DNA methylation, and transcription in mesenchymal stem cells. Quantitative imaging at the nucleus level shows that H3.3, relative to replicative H3.2 or canonical H2B, is enriched in chromatin domains marked by histone modifications of active or potentially active genes. Chromatin immunoprecipitation of epitope-tagged H3.3 and array hybridization identified 1649 H3.3-enriched promoters, a fraction of which is coenriched in H3K4me3 alone or together with H3K27me3, whereas H3K9me3 is excluded, corroborating nucleus-level imaging data. H3.3-enriched promoters are predominantly CpG-rich and preferentially DNA methylated, relative to the proportion of methylated RefSeq promoters in the genome. Most but not all H3.3-enriched promoters are transcriptionally active, and coenrichment of H3.3 with repressive H3K27me3 correlates with an enhanced proportion of expressed genes carrying this mark. H3.3-target genes are enriched in mesodermal differentiation and signaling functions. Our data suggest that in mesenchymal stem cells, H3.3 targets lineage-priming genes with a potential for activation facilitated by H3K4me3 in facultative association with H3K27me3.',
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'id' => '2217',
'antibody_id' => '120',
'name' => 'H3K9me3 Antibody (sample size)',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 9 (H3K9me3)</strong>, using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation Data',
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_ChIP.jpg" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="278" height="189" /></p>
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<div class="small-8 columns">
<p><small> <strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022 ) on the SX-8G IP-Star automated system. A titration of the antibody consisting of 1, 2, 5, and 10 μg per ChIP experiment was analysed. IgG (2 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active c-fos and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq assay" caption="false" width="400" height="358" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " caption="false" width="432" height="214" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="432" height="61" /> <img src="https://www.diagenode.com/img/product/antibodies/C15410056-FigD.jpg" alt="H3K9me3 Antibody validated in ChIP-seq " caption="false" width="700" height="112" /></p>
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<div class="small-6 columns">
<p><small> <strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 0.5 μg of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) on sheared chromatin from 1 million HeLa cells using the “iDeal ChIP-seq” kit (Cat. No. C01010051). The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoter regions of the active GAPDH and EIF4A2 genes, for the coding region of the ZNF510 gene and for the Sat2 satellite repeat (figure 2A). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the BWA algorithm. Figure 2B shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2C and D show the enrichment at ZNF510 and ZNF12 on chromosome 9 and 7, respectively. These results clearly show an enrichment of H3K9me3 at ZNF repeat genes. </small></p>
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" caption="false" width="278" height="212" /></p>
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<div class="small-8 columns">
<p><small> <strong>Figure 3. Determination of the antibody titer</strong><br /> To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (Cat. No. C15410056), crude serum and flow through in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:60,000. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" caption="false" width="400" height="304" /></p>
</div>
<div class="small-8 columns">
<p><small> <strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western Blot" caption="false" width="200" height="213" /></p>
</div>
<div class="small-8 columns">
<p><small> <strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot analysis was performed on histone extracts from HeLa cells (15 μg, lane 1) and on recombinant H3 (1 μg, lane2) using the Diagenode antibody against H3K9me3 (Cat. No. C15410056). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left. </small></p>
</div>
</div>
<div class="row">
<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-IF.jpg" alt="H3K9me3 Antibody validated in Immunofluorescence " caption="false" width="354" height="117" /></p>
</div>
<div class="small-7 columns">
<p><small> <strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, ELISA, DB, WB and IF. Batch-specific data available on the website. Sample size available',
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'name' => 'H3K9me3 Antibody (sample size)',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 9 (H3K9me3)</strong>, using a KLH-conjugated synthetic peptide.</span></p>',
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_ChIP.jpg" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="278" height="189" /></p>
</div>
<div class="small-8 columns">
<p><small> <strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022 ) on the SX-8G IP-Star automated system. A titration of the antibody consisting of 1, 2, 5, and 10 μg per ChIP experiment was analysed. IgG (2 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active c-fos and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq assay" caption="false" width="400" height="358" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " caption="false" width="432" height="214" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="432" height="61" /> <img src="https://www.diagenode.com/img/product/antibodies/C15410056-FigD.jpg" alt="H3K9me3 Antibody validated in ChIP-seq " caption="false" width="700" height="112" /></p>
</div>
<div class="small-6 columns">
<p><small> <strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 0.5 μg of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) on sheared chromatin from 1 million HeLa cells using the “iDeal ChIP-seq” kit (Cat. No. C01010051). The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoter regions of the active GAPDH and EIF4A2 genes, for the coding region of the ZNF510 gene and for the Sat2 satellite repeat (figure 2A). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the BWA algorithm. Figure 2B shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2C and D show the enrichment at ZNF510 and ZNF12 on chromosome 9 and 7, respectively. These results clearly show an enrichment of H3K9me3 at ZNF repeat genes. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" caption="false" width="278" height="212" /></p>
</div>
<div class="small-8 columns">
<p><small> <strong>Figure 3. Determination of the antibody titer</strong><br /> To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (Cat. No. C15410056), crude serum and flow through in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:60,000. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" caption="false" width="400" height="304" /></p>
</div>
<div class="small-8 columns">
<p><small> <strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western Blot" caption="false" width="200" height="213" /></p>
</div>
<div class="small-8 columns">
<p><small> <strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot analysis was performed on histone extracts from HeLa cells (15 μg, lane 1) and on recombinant H3 (1 μg, lane2) using the Diagenode antibody against H3K9me3 (Cat. No. C15410056). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left. </small></p>
</div>
</div>
<div class="row">
<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-IF.jpg" alt="H3K9me3 Antibody validated in Immunofluorescence " caption="false" width="354" height="117" /></p>
</div>
<div class="small-7 columns">
<p><small> <strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the acetylated lysine 27</strong> (<strong>H3K27ac</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<div class="small-6 columns">A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1a.png" width="356" /><br /> B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1b.png" width="356" /></div>
<div class="small-6 columns">
<p><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>Figure 1A ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196) and optimized PCR primer pairs for qPCR. ChIP was performed with the “Auto Histone ChIP-seq” kit on the IP-Star automated system, using sheared chromatin from 1,000,000 cells. A titration consisting of 1, 2, 5 and 10 µg of antibody per ChIP experiment was analyzed. IgG (2 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active EIF4A2 and ACTB genes, used as positive controls, and for the inactive TSH2B and MYT1 genes, used as negative controls.</p>
<p>Figure 1B ChIP assays were performed using human K562 cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196)and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 100,000 cells. A titration consisting of 0.2, 0.5, 1 and 2 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active GAPDH and EIF4A2 genes, used as positive controls, and for the coding regions of the inactive MB and MYT1 genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis)</p>
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<div class="row">
<div class="small-12 columns">
<p><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>ChIP was performed on sheared chromatin from 100,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) as described above. The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A shows the peak distribution along the complete human X-chromosome. Figure 2 B and C show the peak distribution in two regions surrounding the EIF4A2 and GAPDH positive control genes, respectively. The position of the PCR amplicon, used for validating the ChIP assay is indicated with an arrow.</p>
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<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-fig3.jpg" /></center></div>
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<div class="row">
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<p><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (cat. No. C15410196) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions surrounding the EIF2S3 gene on the X-chromosome and the CCT5 gene on chromosome 5 (figure 3A and B, respectively).</p>
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<div class="small-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-ELISA-Fig3.png" /></div>
<div class="small-6 columns">
<p><strong>Figure 4. Determination of the antibody titer</strong></p>
<p>To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:8,300.</p>
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<p><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27ac</strong><br />To test the cross reactivity of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>), a Dot Blot analysis was performed with peptides containing other histone modifications and the unmodified H3K27. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 5 shows a high specificity of the antibody for the modification of interest.</p>
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<p><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27ac</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27ac (Cat. No. C1541196). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The marker (in kDa) is shown on the left.</p>
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<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-IF-Fig6.png" /></div>
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<p><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27ac</strong></p>
<p>HeLa cells were stained with the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/ TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K27ac antibody (top) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown at the bottom.</p>
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<p><small> <strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022 ) on the SX-8G IP-Star automated system. A titration of the antibody consisting of 1, 2, 5, and 10 μg per ChIP experiment was analysed. IgG (2 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active c-fos and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><small> <strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 0.5 μg of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) on sheared chromatin from 1 million HeLa cells using the “iDeal ChIP-seq” kit (Cat. No. C01010051). The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoter regions of the active GAPDH and EIF4A2 genes, for the coding region of the ZNF510 gene and for the Sat2 satellite repeat (figure 2A). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the BWA algorithm. Figure 2B shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2C and D show the enrichment at ZNF510 and ZNF12 on chromosome 9 and 7, respectively. These results clearly show an enrichment of H3K9me3 at ZNF repeat genes. </small></p>
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<p><small> <strong>Figure 3. Determination of the antibody titer</strong><br /> To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (Cat. No. C15410056), crude serum and flow through in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:60,000. </small></p>
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" caption="false" width="400" height="304" /></p>
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<p><small> <strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western Blot" caption="false" width="200" height="213" /></p>
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<p><small> <strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot analysis was performed on histone extracts from HeLa cells (15 μg, lane 1) and on recombinant H3 (1 μg, lane2) using the Diagenode antibody against H3K9me3 (Cat. No. C15410056). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left. </small></p>
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<p><small> <strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
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'description' => 'In contrast to canonical histones, histone variant H3.3 is incorporated into chromatin in a replication-independent manner. Posttranslational modifications of H3.3 have been identified; however, the epigenetic environment of incorporated H3.3 is unclear. We have investigated the genomic distribution of epitope-tagged H3.3 in relation to histone modifications, DNA methylation, and transcription in mesenchymal stem cells. Quantitative imaging at the nucleus level shows that H3.3, relative to replicative H3.2 or canonical H2B, is enriched in chromatin domains marked by histone modifications of active or potentially active genes. Chromatin immunoprecipitation of epitope-tagged H3.3 and array hybridization identified 1649 H3.3-enriched promoters, a fraction of which is coenriched in H3K4me3 alone or together with H3K27me3, whereas H3K9me3 is excluded, corroborating nucleus-level imaging data. H3.3-enriched promoters are predominantly CpG-rich and preferentially DNA methylated, relative to the proportion of methylated RefSeq promoters in the genome. Most but not all H3.3-enriched promoters are transcriptionally active, and coenrichment of H3.3 with repressive H3K27me3 correlates with an enhanced proportion of expressed genes carrying this mark. H3.3-target genes are enriched in mesodermal differentiation and signaling functions. Our data suggest that in mesenchymal stem cells, H3.3 targets lineage-priming genes with a potential for activation facilitated by H3K4me3 in facultative association with H3K27me3.',
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'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, ELISA, DB, WB and IF. Batch specific data available on the website.',
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'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone H3 containing the trimethylated lysine 9 (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1 and 2 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control.<br /> <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for the ZNF510 gene and the Sat2 satellite repeat, used as positive controls, and for the EIF4A2 and GAPDH promoters, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).<br /> <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K9me1, H3K9me2, H3K9me3, H3K4me3, H3K27me3, H3K36me3, H4K20me3 modifications and the unmodified H3K9 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K9me3 modification when using 0.5 or 1 µg. With 2 µg of antibody, some recovery of the H3K27me3 nucleosome is observed.</small></p>
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<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq Grade" /></p>
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<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " /></p>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" /></p>
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<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq4000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoom-in to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B and 2C show the enrichment along the ZNF510 positive control target and at the KCNQ1 imprinted gene.</small></p>
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<p><strong></strong></p>
<p><strong></strong></p>
<p><small><strong>Figure 3. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410056) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:198,000.</small></p>
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<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410056) with peptides containing other modifications of histone H3 and H4 and the unmodified sequence of histone H3. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 4 shows a high specificity of the antibody for the modification of interest.</small></p>
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<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot was performed on 40 µg whole cell extracts from HeLa cells (lane 1) and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K9me3 (cat. No. C15410056). The antibody was diluted 1:2,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right, the marker (in kDa) is shown on the left.</small></p>
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'description' => 'Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Trimethylation of histone H3K9 is associated with satellite repeat regions and ZNF repeat genes.',
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'reactivity' => 'Human, mouse, zebrafish, trout, Daphnia, Arabidopsis, Drosophila, silena latifolia: positive. Other species: not tested.',
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<td>ChIP/ChIP-seq <sup>*</sup></td>
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<td>Fig 1, 2</td>
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1 and 2 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control.<br /> <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for the ZNF510 gene and the Sat2 satellite repeat, used as positive controls, and for the EIF4A2 and GAPDH promoters, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).<br /> <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K9me1, H3K9me2, H3K9me3, H3K4me3, H3K27me3, H3K36me3, H4K20me3 modifications and the unmodified H3K9 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K9me3 modification when using 0.5 or 1 µg. With 2 µg of antibody, some recovery of the H3K27me3 nucleosome is observed.</small></p>
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<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq Grade" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " /></p>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq4000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoom-in to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B and 2C show the enrichment along the ZNF510 positive control target and at the KCNQ1 imprinted gene.</small></p>
<p></p>
</div>
</div>
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<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" /></p>
</div>
<div class="small-6 columns">
<p><strong></strong></p>
<p><strong></strong></p>
<p><small><strong>Figure 3. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410056) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:198,000.</small></p>
<p></p>
<p></p>
<p></p>
<p></p>
<p></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410056) with peptides containing other modifications of histone H3 and H4 and the unmodified sequence of histone H3. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 4 shows a high specificity of the antibody for the modification of interest.</small></p>
<p></p>
<p></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot was performed on 40 µg whole cell extracts from HeLa cells (lane 1) and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K9me3 (cat. No. C15410056). The antibody was diluted 1:2,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right, the marker (in kDa) is shown on the left.</small></p>
</div>
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'type' => 'FRE',
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'slug' => 'h3k9me3-polyclonal-antibody-classic-50-ug',
'meta_title' => 'H3K9me3 Antibody - ChIP-seq Grade (C15410056) | Diagenode',
'meta_keywords' => '',
'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, ELISA, DB, WB and IF. Batch specific data available on the website.',
'modified' => '2021-10-20 09:33:57',
'created' => '2015-06-29 14:08:20',
'locale' => 'zho'
),
'Antibody' => array(
'host' => '*****',
'id' => '120',
'name' => 'H3K9me3 polyclonal antibody',
'description' => 'Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Trimethylation of histone H3K9 is associated with satellite repeat regions and ZNF repeat genes.',
'clonality' => '',
'isotype' => '',
'lot' => 'A2810P',
'concentration' => '1.85 µg/µl',
'reactivity' => 'Human, mouse, zebrafish, trout, Daphnia, Arabidopsis, Drosophila, silena latifolia: positive. Other species: not tested.',
'type' => 'Polyclonal ChIP grade, ChIP-seq grade',
'purity' => 'Affinity purified polyclonal antibody.',
'classification' => 'Classic',
'application_table' => '<table>
<thead>
<tr>
<th>Applications</th>
<th>Suggested dilution</th>
<th>References</th>
</tr>
</thead>
<tbody>
<tr>
<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>0.5 - 1 µg per ChIP</td>
<td>Fig 1, 2</td>
</tr>
<tr>
<td>ELISA</td>
<td>1:1,000 - 1:10,000</td>
<td>Fig 3</td>
</tr>
<tr>
<td>Dot Blotting</td>
<td>1:2,000</td>
<td>Fig 4</td>
</tr>
<tr>
<td>Western Blotting</td>
<td>1:2,000</td>
<td>Fig 5</td>
</tr>
</tbody>
</table>
<p><small><sup>*</sup> Please note that the optimal antibody amount per IP should be determined by the end-user. We recommend testing 0.5-5 µg per IP.</small></p>',
'storage_conditions' => 'Store at -20°C; for long storage, store at -80°C. Avoid multiple freeze-thaw cycles.',
'storage_buffer' => 'PBS containing 0.05% azide.',
'precautions' => 'This product is for research use only. Not for use in diagnostic or therapeutic procedures.',
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'modified' => '2021-07-28 12:12:46',
'created' => '0000-00-00 00:00:00',
'select_label' => '120 - H3K9me3 polyclonal antibody (A2810P - 1.85 µg/µl - Human, mouse, zebrafish, trout, Daphnia, Arabidopsis, Drosophila, silena latifolia: positive. Other species: not tested. - Affinity purified polyclonal antibody. - Rabbit)'
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'name' => 'H3K9me3 Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 9</strong> (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation data',
'info1' => '<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_ChIP.jpg" alt="H3K9me3 Antibody ChIP Grade" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1 and 2 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control.<br /> <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for the ZNF510 gene and the Sat2 satellite repeat, used as positive controls, and for the EIF4A2 and GAPDH promoters, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).<br /> <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K9me1, H3K9me2, H3K9me3, H3K4me3, H3K27me3, H3K36me3, H4K20me3 modifications and the unmodified H3K9 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K9me3 modification when using 0.5 or 1 µg. With 2 µg of antibody, some recovery of the H3K27me3 nucleosome is observed.</small></p>
</div>
</div>
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<div class="extra-spaced"></div>
<div class="row">
<div class="small-12 columns">
<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq Grade" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " /></p>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq4000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoom-in to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B and 2C show the enrichment along the ZNF510 positive control target and at the KCNQ1 imprinted gene.</small></p>
<p></p>
</div>
</div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" /></p>
</div>
<div class="small-6 columns">
<p><strong></strong></p>
<p><strong></strong></p>
<p><small><strong>Figure 3. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410056) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:198,000.</small></p>
<p></p>
<p></p>
<p></p>
<p></p>
<p></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410056) with peptides containing other modifications of histone H3 and H4 and the unmodified sequence of histone H3. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 4 shows a high specificity of the antibody for the modification of interest.</small></p>
<p></p>
<p></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot was performed on 40 µg whole cell extracts from HeLa cells (lane 1) and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K9me3 (cat. No. C15410056). The antibody was diluted 1:2,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right, the marker (in kDa) is shown on the left.</small></p>
</div>
</div>',
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'format' => '50 µg',
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'sf_code' => 'C15410056-D001-000581',
'type' => 'FRE',
'search_order' => '03-Antibody',
'price_EUR' => '380',
'price_USD' => '380',
'price_GBP' => '340',
'price_JPY' => '59525',
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'price_AUD' => '950',
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'slug' => 'h3k9me3-polyclonal-antibody-classic-50-ug',
'meta_title' => 'H3K9me3 Antibody - ChIP-seq Grade (C15410056) | Diagenode',
'meta_keywords' => '',
'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, ELISA, DB, WB and IF. Batch specific data available on the website.',
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(int) 0 => array(
'id' => '1836',
'antibody_id' => null,
'name' => 'iDeal ChIP-seq kit for Histones',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/ideal-chipseq-for-histones-complete-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>Don’t risk wasting your precious sequencing samples. Diagenode’s validated <strong>iDeal ChIP-seq kit for Histones</strong> has everything you need for a successful start-to-finish <strong>ChIP of histones prior to Next-Generation Sequencing</strong>. The complete kit contains all buffers and reagents for cell lysis, chromatin shearing, immunoprecipitation and DNA purification. In addition, unlike competing solutions, the kit contains positive and negative control antibodies (H3K4me3 and IgG, respectively) as well as positive and negative control PCR primers pairs (GAPDH TSS and Myoglobin exon 2, respectively) for your convenience and a guarantee of optimal results. The kit has been validated on multiple histone marks.</p>
<p> The iDeal ChIP-seq kit for Histones<strong> </strong>is perfect for <strong>cells</strong> (<strong>100,000 cells</strong> to <strong>1,000,000 cells</strong> per IP) and has been validated for <strong>tissues</strong> (<strong>1.5 mg</strong> to <strong>5 mg</strong> of tissue per IP).</p>
<p> The iDeal ChIP-seq kit is the only kit on the market validated for the major sequencing systems. Our expertise in ChIP-seq tools allows reproducible and efficient results every time.</p>
<p></p>
<p> <strong></strong></p>
<p></p>',
'label1' => 'Characteristics',
'info1' => '<ul style="list-style-type: disc;">
<li>Highly <strong>optimized</strong> protocol for ChIP-seq from cells and tissues</li>
<li><strong>Validated</strong> for ChIP-seq with multiple histones marks</li>
<li>Most <strong>complete</strong> kit available (covers all steps, including the control antibodies and primers)</li>
<li>Optimized chromatin preparation in combination with the Bioruptor ensuring the best <strong>epitope integrity</strong></li>
<li>Magnetic beads make ChIP easy, fast and more <strong>reproducible</strong></li>
<li>Combination with Diagenode ChIP-seq antibodies provides high yields with excellent <strong>specificity</strong> and <strong>sensitivity</strong></li>
<li>Purified DNA suitable for any downstream application</li>
<li>Easy-to-follow protocol</li>
</ul>
<p>Note: to obtain optimal results, this kit should be used in combination with the DiaMag1.5 - magnetic rack.</p>
<h3>ChIP-seq on cells</h3>
<p><img src="https://www.diagenode.com/img/product/kits/iDeal-kit-C01010053-figure-1.jpg" alt="Figure 1A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 1A. The high consistency of the iDeal ChIP-seq kit on the Ion Torrent™ PGM™ (Life Technologies) and GAIIx (Illumina<sup>®</sup>)</strong><br /> ChIP was performed on sheared chromatin from 1 million HelaS3 cells using the iDeal ChIP-seq kit and 1 µg of H3K4me3 positive control antibody. Two different biological samples have been analyzed using two different sequencers - GAIIx (Illumina<sup>®</sup>) and PGM™ (Ion Torrent™). The expected ChIP-seq profile for H3K4me3 on the GAPDH promoter region has been obtained.<br /> Image A shows a several hundred bp along chr12 with high similarity of read distribution despite the radically different sequencers. Image B is a close capture focusing on the GAPDH that shows that even the peak structure is similar.</p>
<p class="text-center"><strong>Perfect match between ChIP-seq data obtained with the iDeal ChIP-seq workflow and reference dataset</strong></p>
<p><img src="https://www.diagenode.com/img/product/kits/perfect-match-between-chipseq-data.png" alt="Figure 1B" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 1B.</strong> The ChIP-seq dataset from this experiment has been compared with a reference dataset from the Broad Institute. We observed a perfect match between the top 40% of Diagenode peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>
<p><img src="https://www.diagenode.com/img/product/kits/iDeal-kit-C01010053-figure-2.jpg" alt="Figure 2" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 2. Efficient and easy chromatin shearing using the Bioruptor<sup>®</sup> and Shearing buffer iS1 from the iDeal ChIP-seq kit</strong><br /> Chromatin from 1 million of Hela cells was sheared using the Bioruptor<sup>®</sup> combined with the Bioruptor<sup>®</sup> Water cooler (Cat No. BioAcc-cool) during 3 rounds of 10 cycles of 30 seconds “ON” / 30 seconds “OFF” at HIGH power setting (position H). Diagenode 1.5 ml TPX tubes (Cat No. M-50001) were used for chromatin shearing. Samples were gently vortexed before and after performing each sonication round (rounds of 10 cycles), followed by a short centrifugation at 4°C to recover the sample volume at the bottom of the tube. The sheared chromatin was then decross-linked as described in the kit manual and analyzed by agarose gel electrophoresis.</p>
<p><img src="https://www.diagenode.com/img/product/kits/iDeal-kit-C01010053-figure-3.jpg" alt="Figure 3" style="display: block; margin-left: auto; margin-right: auto;" width="264" height="320" /></p>
<p><strong>Figure 3. Validation of ChIP by qPCR: reliable results using Diagenode’s ChIP-seq grade H3K4me3 antibody, isotype control and sets of validated primers</strong><br /> Specific enrichment on positive loci (GAPDH, EIF4A2, c-fos promoter regions) comparing to no enrichment on negative loci (TSH2B promoter region and Myoglobin exon 2) was detected by qPCR. Samples were prepared using the Diagenode iDeal ChIP-seq kit. Diagenode ChIP-seq grade antibody against H3K4me3 and the corresponding isotype control IgG were used for immunoprecipitation. qPCR amplification was performed with sets of validated primers.</p>
<h3>ChIP-seq on tissue</h3>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-figure-h3k4me3.jpg" alt="Figure 4A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 4A.</strong> Chromatin Immunoprecipitation has been performed using chromatin from mouse liver tissue, the iDeal ChIP-seq kit for Histones and the Diagenode ChIP-seq-grade H3K4me3 (Cat. No. C15410003) antibody. The IP'd DNA was subsequently analysed on an Illumina® HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. This figure shows the peak distribution in a region surrounding the GAPDH positive control gene.</p>
<p><img src="https://www.diagenode.com/img/product/kits/match-of-the-top40-peaks-2.png" alt="Figure 4B" caption="false" style="display: block; margin-left: auto; margin-right: auto;" width="700" height="280" /></p>
<p><strong>Figure 4B.</strong> The ChIP-seq dataset from this experiment has been compared with a reference dataset from the Broad Institute. We observed a perfect match between the top 40% of Diagenode peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>',
'label2' => 'Species, cell lines, tissues tested',
'info2' => '<p>The iDeal ChIP-seq Kit for Histones is compatible with a broad variety of cell lines, tissues and species - some examples are shown below. Other species / cell lines / tissues can be used with this kit.</p>
<p><u>Cell lines:</u></p>
<p>Human: A549, A673, CD8+ T, Blood vascular endothelial cells, Lymphatic endothelial cells, fibroblasts, K562, MDA-MB231</p>
<p>Pig: Alveolar macrophages</p>
<p>Mouse: C2C12, primary HSPC, synovial fibroblasts, HeLa-S3, FACS sorted cells from embryonic kidneys, macrophages, mesodermal cells, myoblasts, NPC, salivary glands, spermatids, spermatocytes, skeletal muscle stem cells, stem cells, Th2</p>
<p>Hamster: CHO</p>
<p>Other cell lines / species: compatible, not tested</p>
<p><u>Tissues</u></p>
<p>Bee – brain</p>
<p>Daphnia – whole animal</p>
<p>Horse – brain, heart, lamina, liver, lung, skeletal muscles, ovary</p>
<p>Human – Erwing sarcoma tumor samples</p>
<p>Other tissues: compatible, not tested</p>
<p>Did you use the iDeal ChIP-seq for Histones Kit on other cell line / tissue / species? <a href="mailto:agnieszka.zelisko@diagenode.com?subject=Species, cell lines, tissues tested with the iDeal ChIP-seq Kit for TF&body=Dear Customer,%0D%0A%0D%0APlease, leave below your feedback about the iDeal ChIP-seq for Transcription Factors (cell / tissue type, species, other information...).%0D%0A%0D%0AThank you for sharing with us your experience !%0D%0A%0D%0ABest regards,%0D%0A%0D%0AAgnieszka Zelisko-Schmidt, PhD">Let us know!</a></p>',
'label3' => ' Additional solutions compatible with iDeal ChIP-seq Kit for Histones',
'info3' => '<p><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin EasyShear Kit - Ultra Low SDS </a>optimizes chromatin shearing, a critical step for ChIP.</p>
<p> The <a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq">MicroPlex Library Preparation Kit </a>provides easy and optimal library preparation of ChIPed samples.</p>
<p><a href="../categories/chip-seq-grade-antibodies">ChIP-seq grade anti-histone antibodies</a> provide high yields with excellent specificity and sensitivity.</p>
<p> Plus, for our IP-Star Automation users for automated ChIP, check out our <a href="../p/auto-ideal-chip-seq-kit-for-histones-x24-24-rxns">automated</a> version of this kit.</p>',
'format' => '4 chrom. prep./24 IPs',
'catalog_number' => 'C01010051',
'old_catalog_number' => 'AB-001-0024',
'sf_code' => 'C01010051-',
'type' => 'RFR',
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'slug' => 'ideal-chip-seq-kit-x24-24-rxns',
'meta_title' => 'iDeal ChIP-seq kit x24',
'meta_keywords' => '',
'meta_description' => 'iDeal ChIP-seq kit x24',
'modified' => '2023-04-20 16:00:20',
'created' => '2015-06-29 14:08:20',
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(int) 1 => array(
'id' => '1856',
'antibody_id' => null,
'name' => 'True MicroChIP-seq Kit',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/truemicrochipseq-kit-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>The <b>True </b><b>MicroChIP-seq</b><b> kit </b>provides a robust ChIP protocol suitable for the investigation of histone modifications within chromatin from as few as <b>10 000 cells</b>, including <b>FACS sorted cells</b>. The kit can be used for chromatin preparation for downstream ChIP-qPCR or ChIP-seq analysis. The <b>complete kit</b> contains everything you need for start-to-finish ChIP including all validated buffers and reagents for chromatin shearing, immunoprecipitation and DNA purification for exceptional <strong>ChIP-qPCR</strong> or <strong>ChIP-seq</strong> results. In addition, positive control antibodies and negative control PCR primers are included for your convenience and assurance of result sensitivity and specificity.</p>
<p>The True MicroChIP-seq kit offers unique benefits:</p>
<ul>
<li>An <b>optimized chromatin preparation </b>protocol compatible with low number of cells (<b>10.000</b>) in combination with the Bioruptor™ shearing device</li>
<li>Most <b>complete kit </b>available (covers all steps and includes control antibodies and primers)</li>
<li><b>Magnetic beads </b>make ChIP easy, fast, and more reproducible</li>
<li>MicroChIP DiaPure columns (included in the kit) enable the <b>maximum recovery </b>of immunoprecipitation DNA suitable for any downstream application</li>
<li><b>Excellent </b><b>ChIP</b><b>-seq </b>result when combined with <a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq">MicroPlex</a><a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq"> Library Preparation kit </a>adapted for low input</li>
</ul>
<p>For fast ChIP-seq on low input – check out Diagenode’s <a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns">µ</a><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns">ChIPmentation</a><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns"> for histones</a>.</p>
<p><sub>The True MicroChIP-seq kit, Cat. No. C01010132 is an upgraded version of the kit True MicroChIP, Cat. No. C01010130, with the new validated protocols (e.g. FACS sorted cells) and MicroChIP DiaPure columns included in the kit.</sub></p>',
'label1' => 'Characteristics',
'info1' => '<ul>
<li><b>Revolutionary:</b> Only 10,000 cells needed for complete ChIP-seq procedure</li>
<li><b>Validated on</b> studies for histone marks</li>
<li><b>Automated protocol </b>for the IP-Star<sup>®</sup> Compact Automated Platform available</li>
</ul>
<p></p>
<p>The True MicroChIP-seq kit protocol has been optimized for the use of 10,000 - 100,000 cells per immunoprecipitation reaction. Regarding chromatin immunoprecipitation, three protocol variants have been optimized:<br />starting with a batch, starting with an individual sample and starting with the FACS-sorted cells.</p>
<div><button id="readmorebtn" style="background-color: #b02736; color: white; border-radius: 5px; border: none; padding: 5px;">Show Workflow</button></div>
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<div class="container">
<div class="row" style="background: rgba(255,255,255,0.1);">
<div class="large-12 columns truemicro-slider" id="truemicro-slider">
<div>
<h3>High efficiency ChIP on 10,000 cells</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-histone-results.png" width="800px" /></div>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center>
<p><small><strong>Figure 1. </strong>ChIP efficiency on 10,000 cells. ChIP was performed on human Hela cells using the Diagenode antibodies <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (Cat. No. C15410003), <a href="https://www.diagenode.com/en/p/h3k27ac-polyclonal-antibody-classic-50-mg-42-ml">H3K27ac</a> (C15410174), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-classic-50-ug">H3K9me3</a> (C15410056) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-classic-50-mg-34-ml">H3K27me3</a> (C15410069). Sheared chromatin from 10,000 cells and 0.1 µg (H3K27ac), 0.25 µg (H3K4me3 and H3K27me3) or 0.5 µg (H3K9me3) of the antibody were used per IP. Corresponding amount of IgG was used as control. Quantitative PCR was performed with primers for corresponding positive and negative loci. Figure shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
</center></div>
</div>
<div>
<h3>True MicroChIP-seq protocol in a combination with MicroPlex library preparation kit results in reliable and accurate sequencing data</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><img src="https://www.diagenode.com/img/product/kits/fig2-truemicro.jpg" alt="True MicroChip results" width="800px" /></div>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center>
<p><small><strong>Figure 2.</strong> Integrative genomics viewer (IGV) visualization of ChIP-seq experiments using 50.000 of K562 cells. ChIP has been performed accordingly to True MicroChIP protocol followed by the library preparation using MicroPlex Library Preparation Kit (C05010001). The above figure shows the peaks from ChIP-seq experiments using the following antibodies: H3K4me1 (C15410194), H3K9/14ac (C15410200), H3K27ac (C15410196) and H3K36me3 (C15410192).</small></p>
</center></div>
</div>
<div>
<h3>Successful chromatin profiling from 10.000 of FACS-sorted cells</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><img src="https://www.diagenode.com/img/product/kits/fig3ab-truemicro.jpg" alt="small non coding RNA" width="800px" /></div>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center>
<p><small><strong>Figure 3.</strong> (A) Integrative genomics viewer (IGV) visualization of ChIP-seq experiments and heatmap 3kb upstream and downstream of the TSS (B) for H3K4me3. ChIP has been performed using 10.000 of FACS-sorted cells (K562) and H3K4me3 antibody (C15410003) accordingly to True MicroChIP protocol followed by the library preparation using MicroPlex Library Preparation Kit (C05010001). Data were compared to ENCODE standards.</small></p>
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'label2' => 'Additional solutions compatible with the True MicroChIP-seq Kit',
'info2' => '<p><span style="font-weight: 400;">The <a href="https://www.diagenode.com/en/p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin EasyShear Kit – High SDS</a></span><span style="font-weight: 400;"> Recommended for the optimizing chromatin shearing.</span></p>
<p><a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies"><span style="font-weight: 400;">ChIP-seq grade antibodies</span></a><span style="font-weight: 400;"> for high yields, specificity, and sensitivity.</span></p>
<p><span style="font-weight: 400;">Check the list of available </span><a href="https://www.diagenode.com/en/categories/primer-pairs"><span style="font-weight: 400;">primer pairs</span></a><span style="font-weight: 400;"> designed for high specificity to specific genomic regions.</span></p>
<p><span style="font-weight: 400;">For library preparation of immunoprecipitated samples we recommend to use the </span><b> </b><a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq"><span style="font-weight: 400;">MicroPlex Library Preparation Kit</span></a><span style="font-weight: 400;"> - validated for library preparation from picogram inputs.</span></p>
<p><span style="font-weight: 400;">For IP-Star Automation users, check out the </span><a href="https://www.diagenode.com/en/p/auto-true-microchip-kit-16-rxns"><span style="font-weight: 400;">automated version</span></a><span style="font-weight: 400;"> of this kit.</span></p>
<p><span style="font-weight: 400;">Application note: </span><a href="https://www.diagenode.com/files/application_notes/Diagenode_AATI_Joint.pdf"><span style="font-weight: 400;">Best Workflow Practices for ChIP-seq Analysis with Small Samples</span></a></p>
<p></p>',
'label3' => 'Species, cell lines, tissues tested',
'info3' => '<p>The True MicroChIP-seq kit is compatible with a broad variety of cell lines, tissues and species - some examples are shown below. Other species / cell lines / tissues can be used with this kit.</p>
<p><strong>Cell lines:</strong></p>
<p>Bovine: blastocysts,<br />Drosophila: embryos, salivary glands<br />Human: EndoC-ẞH1 cells, HeLa cells, PBMC, urothelial cells<br />Mouse: adipocytes, B cells, blastocysts, pre-B cells, BMDM cells, chondrocytes, embryonic stem cells, KH2 cells, LSK cells, macrophages, MEP cells, microglia, NK cells, oocytes, pancreatic cells, P19Cl6 cells, RPE cells,</p>
<p>Other cell lines / species: compatible, not tested</p>
<p><strong>Tissues:</strong></p>
<p>Horse: adipose tissue</p>
<p>Mice: intestine tissue</p>
<p>Other tissues: not tested</p>',
'format' => '20 rxns',
'catalog_number' => 'C01010132',
'old_catalog_number' => 'C01010130',
'sf_code' => 'C01010132-',
'type' => 'RFR',
'search_order' => '04-undefined',
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'price_AUD' => '1700',
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'slug' => 'true-microchip-kit-x16-16-rxns',
'meta_title' => 'True MicroChIP-seq Kit | Diagenode C01010132',
'meta_keywords' => '',
'meta_description' => 'True MicroChIP-seq Kit provides a robust ChIP protocol suitable for the investigation of histone modifications within chromatin from as few as 10 000 cells, including FACS sorted cells. Compatible with ChIP-qPCR as well as ChIP-seq.',
'modified' => '2023-04-20 16:06:10',
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'id' => '1927',
'antibody_id' => null,
'name' => 'MicroPlex Library Preparation Kit v2 (12 indexes)',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/MicroPlex-Libary-Prep-Kit-v2-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p><span><strong>Specifically optimized for ChIP-seq</strong></span><br /><br /><span>The MicroPlex Library Preparation™ kit is the only kit on the market which is validated for ChIP-seq and which allows the preparation of indexed libraries from just picogram inputs. In combination with the </span><a href="./true-microchip-kit-x16-16-rxns">True MicroChIP kit</a><span>, it allows for performing ChIP-seq on as few as 10,000 cells. Less input, fewer steps, fewer supplies, faster time to results! </span></p>
<p>The MicroPlex v2 kit (Cat. No. C05010012) contains all necessary reagents including single indexes for multiplexing up to 12 samples using single barcoding. For higher multiplexing (using dual indexes) check <a href="https://www.diagenode.com/en/p/microplex-lib-prep-kit-v3-48-rxns">MicroPlex Library Preparation Kits v3</a>.</p>',
'label1' => 'Characteristics',
'info1' => '<ul>
<li><strong>1 tube, 2 hours, 3 steps</strong> protocol</li>
<li><strong>Input: </strong>50 pg – 50 ng</li>
<li><strong>Reduce potential bias</strong> - few PCR amplification cycles needed</li>
<li><strong>High sensitivity ChIP-seq</strong> - low PCR duplication rate</li>
<li><strong>Great multiplexing flexibility</strong> with 12 barcodes (8 nt) included</li>
<li><strong>Validated with the <a href="https://www.diagenode.com/p/sx-8g-ip-star-compact-automated-system-1-unit" title="IP-Star Automated System">IP-Star<sup>®</sup> Automated Platform</a></strong></li>
</ul>
<h3>How it works</h3>
<center><img src="https://www.diagenode.com/img/product/kits/microplex-method-overview-v2.png" /></center>
<p style="margin-bottom: 0;"><small><strong>Microplex workflow - protocol with single indexes</strong><br />An input of 50 pg to 50 ng of fragmented dsDNA is converted into sequencing-ready libraries for Illumina® NGS platforms using a fast and simple 3-step protocol</small></p>
<ul class="accordion" data-accordion="" id="readmore" style="margin-left: 0;">
<li class="accordion-navigation"><a href="#first" style="background: #ffffff; padding: 0rem; margin: 0rem; color: #13b2a2;"><small>Read more about MicroPlex workflow</small></a>
<div id="first" class="content">
<p><small><strong>Step 1. Template Preparation</strong> provides efficient repair of the fragmented double-stranded DNA input.</small></p>
<p><small>In this step, the DNA is repaired and yields molecules with blunt ends.</small></p>
<p><small><strong>Step 2. Library Synthesis.</strong> enables ligation of MicroPlex patented stem- loop adapters.</small></p>
<p><small>In the next step, stem-loop adaptors with blocked 5’ ends are ligated with high efficiency to the 5’ end of the genomic DNA, leaving a nick at the 3’ end. The adaptors cannot ligate to each other and do not have single- strand tails, both of which contribute to non-specific background found with many other NGS preparations.</small></p>
<p><small><strong>Step 3. Library Amplification</strong> enables extension of the template, cleavage of the stem-loop adaptors, and amplification of the library. Illumina- compatible indexes are also introduced using a high-fidelity, highly- processive, low-bias DNA polymerase.</small></p>
<p><small>In the final step, the 3’ ends of the genomic DNA are extended to complete library synthesis and Illumina-compatible indexes are added through a high-fidelity amplification. Any remaining free adaptors are destroyed. Hands-on time and the risk of contamination are minimized by using a single tube and eliminating intermediate purifications.</small></p>
<p><small>Obtained libraries are purified, quantified and sized. The libraries pooling can be performed as well before sequencing.</small></p>
</div>
</li>
</ul>
<p></p>
<h3>Reliable detection of enrichments in ChIP-seq</h3>
<p><img src="https://www.diagenode.com/img/product/kits/microplex-library-prep-kit-figure-a.png" alt="Reliable detection of enrichments in ChIP-seq figure 1" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure A.</strong> ChIP has been peformed with H3K4me3 antibody, amplification of 17 pg of DNA ChIP'd from 10.000 cells and amplification of 35 pg of DNA ChIP'd from 100.000 cells (control experiment). The IP'd DNA was amplified and transformed into a sequencing-ready preparation for the Illumina plateform with the MicroPlex Library Preparation kit. The library was then analysed on an Illumina<sup>®</sup> Genome Analyzer. Cluster generation and sequencing were performed according to the manufacturer's instructions.</p>
<p><img src="https://www.diagenode.com/img/product/kits/microplex-library-prep-kit-figure-b.png" alt="Reliable detection of enrichments in ChIP-seq figure 2" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure B.</strong> We observed a perfect match between the top 40% of True MicroChIP peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>',
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'meta_title' => 'MicroPlex Library Preparation Kit v2 x12 (12 indices)',
'meta_keywords' => '',
'meta_description' => 'MicroPlex Library Preparation Kit v2 x12 (12 indices)',
'modified' => '2023-04-20 15:01:16',
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'id' => '2264',
'antibody_id' => '121',
'name' => 'H3K9me3 Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone<strong> H3 containing the trimethylated lysine 9</strong> (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation Data',
'info1' => '<div class="row">
<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig1.png" /></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (cat. No. C15410193) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). A titration of the antibody consisting of 0.5, 1, 2, and 5 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2a.png" width="700" /></center><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2b.png" width="700" /></center><center>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2c.png" width="700" /></center><center>D.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2d.png" width="700" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with 0.5 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410193) on sheared chromatin from 1,000,000 HeLa cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq 2000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B, 2C and 2D show the enrichment along the ZNF510 positive control target and at the H19 and KCNQ1 imprinted genes.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-CT-Fig3a.png" width="700" /></center><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-CT-Fig3b.png" width="700" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K9me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410193) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in a genomic regions on chromosome 1 containing several ZNF repeat genes and in a genomic region surrounding the KCNQ1 imprinting control gene on chromosome 11 (figure 3A and B, respectively).</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-Elisa-Fig4.png" /></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410193) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:87,000.</small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-DB-Fig5.png" /></center></div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410193) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 5 shows a high specificity of the antibody for the modification of interest.</small></p>
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<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-WB-Fig6.png" /></center></div>
<div class="small-8 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K9me3 (cat. No. C15410193). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-IF-Fig7.png" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br />HeLa cells were stained with the Diagenode antibody against H3K9me3 (cat. No. C15410193) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (middle) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The left panel shows staining of the nuclei with DAPI. A merge of both stainings is shown on the right.</small></p>
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'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 4</strong> (<strong>H3K4me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" /></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me3</strong><br />ChIP assays were performed using human K562 cells, the Diagenode antibody against H3K4me3 (cat. No. C15410003) and optimized PCR primer pairs for qPCR. ChIP was performed with the iDeal ChIP-seq kit (cat. No. C01010051), using sheared chromatin from 500,000 cells. A titration consisting of 0.5, 1, 2 and 5 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers specific for the promoter of the active genes GAPDH and EIF4A2, used as positive controls, and for the inactive MYOD1 gene and the Sat2 satellite repeat, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p></p>
<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2a-ChIP-seq.jpg" width="800" /></center><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2b-ChIP-seq.jpg" width="800" /></center><center>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2c-ChIP-seq.jpg" width="800" /></center><center>D.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2d-ChIP-seq.jpg" width="800" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me3</strong><br />ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using 1 µg of the Diagenode antibody against H3K4me3 (cat. No. C15410003) as described above. The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2 shows the peak distribution along the complete sequence and a 600 kb region of the X-chromosome (figure 2A and B) and in two regions surrounding the GAPDH and EIF4A2 positive control genes, respectively (figure 2C and D). These results clearly show an enrichment of the H3K4 trimethylation at the promoters of active genes.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-cuttag-a.png" width="800" /></center></div>
<div class="small-12 columns"><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-cuttag-b.png" width="800" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K4me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 0.5 µg of the Diagenode antibody against H3K4me3 (cat. No. C15410003) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions surrounding the FOS gene on chromosome 14 and the ACTB gene on chromosome 7 (figure 3A and B, respectively).</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig3-ELISA.jpg" width="350" /></center><center></center><center></center><center></center><center></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody against H3K4me3 (cat. No. C15410003). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:11,000.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig4-DB.jpg" /></div>
<div class="small-6 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K4me3</strong><br />To test the cross reactivity of the Diagenode antibody against H3K4me3 (cat. No. C15410003), a Dot Blot analysis was performed with peptides containing other histone modifications and the unmodified H3K4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 5A shows a high specificity of the antibody for the modification of interest.</small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig5-WB.jpg" /></div>
<div class="small-8 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K4me3</strong><br />Western blot was performed on whole cell extracts (40 µg, lane 1) from HeLa cells, and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K4me3 (cat. No. C15410003). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig6-if.jpg" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K4me3</strong><br />HeLa cells were stained with the Diagenode antibody against H3K4me3 (cat. No. C15410003) and with DAPI. Cells were fixed with 4% formaldehyde for 20’ and blocked with PBS/TX-100 containing 5% normal goat serum. The cells were immunofluorescently labelled with the H3K4me3 antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa568 or with DAPI (middle), which specifically labels DNA. The right picture shows a merge of both stainings.</small></p>
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'info2' => '<p>Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called "histone code". Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Methylation of histone H3K4 is associated with activation of gene transcription.</p>
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'meta_title' => 'H3K4me3 Antibody - ChIP-seq Grade (C15410003) | Diagenode',
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'meta_description' => 'H3K4me3 (Histone H3 trimethylated at lysine 4) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, CUT&Tag, ELISA, DB, WB and IF. Specificity confirmed by Peptide array. Batch-specific data available on the website. Sample size available.',
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'id' => '2268',
'antibody_id' => '70',
'name' => 'H3K27me3 Antibody',
'description' => '<p>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 27</strong> (<strong>H3K27me3</strong>), using a KLH-conjugated synthetic peptide.</p>',
'label1' => 'Validation Data',
'info1' => '<div class="row">
<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig1.png" alt="H3K27me3 Antibody ChIP Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2.png" alt="H3K27me3 Antibody for ChIP" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 1 million cells. The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation. A titration consisting of 0.5, 1, 2 and 5 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control.</small></p>
<p><small><strong>Figure 1A.</strong> Quantitative PCR was performed with primers specific for the promoter of the active GAPDH and EIF4A2 genes, used as negative controls, and for the inactive TSH2B and MYT1 genes, used as positive controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
<p><small><strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K27me1, H3K27me2, H3K27me3, H3K4me3, H3K9me3 and H3K36me3 modifications and the unmodified H3K27 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K27me3 modification.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2a.png" alt="H3K27me3 Antibody ChIP-seq Grade" /></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-12 columns">
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2b.png" alt="H3K27me3 Antibody for ChIP-seq" /></p>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2c.png" alt="H3K27me3 Antibody for ChIP-seq assay" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2d.png" alt="H3K27me3 Antibody validated in ChIP-seq" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP was performed on sheared chromatin from 1 million HeLa cells using 1 µg of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2 shows the enrichment in genomic regions of chromosome 6 and 20, surrounding the TSH2B and MYT1 positive control genes (fig 2A and 2B, respectively), and in two genomic regions of chromosome 1 and X (figure 2C and D).</small></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3A.png" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3B.png" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27me3 (cat. No. C15410195) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions on chromosome and 13 and 20 (figure 3A and B, respectively).</small></p>
</div>
</div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-ELISA-Fig4.png" alt="H3K27me3 Antibody ELISA Validation " /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K27me3 (Cat. No. C15410195). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:3,000.</small></p>
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</div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-DB-Fig5a.png" alt="H3K27me3 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) with peptides containing other modifications of histone H3 and H4 and the unmodified H3K27 sequence. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:5,000. Figure 5 shows a high specificity of the antibody for the modification of interest. Please note that the antibody also recognizes the modification if S28 is phosphorylated.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-WB-Fig6.png" alt="H3K27me3 Antibody validated in Western Blot" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27me3</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27me3 (cat. No. C15410195) diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-IF-Fig7.png" alt="H3K27me3 Antibody validated for Immunofluorescence" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27me3</strong><br />Human HeLa cells were stained with the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K27me3 antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.</small></p>
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'name' => 'H3K27ac Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the acetylated lysine 27</strong> (<strong>H3K27ac</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation Data',
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<div class="small-6 columns">A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1a.png" width="356" /><br /> B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1b.png" width="356" /></div>
<div class="small-6 columns">
<p><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>Figure 1A ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196) and optimized PCR primer pairs for qPCR. ChIP was performed with the “Auto Histone ChIP-seq” kit on the IP-Star automated system, using sheared chromatin from 1,000,000 cells. A titration consisting of 1, 2, 5 and 10 µg of antibody per ChIP experiment was analyzed. IgG (2 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active EIF4A2 and ACTB genes, used as positive controls, and for the inactive TSH2B and MYT1 genes, used as negative controls.</p>
<p>Figure 1B ChIP assays were performed using human K562 cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196)and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 100,000 cells. A titration consisting of 0.2, 0.5, 1 and 2 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active GAPDH and EIF4A2 genes, used as positive controls, and for the coding regions of the inactive MB and MYT1 genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis)</p>
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<div class="small-12 columns"><center>
<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2a.png" /></p>
</center><center>
<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2b.png" /></p>
</center><center>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2c.png" /></p>
</center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>ChIP was performed on sheared chromatin from 100,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) as described above. The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A shows the peak distribution along the complete human X-chromosome. Figure 2 B and C show the peak distribution in two regions surrounding the EIF4A2 and GAPDH positive control genes, respectively. The position of the PCR amplicon, used for validating the ChIP assay is indicated with an arrow.</p>
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<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-fig3.jpg" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (cat. No. C15410196) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions surrounding the EIF2S3 gene on the X-chromosome and the CCT5 gene on chromosome 5 (figure 3A and B, respectively).</p>
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<div class="row">
<div class="small-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-ELISA-Fig3.png" /></div>
<div class="small-6 columns">
<p><strong>Figure 4. Determination of the antibody titer</strong></p>
<p>To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:8,300.</p>
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<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-DB-Fig4.png" /></center></div>
<div class="small-8 columns">
<p><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27ac</strong><br />To test the cross reactivity of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>), a Dot Blot analysis was performed with peptides containing other histone modifications and the unmodified H3K27. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 5 shows a high specificity of the antibody for the modification of interest.</p>
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<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-WB-Fig5.png" /></center></div>
<div class="small-8 columns">
<p><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27ac</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27ac (Cat. No. C1541196). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The marker (in kDa) is shown on the left.</p>
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<div class="row">
<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-IF-Fig6.png" /></div>
<div class="small-8 columns">
<p><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27ac</strong></p>
<p>HeLa cells were stained with the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/ TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K27ac antibody (top) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown at the bottom.</p>
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<p>Learn more about: <a href="https://www.diagenode.com/applications/western-blot">Loading control, MW marker visualization</a><em>. <br /></em></p>
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<p><span style="font-weight: 400;">Diagenode provides leading solutions for epigenetic research. Because ChIP-seq is a widely-used technique, we validate our antibodies in ChIP and ChIP-seq experiments (in addition to conventional methods like Western blot, Dot blot, ELISA, and immunofluorescence) to provide the highest quality antibody. We standardize our validation and production to guarantee high product quality without technical bias. Diagenode guarantees ChIP-seq grade antibody performance under our suggested conditions.</span></p>
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<div class="small-12 medium-9 large-9 columns">
<p><strong>ChIP-seq profile</strong> of active (H3K4me3 and H3K36me3) and inactive (H3K27me3) marks using Diagenode antibodies.</p>
<img src="https://www.diagenode.com/img/categories/antibodies/chip-seq-grade-antibodies.png" /></div>
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<p><small> ChIP was performed on sheared chromatin from 100,000 K562 cells using iDeal ChIP-seq kit for Histones (cat. No. C01010051) with 1 µg of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 µg of the antibody against H3K36me3 (cat. No. C15410192). The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. The figure shows the signal distribution along the complete sequence of human chromosome 3, a zoomin to a 10 Mb region and a further zoomin to a 1.5 Mb region. </small></p>
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<p>Diagenode’s highly validated antibodies:</p>
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<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
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'description' => '<p>Histones are the main protein components of chromatin involved in the compaction of DNA into nucleosomes, the basic units of chromatin. A <strong>nucleosome</strong> consists of one pair of each of the core histones (<strong>H2A</strong>, <strong>H2B</strong>, <strong>H3</strong> and <strong>H4</strong>) forming an octameric structure wrapped by 146 base pairs of DNA. The different nucleosomes are linked by the linker histone<strong> H1, </strong>allowing for further condensation of chromatin.</p>
<p>The core histones have a globular structure with large unstructured N-terminal tails protruding from the nucleosome. They can undergo to multiple post-translational modifications (PTM), mainly at the N-terminal tails. These <strong>post-translational modifications </strong>include methylation, acetylation, phosphorylation, ubiquitinylation, citrullination, sumoylation, deamination and crotonylation. The most well characterized PTMs are <strong>methylation,</strong> <strong>acetylation and phosphorylation</strong>. Histone methylation occurs mainly on lysine (K) residues, which can be mono-, di- or tri-methylated, and on arginines (R), which can be mono-methylated and symmetrically or asymmetrically di-methylated. Histone acetylation occurs on lysines and histone phosphorylation mainly on serines (S), threonines (T) and tyrosines (Y).</p>
<p>The PTMs of the different residues are involved in numerous processes such as DNA repair, DNA replication and chromosome condensation. They influence the chromatin organization and can be positively or negatively associated with gene expression. Trimethylation of H3K4, H3K36 and H3K79, and lysine acetylation generally result in an open chromatin configuration (figure below) and are therefore associated with <strong>euchromatin</strong> and gene activation. Trimethylation of H3K9, K3K27 and H4K20, on the other hand, is enriched in <strong>heterochromatin </strong>and associated with gene silencing. The combination of different histone modifications is called the "<strong>histone code</strong>”, analogous to the genetic code.</p>
<p><img src="https://www.diagenode.com/img/categories/antibodies/histone-marks-illustration.png" /></p>
<p>Diagenode is proud to offer a large range of antibodies against histones and histone modifications. Our antibodies are highly specific and have been validated in many applications, including <strong>ChIP</strong> and <strong>ChIP-seq</strong>.</p>
<p>Diagenode’s collection includes antibodies recognizing:</p>
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<li><strong>Histone H1 variants</strong></li>
<li><strong>Histone H2A, H2A variants and histone H2A</strong> <strong>modifications</strong> (serine phosphorylation, lysine acetylation, lysine ubiquitinylation)</li>
<li><strong>Histone H2B and H2B</strong> <strong>modifications </strong>(serine phosphorylation, lysine acetylation)</li>
<li><strong>Histone H3 and H3 modifications </strong>(lysine methylation (mono-, di- and tri-methylated), lysine acetylation, serine phosphorylation, threonine phosphorylation, arginine methylation (mono-methylated, symmetrically and asymmetrically di-methylated))</li>
<li><strong>Histone H4 and H4 modifications (</strong>lysine methylation (mono-, di- and tri-methylated), lysine acetylation, arginine methylation (mono-methylated and symmetrically di-methylated), serine phosphorylation )</li>
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<p><span style="font-weight: 400;"><strong>HDAC's HAT's, HMT's and other</strong> <strong>enzymes</strong> which modify histones can be found in the category <a href="../categories/chromatin-modifying-proteins-histone-transferase">Histone modifying enzymes</a><br /></span></p>
<p><span style="font-weight: 400;"> Diagenode’s highly validated antibodies:</span></p>
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<li><span style="font-weight: 400;"> Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> Expert technical support</span></li>
<li><span style="font-weight: 400;"> Sample sizes available</span></li>
<li><span style="font-weight: 400;"> 100% satisfaction guarantee</span></li>
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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
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<li>Highly sensitive and specific</li>
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<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
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<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
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<div class="small-12 medium-6 large-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" alt="" width="400" height="315" /> </div>
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<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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'name' => 'Epigenetic Antibodies Brochure',
'description' => '<p>More than in any other immuoprecipitation assays, quality antibodies are critical tools in many epigenetics experiments. Since 10 years, Diagenode has developed the most stringent quality production available on the market for antibodies exclusively focused on epigenetic uses. All our antibodies have been qualified to work in epigenetic applications.</p>',
'image_id' => null,
'type' => 'Brochure',
'url' => 'files/brochures/Epigenetic_Antibodies_Brochure.pdf',
'slug' => 'epigenetic-antibodies-brochure',
'meta_keywords' => '',
'meta_description' => '',
'modified' => '2016-06-15 11:24:06',
'created' => '2015-07-03 16:05:27',
'ProductsDocument' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'id' => '11',
'name' => 'Antibodies you can trust',
'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
'image_id' => null,
'type' => 'Poster',
'url' => 'files/posters/Antibodies_you_can_trust_Poster.pdf',
'slug' => 'antibodies-you-can-trust-poster',
'meta_keywords' => '',
'meta_description' => '',
'modified' => '2015-10-01 20:18:31',
'created' => '2015-07-03 16:05:15',
'ProductsDocument' => array(
[maximum depth reached]
)
)
),
'Feature' => array(),
'Image' => array(
(int) 0 => array(
'id' => '1783',
'name' => 'product/antibodies/chipseq-grade-ab-icon.png',
'alt' => 'ChIP-seq Grade',
'modified' => '2020-11-27 07:04:40',
'created' => '2018-03-15 15:54:09',
'ProductsImage' => array(
[maximum depth reached]
)
)
),
'Promotion' => array(),
'Protocol' => array(),
'Publication' => array(
(int) 0 => array(
'id' => '4844',
'name' => 'SMYD3 represses tumor-intrinsic interferon response in HPV-negativesquamous cell carcinoma of the head and neck.',
'authors' => 'Nigam N. et al.',
'description' => '<p>Cancers often display immune escape, but the mechanisms are incompletely understood. Herein, we identify SMYD3 as a mediator of immune escape in human papilloma virus (HPV)-negative head and neck squamous cell carcinoma (HNSCC), an aggressive disease with poor response to immunotherapy with pembrolizumab. SMYD3 depletion induces upregulation of multiple type I interferon (IFN) response and antigen presentation machinery genes in HNSCC cells. Mechanistically, SMYD3 binds to and regulates the transcription of UHRF1, encoding for a reader of H3K9me3, which binds to H3K9me3-enriched promoters of key immune-related genes, recruits DNMT1, and silences their expression. SMYD3 further maintains the repression of immune-related genes through intragenic deposition of H4K20me3. In vivo, Smyd3 depletion induces influx of CD8 T cells and increases sensitivity to anti-programmed death 1 (PD-1) therapy. SMYD3 overexpression is associated with decreased CD8 T cell infiltration and poor response to neoadjuvant pembrolizumab. These data support combining SMYD3 depletion strategies with checkpoint blockade to overcome anti-PD-1 resistance in HPV-negative HNSCC.</p>',
'date' => '2023-07-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37463106',
'doi' => '10.1016/j.celrep.2023.112823',
'modified' => '2023-08-01 14:15:28',
'created' => '2023-08-01 15:59:38',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'id' => '4822',
'name' => 'RUNX1 colludes with NOTCH1 to reprogram chromatin in T-cell acutelymphoblastic leukemia',
'authors' => 'Islam R. et al.',
'description' => '<p><span>Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including </span><em>MYC, DTX1, HES4, IL7R,</em><span><span> </span>and<span> </span></span><em>NOTCH3</em><span>. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.</span></p>',
'date' => '2023-05-01',
'pmid' => 'https://doi.org/10.1016%2Fj.isci.2023.106795',
'doi' => '10.1016/j.isci.2023.106795',
'modified' => '2023-06-19 10:14:27',
'created' => '2023-06-13 21:11:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'id' => '4605',
'name' => 'Gene Regulatory Interactions at Lamina-Associated Domains',
'authors' => 'Madsen-Østerbye J. et al.',
'description' => '<p>The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are inactive, over ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to interact with regulatory elements remain unclear. Here, we integrate publicly available enhancer-capture Hi-C data with our own chromatin state and transcriptomic datasets to show that inferred enhancers of active genes in LADs are able to form connections with other enhancers within LADs and outside LADs. Fluorescence in situ hybridization analyses show proximity changes between differentially expressed genes in LADs and distant enhancers upon the induction of adipogenic differentiation. We also provide evidence of involvement of lamin A/C, but not lamin B1, in repressing genes at the border of an in-LAD active region within a topological domain. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with gene expression in this dynamic nuclear compartment.</p>',
'date' => '2023-01-01',
'pmid' => 'https://doi.org/10.3390%2Fgenes14020334',
'doi' => '10.3390/genes14020334',
'modified' => '2023-04-04 08:57:32',
'created' => '2023-02-21 09:59:46',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'id' => '4566',
'name' => 'Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing.',
'authors' => 'O'Geen H.et al.',
'description' => '<p>Precision epigenome editing has gained significant attention as a method to modulate gene expression without altering genetic information. However, a major limiting factor has been that the gene expression changes are often transient, unlike the life-long epigenetic changes that occur frequently in nature. Here, we systematically interrogate the ability of CRISPR/dCas9-based epigenome editors (Epi-dCas9) to engineer persistent epigenetic silencing. We elucidated cis regulatory features that contribute to the differential stability of epigenetic reprogramming, such as the active transcription histone marks H3K36me3 and H3K27ac strongly correlating with resistance to short-term repression and resistance to long-term silencing, respectively. H3K27ac inversely correlates with increased DNA methylation. Interestingly, the dependance on H3K27ac was only observed when a combination of KRAB-dCas9 and targetable DNA methyltransferases (DNMT3A-dCas9 + DNMT3L) was used, but not when KRAB was replaced with the targetable H3K27 histone methyltransferase Ezh2. In addition, programmable Ezh2/DNMT3A + L treatment demonstrated enhanced engineering of localized DNA methylation and was not sensitive to a divergent chromatin state. Our results highlight the importance of local chromatin features for heritability of programmable silencing and the differential response to KRAB- and Ezh2-based epigenetic editing platforms. The information gained in this study provides fundamental insights into understanding contextual cues to more predictably engineer persistent silencing.</p>',
'date' => '2022-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35234927',
'doi' => '10.1093/nar/gkac123',
'modified' => '2022-11-24 09:26:11',
'created' => '2022-11-24 08:49:52',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'id' => '4292',
'name' => 'The prolyl-isomerase PIN1 is essential for nuclear Lamin-Bstructure and function and protects heterochromatin under mechanicalstress.',
'authors' => 'Napoletano Francesco et al.',
'description' => '<p>Chromatin organization plays a crucial role in tissue homeostasis. Heterochromatin relaxation and consequent unscheduled mobilization of transposable elements (TEs) are emerging as key contributors of aging and aging-related pathologies, including Alzheimer's disease (AD) and cancer. However, the mechanisms governing heterochromatin maintenance or its relaxation in pathological conditions remain poorly understood. Here we show that PIN1, the only phosphorylation-specific cis/trans prolyl isomerase, whose loss is associated with premature aging and AD, is essential to preserve heterochromatin. We demonstrate that this PIN1 function is conserved from Drosophila to humans and prevents TE mobilization-dependent neurodegeneration and cognitive defects. Mechanistically, PIN1 maintains nuclear type-B Lamin structure and anchoring function for heterochromatin protein 1α (HP1α). This mechanism prevents nuclear envelope alterations and heterochromatin relaxation under mechanical stress, which is a key contributor to aging-related pathologies.</p>',
'date' => '2021-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34525372',
'doi' => '10.1016/j.celrep.2021.109694',
'modified' => '2022-05-24 09:18:40',
'created' => '2022-05-19 10:41:50',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '4174',
'name' => 'Dynamic association of the H3K64 trimethylation mark with genes encodingexported proteins in Plasmodium falciparum.',
'authors' => 'Jabeena, C A et al.',
'description' => '<p>Epigenetic modifications have emerged as critical regulators of virulence genes and stage-specific gene expression in Plasmodium falciparum. However, the specific roles of histone core epigenetic modifications in regulating the stage-specific gene expression are not well understood. In this study, we report an unconventional trimethylation at lysine 64 on histone 3 (H3K64me3) and characterize its functional relevance in P. falciparum. We show that PfSET4 and PfSET5 proteins of P. falciparum methylate H3K64 and that they prefer the nucleosome as a substrate over free histone 3 proteins. Structural analysis of PfSET5 revealed that it interacts with the nucleosome as a dimer. The H3K64me3 mark is dynamic, being enriched in the ring and trophozoite stages and drastically reduced in schizont stages. Stage-specific global ChIP-sequencing analysis of the H3K64me3 mark revealed the selective enrichment of this methyl mark on the genes of exported family proteins in the ring and trophozoite stages, and a significant reduction of the same in the schizont stages. Collectively, our data identify a novel epigenetic mark that are associated with the subset of genes encoding for exported proteins which may regulate their expression in different stages of P. falciparum.</p>',
'date' => '2021-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33839154',
'doi' => '10.1016/j.jbc.2021.100614',
'modified' => '2021-12-21 16:07:05',
'created' => '2021-12-06 15:53:19',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'id' => '4149',
'name' => 'Restricted nucleation and piRNA-mediated establishment of heterochromatinduring embryogenesis in Drosophila miranda',
'authors' => 'Wei, K. et al.',
'description' => '<p>Heterochromatin is a key architectural feature of eukaryotic genomes, crucial for silencing of repetitive elements and maintaining genome stability. Heterochromatin shows stereotypical enrichment patterns around centromeres and repetitive sequences, but the molecular details of how heterochromatin is established during embryogenesis are poorly understood. Here, we map the genome-wide distribution of H3K9me3-dependent heterochromatin in individual embryos of D. miranda at precisely staged developmental time points. We find that canonical H3K9me3 enrichment patterns are established early on before cellularization, and mature into stable and broad heterochromatin domains through development. Intriguingly, initial nucleation sites of H3K9me3 enrichment appear as early as embryonic stage3 (nuclear cycle 9) over transposable elements (TE) and progressively broaden, consistent with spreading to neighboring nucleosomes. The earliest nucleation sites are limited to specific regions of a small number of TE families and often appear over promoter regions, while late nucleation develops broadly across most TEs. Early nucleating TEs are highly targeted by maternal piRNAs and show early zygotic transcription, consistent with a model of co-transcriptional silencing of TEs by small RNAs. Interestingly, truncated TE insertions lacking nucleation sites show significantly reduced enrichment across development, suggesting that the underlying sequences play an important role in recruiting histone methyltransferases for heterochromatin</p>',
'date' => '2021-02-01',
'pmid' => 'https://doi.org/10.1101%2F2021.02.16.431328',
'doi' => '10.1101/2021.02.16.431328',
'modified' => '2021-12-14 09:28:27',
'created' => '2021-12-06 15:53:19',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'id' => '3995',
'name' => 'Epigenetic, transcriptional and phenotypic responses in Daphnia magna exposed to low-level ionizing radiation',
'authors' => 'Thaulow Jens, Song You, Lindeman Leif C., Kamstra Jorke H., Lee YeonKyeong, Xie Li, Aleström Peter, Salbu Brit, Tollefsen Knut Erik',
'description' => '<p>Ionizing radiation is known to induce oxidative stress and DNA damage as well as epigenetic effects in aquatic organisms. Epigenetic changes can be part of the adaptive responses to protect organisms from radiation-induced damage, or act as drivers of toxicity pathways leading to adverse effects. To investigate the potential roles of epigenetic mechanisms in low-dose ionizing radiation-induced stress responses, an ecologically relevant crustacean, adult Daphnia magna were chronically exposed to low and medium level external 60Co gamma radiation ranging from 0.4, 1, 4, 10, and 40 mGy/h for seven days. Biological effects at the molecular (global DNA methylation, histone modification, gene expression), cellular (reactive oxygen species formation), tissue/organ (ovary, gut and epidermal histology) and organismal (fecundity) levels were investigated using a suite of effect assessment tools. The results showed an increase in global DNA methylation associated with loci-specific alterations of histone H3K9 methylation and acetylation, and downregulation of genes involved in DNA methylation, one-carbon metabolism, antioxidant defense, DNA repair, apoptosis, calcium signaling and endocrine regulation of development and reproduction. Temporal changes of reactive oxygen species (ROS) formation were also observed with an apparent transition from ROS suppression to induction from 2-7 days after gamma exposure. The cumulative fecundity, however, was not significantly changed by the gamma exposure. On the basis of the new experimental evidence and existing knowledge, a hypothetical model was proposed to provide in-depth mechanistic understanding of the roles of epigenetic mechanisms in low dose ionizing radiation induced stress responses in D. magna.</p>',
'date' => '2020-07-18',
'pmid' => 'https://www.sciencedirect.com/science/article/pii/S0013935120308252',
'doi' => '10.1016/j.envres.2020.109930',
'modified' => '2020-09-01 14:51:16',
'created' => '2020-08-21 16:41:39',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 8 => array(
'id' => '3964',
'name' => 'The 20S proteasome activator PA28γ controls the compaction of chromatin',
'authors' => 'Didier Fesquet, David Llères, Cristina Viganò, Francisca Méchali, Séverine Boulon, Robert Feil, Olivier Coux, Catherine Bonne-Andrea, Véronique Baldin',
'description' => '<p>The nuclear PA28γ is known to activate the 20S proteasome, but its precise cellular functions remains unclear. Here, we identify PA28γ as a key factor that structures heterochromatin. We find that in human cells, a fraction of PA28γ-20S proteasome complexes localizes within HP1-linked heterochromatin foci. Our biochemical studies show that PA28γ interacts with HP1 proteins, particularly HP1β, which recruits the PA28γ-20S proteasome complexes to heterochromatin. Loss of PA28γ does not modify the localization of HP1β, its mobility within nuclear foci, or the level of H3K9 tri-methylation, but reduces H4K20 mono- and tri-methylation, modifications involved in heterochromatin establishment. Concordantly, using a quantitative FRET-based microscopy assay to monitor nanometer-scale proximity between nucleosomes in living cells, we find that PA28γ regulates nucleosome proximity within heterochromatin, and thereby controls its compaction. This function of PA28γ is independent of the 20S proteasome. Importantly, HP1β on its own is unable to drive heterochromatin compaction without PA28γ. Combined, our data reveal an unexpected chromatin structural role of PA28γ, and provide new insights into the mechanism that controls HP1β-mediated heterochromatin compaction.</p>',
'date' => '2020-05-28',
'pmid' => 'https://www.biorxiv.org/content/10.1101/716332v1.article-info',
'doi' => 'https://doi.org/10.1101/716332',
'modified' => '2020-08-12 09:44:09',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'id' => '3965',
'name' => 'Histone post-translational modifications in Silene latifolia X and Y chromosomes suggest a mammal-like dosage compensation system',
'authors' => 'Luis Rodríguez Lorenzo José, Hubinský Marcel, Vyskot Boris, Hobza Roman',
'description' => '<p>Silene latifolia is a model organism to study evolutionary young heteromorphic sex chromosome evolution in plants. Previous research indicates a Y-allele gene degeneration and a dosage compensation system already operating. Here, we propose an epigenetic approach based on analysis of several histone post-translational modifications (PTMs) to find the first epigenetic hints of the X:Y sex chromosome system regulation in S. latifolia. Through chromatin immunoprecipitation we interrogated six genes from X and Y alleles. Several histone PTMS linked to DNA methylation and transcriptional repression (H3K27me3, H3K23me, H3K9me2 and H3K9me3) and to transcriptional activation (H3K4me3 and H4K5, 8, 12, 16ac) were used. DNA enrichment (Immunoprecipitated DNA/input DNA) was analyzed and showed three main results: i) promoters of the Y allele are associated with heterochromatin marks, ii) promoters of the X allele in males are associated with activation of transcription marks and finally, iii) promoters of X alleles in females are associated with active and repressive marks. Our finding indicates a transcription activation of X allele and transcription repression of Y allele in males. In females we found a possible differential regulation (up X1, down X2) of each female X allele. These results agree with the mammal-like epigenetic dosage compensation regulation.</p>',
'date' => '2020-05-24',
'pmid' => 'https://www.sciencedirect.com/science/article/abs/pii/S0168945220301333',
'doi' => '10.1016/j.plantsci.2020.110528',
'modified' => '2020-08-12 09:42:21',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 10 => array(
'id' => '3943',
'name' => 'SETDB2 promoted breast cancer stem cell maintenance by interaction with and stabilization of ΔNp63α protein',
'authors' => 'Ying Liu, Fei Xie, Jialun Li, Jianpeng Xiao, Jie Wang, Zhaolin Mei, Hongjia Fan, Huan Fang, Sha Li, Qiuju Wu, Lin Yuan, Cuicui Liu, You Peng, Weiwei Zhao, Lulu Wang, Jiemin Wong, Jing Li, Jing Feng',
'description' => '<p>The histone H3K9 methyltransferase SETDB2 is involved in cell cycle dysregulation in acute leukemia and has oncogenic roles in gastric cancer. In our study, we found that SETDB2 plays essential roles in breast cancer stem cell maintenance. Depleted SETDB2 significantly decreased the breast cancer stem cell population and mammosphere formation in vitro and also inhibited breast tumor initiation and growth in vivo. Restoring SETDB2 expression rescued the defect in breast cancer stem cell maintenance. A mechanistic analysis showed that SETDB2 upregulated the transcription of the ΔNp63α downstream Hedgehog pathway gene. SETDB2 also interacted with and methylated ΔNp63α, and stabilized ΔNp63α protein. Restoring ΔNp63α expression rescued the breast cancer stem cell maintenance defect which mediated by SETDB2 knockdown. In conclusion, our study reveals a novel function of SETDB2 in cancer stem cell maintenance in breast cancer.</p>',
'date' => '2020-04-28',
'pmid' => 'https://www.ijbs.com/v16p2180',
'doi' => '10.7150/ijbs.43611',
'modified' => '2020-08-17 10:17:33',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 11 => array(
'id' => '3762',
'name' => 'Transit amplifying cells coordinate mouse incisor mesenchymal stem cell activation.',
'authors' => 'Walker JV, Zhuang H, Singer D, Illsley CS, Kok WL, Sivaraj KK, Gao Y, Bolton C, Liu Y, Zhao M, Grayson PRC, Wang S, Karbanová J, Lee T, Ardu S, Lai Q, Liu J, Kassem M, Chen S, Yang K, Bai Y, Tredwin C, Zambon AC, Corbeil D, Adams R, Abdallah BM, Hu B',
'description' => '<p>Stem cells (SCs) receive inductive cues from the surrounding microenvironment and cells. Limited molecular evidence has connected tissue-specific mesenchymal stem cells (MSCs) with mesenchymal transit amplifying cells (MTACs). Using mouse incisor as the model, we discover a population of MSCs neibouring to the MTACs and epithelial SCs. With Notch signaling as the key regulator, we disclose molecular proof and lineage tracing evidence showing the distinct MSCs contribute to incisor MTACs and the other mesenchymal cell lineages. MTACs can feedback and regulate the homeostasis and activation of CL-MSCs through Delta-like 1 homolog (Dlk1), which balances MSCs-MTACs number and the lineage differentiation. Dlk1's function on SCs priming and self-renewal depends on its biological forms and its gene expression is under dynamic epigenetic control. Our findings can be validated in clinical samples and applied to accelerate tooth wound healing, providing an intriguing insight of how to direct SCs towards tissue regeneration.</p>',
'date' => '2019-08-09',
'pmid' => 'http://www.pubmed.gov/31399601',
'doi' => '10.1038/s41467-019-11611-0',
'modified' => '2019-10-03 10:03:31',
'created' => '2019-10-02 16:16:55',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 12 => array(
'id' => '3715',
'name' => 'Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner.',
'authors' => 'O'Geen H, Bates SL, Carter SS, Nisson KA, Halmai J, Fink KD, Rhie SK, Farnham PJ, Segal DJ',
'description' => '<p>BACKGROUND: Rewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve in a predictable manner using targeted systems. RESULTS: Here, we report that persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). We demonstrate that the histone methyltransferase requirement can be locus specific. Co-targeting Ezh2-dCas9, but not KRAB-dCas9, with DNMT3A-dCas9 and DNMT3L induced long-term HER2 repression over at least 50 days (approximately 57 cell divisions) and triggered an epigenetic switch to a heterochromatic environment. An increase in H3K27 trimethylation and DNA methylation was stably maintained and accompanied by a sustained loss of H3K27 acetylation. Interestingly, substitution of Ezh2-dCas9 with KRAB-dCas9 enabled long-term repression at some target genes (e.g., SNURF) but not at HER2, at which H3K9me3 and DNA methylation were transiently acquired and subsequently lost. Off-target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the off-target loci tested. Conversely, robust hypermethylation was observed at HER2. We further demonstrated that Ezh2-dCas9 required full-length DNMT3L for maximal activity and that co-targeting DNMT3L was sufficient for persistent repression by Ezh2-dCas9 or KRAB-dCas9. CONCLUSIONS: These data demonstrate that targeting different combinations of histone and DNA methyltransferases is required to achieve maximal repression at different loci. Fine-tuning of targeting tools is a necessity to engineer epigenetic memory at any given locus in any given cell type.</p>',
'date' => '2019-05-03',
'pmid' => 'http://www.pubmed.gov/31053162',
'doi' => '10.1186/s13072-019-0275-8',
'modified' => '2019-07-05 13:15:49',
'created' => '2019-07-04 10:42:34',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 13 => array(
'id' => '3709',
'name' => 'Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation.',
'authors' => 'Paulsen J, Liyakat Ali TM, Nekrasov M, Delbarre E, Baudement MO, Kurscheid S, Tremethick D, Collas P',
'description' => '<p>Genomic information is selectively used to direct spatial and temporal gene expression during differentiation. Interactions between topologically associating domains (TADs) and between chromatin and the nuclear lamina organize and position chromosomes in the nucleus. However, how these genomic organizers together shape genome architecture is unclear. Here, using a dual-lineage differentiation system, we report long-range TAD-TAD interactions that form constitutive and variable TAD cliques. A differentiation-coupled relationship between TAD cliques and lamina-associated domains suggests that TAD cliques stabilize heterochromatin at the nuclear periphery. We also provide evidence of dynamic TAD cliques during mouse embryonic stem-cell differentiation and somatic cell reprogramming and of inter-TAD associations in single-cell high-resolution chromosome conformation capture (Hi-C) data. TAD cliques represent a level of four-dimensional genome conformation that reinforces the silencing of repressed developmental genes.</p>',
'date' => '2019-05-01',
'pmid' => 'http://www.pubmed.gov/31011212',
'doi' => '10.1038/s41588-019-0392-0',
'modified' => '2019-07-05 14:33:38',
'created' => '2019-07-04 10:42:34',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 14 => array(
'id' => '3692',
'name' => 'PML modulates H3.3 targeting to telomeric and centromeric repeats in mouse fibroblasts.',
'authors' => 'Spirkoski J, Shah A, Reiner AH, Collas P, Delbarre E',
'description' => '<p>Targeted deposition of histone variant H3.3 into chromatin is paramount for proper regulation of chromatin integrity, particularly in heterochromatic regions including repeats. We have recently shown that the promyelocytic leukemia (PML) protein prevents H3.3 from being deposited in large heterochromatic PML-associated domains (PADs). However, to what extent PML modulates H3.3 loading on chromatin in other areas of the genome remains unexplored. Here, we examined the impact of PML on targeting of H3.3 to genes and repeat regions that reside outside PADs. We show that loss of PML increases H3.3 deposition in subtelomeric, telomeric, pericentric and centromeric repeats in mouse embryonic fibroblasts, while other repeat classes are not affected. Expression of major satellite, minor satellite and telomeric non-coding transcripts is altered in Pml-null cells. In particular, telomeric Terra transcripts are strongly upregulated, in concordance with a marked reduction in H4K20me3 at these sites. Lastly, for most genes H3.3 enrichment or gene expression outcomes are independent of PML. Our data argue towards the importance of a PML-H3.3 axis in preserving a heterochromatin state at centromeres and telomeres.</p>',
'date' => '2019-04-16',
'pmid' => 'http://www.pubmed.gov/30850162',
'doi' => '10.1016/j.bbrc.2019.02.087',
'modified' => '2019-06-28 13:50:40',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 15 => array(
'id' => '3644',
'name' => 'Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs.',
'authors' => 'Pontis J, Planet E, Offner S, Turelli P, Duc J, Coudray A, Theunissen TW, Jaenisch R, Trono D',
'description' => '<p>Expansion of transposable elements (TEs) coincides with evolutionary shifts in gene expression. TEs frequently harbor binding sites for transcriptional regulators, thus enabling coordinated genome-wide activation of species- and context-specific gene expression programs, but such regulation must be balanced against their genotoxic potential. Here, we show that Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) control the timely and pleiotropic activation of TE-derived transcriptional cis regulators during early embryogenesis. Evolutionarily recent SVA, HERVK, and HERVH TE subgroups contribute significantly to chromatin opening during human embryonic genome activation and are KLF-stimulated enhancers in naive human embryonic stem cells (hESCs). KZFPs of corresponding evolutionary ages are simultaneously induced and repress the transcriptional activity of these TEs. Finally, the same KZFP-controlled TE-based enhancers later serve as developmental and tissue-specific enhancers. Thus, by controlling the transcriptional impact of TEs during embryogenesis, KZFPs facilitate their genome-wide incorporation into transcriptional networks, thereby contributing to human genome regulation.</p>',
'date' => '2019-03-27',
'pmid' => 'http://www.pubmed.gov/31006620',
'doi' => '10.1016/j.stem.2019.03.012',
'modified' => '2019-06-07 10:16:36',
'created' => '2019-06-06 12:11:18',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 16 => array(
'id' => '3686',
'name' => 'Gamma radiation induces locus specific changes to histone modification enrichment in zebrafish and Atlantic salmon.',
'authors' => 'Lindeman LC, Kamstra JH, Ballangby J, Hurem S, Martín LM, Brede DA, Teien HC, Oughton DH, Salbu B, Lyche JL, Aleström P',
'description' => '<p>Ionizing radiation is a recognized genotoxic agent, however, little is known about the role of the functional form of DNA in these processes. Post translational modifications on histone proteins control the organization of chromatin and hence control transcriptional responses that ultimately affect the phenotype. The purpose of this study was to investigate effects on chromatin caused by ionizing radiation in fish. Direct exposure of zebrafish (Danio rerio) embryos to gamma radiation (10.9 mGy/h for 3h) induced hyper-enrichment of H3K4me3 at the genes hnf4a, gmnn and vegfab. A similar relative hyper-enrichment was seen at the hnf4a loci of irradiated Atlantic salmon (Salmo salar) embryos (30 mGy/h for 10 days). At the selected genes in ovaries of adult zebrafish irradiated during gametogenesis (8.7 and 53 mGy/h for 27 days), a reduced enrichment of H3K4me3 was observed, which was correlated with reduced levels of histone H3 was observed. F1 embryos of the exposed parents showed hyper-methylation of H3K4me3, H3K9me3 and H3K27me3 on the same three loci, while these differences were almost negligible in F2 embryos. Our results from three selected loci suggest that ionizing radiation can affect chromatin structure and organization, and that these changes can be detected in F1 offspring, but not in subsequent generations.</p>',
'date' => '2019-01-01',
'pmid' => 'http://www.pubmed.gov/30759148',
'doi' => '10.1371/journal.pone.0212123',
'modified' => '2019-06-28 13:57:39',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 17 => array(
'id' => '3635',
'name' => 'TIP60: an actor in acetylation of H3K4 and tumor development in breast cancer.',
'authors' => 'Judes G, Dubois L, Rifaï K, Idrissou M, Mishellany F, Pajon A, Besse S, Daures M, Degoul F, Bignon YJ, Penault-Llorca F, Bernard-Gallon D',
'description' => '<p>AIM: The acetyltransferase TIP60 is reported to be downregulated in several cancers, in particular breast cancer, but the molecular mechanisms resulting from its alteration are still unclear. MATERIALS & METHODS: In breast tumors, H3K4ac enrichment and its link with TIP60 were evaluated by chromatin immunoprecipitation-qPCR and re-chromatin immunoprecipitation techniques. To assess the biological roles of TIP60 in breast cancer, two cell lines of breast cancer, MDA-MB-231 (ER-) and MCF-7 (ER+) were transfected with shRNA specifically targeting TIP60 and injected to athymic Balb-c mice. RESULTS: We identified a potential target of TIP60, H3K4. We show that an underexpression of TIP60 could contribute to a reduction of H3K4 acetylation in breast cancer. An increase in tumor development was noted in sh-TIP60 MDA-MB-231 xenografts and a slowdown of tumor growth in sh-TIP60 MCF-7 xenografts. CONCLUSION: This is evidence that the underexpression of TIP60 observed in breast cancer can promote the tumorigenesis of ER-negative tumors.</p>',
'date' => '2018-11-01',
'pmid' => 'http://www.pubmed.gov/30324811',
'doi' => '10.2217/epi-2018-0004',
'modified' => '2019-06-07 10:29:04',
'created' => '2019-06-06 12:11:18',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 18 => array(
'id' => '3556',
'name' => 'PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex.',
'authors' => 'Link S, Spitzer RMM, Sana M, Torrado M, Völker-Albert MC, Keilhauer EC, Burgold T, Pünzeler S, Low JKK, Lindström I, Nist A, Regnard C, Stiewe T, Hendrich B, Imhof A, Mann M, Mackay JP, Bartkuhn M, Hake SB',
'description' => '<p>Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified that PWWP2A tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial-facial development. Here, using in vitro assays, we show that distinct domains of PWWP2A mediate binding to free linker DNA as well as H3K36me3 nucleosomes. In vivo, PWWP2A strongly recognizes H2A.Z-containing regulatory regions and weakly binds H3K36me3-containing gene bodies. Further, PWWP2A binds to an MTA1-specific subcomplex of the NuRD complex (M1HR), which consists solely of MTA1, HDAC1, and RBBP4/7, and excludes CHD, GATAD2 and MBD proteins. Depletion of PWWP2A leads to an increase of acetylation levels on H3K27 as well as H2A.Z, presumably by impaired chromatin recruitment of M1HR. Thus, this study identifies PWWP2A as a complex chromatin-binding protein that serves to direct the deacetylase complex M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels.</p>',
'date' => '2018-10-16',
'pmid' => 'http://www.pubmed.gov/30327463',
'doi' => '10.1038/s41467-018-06665-5',
'modified' => '2019-07-22 09:17:39',
'created' => '2019-03-21 14:12:08',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 19 => array(
'id' => '3551',
'name' => 'HIV-2/SIV viral protein X counteracts HUSH repressor complex.',
'authors' => 'Ghina Chougui, Soundasse Munir-Matloob, Roy Matkovic, Michaël M Martin, Marina Morel, Hichem Lahouassa, Marjorie Leduc, Bertha Cecilia Ramirez, Lucie Etienne and Florence Margottin-Goguet',
'description' => '<p>To evade host immune defences, human immunodeficiency viruses 1 and 2 (HIV-1 and HIV-2) have evolved auxiliary proteins that target cell restriction factors. Viral protein X (Vpx) from the HIV-2/SIVsmm lineage enhances viral infection by antagonizing SAMHD1 (refs ), but this antagonism is not sufficient to explain all Vpx phenotypes. Here, through a proteomic screen, we identified another Vpx target-HUSH (TASOR, MPP8 and periphilin)-a complex involved in position-effect variegation. HUSH downregulation by Vpx is observed in primary cells and HIV-2-infected cells. Vpx binds HUSH and induces its proteasomal degradation through the recruitment of the DCAF1 ubiquitin ligase adaptor, independently from SAMHD1 antagonism. As a consequence, Vpx is able to reactivate HIV latent proviruses, unlike Vpx mutants, which are unable to induce HUSH degradation. Although antagonism of human HUSH is not conserved among all lentiviral lineages including HIV-1, it is a feature of viral protein R (Vpr) from simian immunodeficiency viruses (SIVs) of African green monkeys and from the divergent SIV of l'Hoest's monkey, arguing in favour of an ancient lentiviral species-specific vpx/vpr gene function. Altogether, our results suggest the HUSH complex as a restriction factor, active in primary CD4 T cells and counteracted by Vpx, therefore providing a molecular link between intrinsic immunity and epigenetic control.</p>',
'date' => '2018-08-01',
'pmid' => 'http://www.pubmed.gov/29891865',
'doi' => '10.1038/s41564-018-0179-6',
'modified' => '2019-02-28 10:20:23',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 20 => array(
'id' => '3470',
'name' => 'Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes.',
'authors' => 'Lomberk G, Blum Y, Nicolle R, Nair A, Gaonkar KS, Marisa L, Mathison A, Sun Z, Yan H, Elarouci N, Armenoult L, Ayadi M, Ordog T, Lee JH, Oliver G, Klee E, Moutardier V, Gayet O, Bian B, Duconseil P, Gilabert M, Bigonnet M, Garcia S, Turrini O, Delpero JR,',
'description' => '<p>Recent studies have offered ample insight into genome-wide expression patterns to define pancreatic ductal adenocarcinoma (PDAC) subtypes, although there remains a lack of knowledge regarding the underlying epigenomics of PDAC. Here we perform multi-parametric integrative analyses of chromatin immunoprecipitation-sequencing (ChIP-seq) on multiple histone modifications, RNA-sequencing (RNA-seq), and DNA methylation to define epigenomic landscapes for PDAC subtypes, which can predict their relative aggressiveness and survival. Moreover, we describe the state of promoters, enhancers, super-enhancers, euchromatic, and heterochromatic regions for each subtype. Further analyses indicate that the distinct epigenomic landscapes are regulated by different membrane-to-nucleus pathways. Inactivation of a basal-specific super-enhancer associated pathway reveals the existence of plasticity between subtypes. Thus, our study provides new insight into the epigenetic landscapes associated with the heterogeneity of PDAC, thereby increasing our mechanistic understanding of this disease, as well as offering potential new markers and therapeutic targets.</p>',
'date' => '2018-05-17',
'pmid' => 'http://www.pubmed.gov/29773832',
'doi' => '10.1038/s41467-018-04383-6',
'modified' => '2019-02-15 21:08:07',
'created' => '2019-02-14 15:01:22',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 21 => array(
'id' => '3536',
'name' => 'PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites.',
'authors' => 'Diagouraga B, Clément JAJ, Duret L, Kadlec J, de Massy B, Baudat F',
'description' => '<p>The programmed formation of hundreds of DNA double-strand breaks (DSBs) is essential for proper meiosis and fertility. In mice and humans, the location of these breaks is determined by the meiosis-specific protein PRDM9, through the DNA-binding specificity of its zinc-finger domain. PRDM9 also has methyltransferase activity. Here, we show that this activity is required for H3K4me3 and H3K36me3 deposition and for DSB formation at PRDM9-binding sites. By analyzing mice that express two PRDM9 variants with distinct DNA-binding specificities, we show that each variant generates its own set of H3K4me3 marks independently from the other variant. Altogether, we reveal several basic principles of PRDM9-dependent DSB site determination, in which an excess of sites are designated through PRDM9 binding and subsequent histone methylation, from which a subset is selected for DSB formation.</p>',
'date' => '2018-03-01',
'pmid' => 'http://www.pubmed.gov/29478809',
'doi' => '10.1016/j.molcel.2018.01.033',
'modified' => '2019-02-28 10:51:44',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 22 => array(
'id' => '3276',
'name' => 'DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease',
'authors' => 'Jeziorska D.M. et al.',
'description' => '<p>The human genome contains ∼30,000 CpG islands (CGIs). While CGIs associated with promoters nearly always remain unmethylated, many of the ∼9,000 CGIs lying within gene bodies become methylated during development and differentiation. Both promoter and intragenic CGIs may also become abnormally methylated as a result of genome rearrangements and in malignancy. The epigenetic mechanisms by which some CGIs become methylated but others, in the same cell, remain unmethylated in these situations are poorly understood. Analyzing specific loci and using a genome-wide analysis, we show that transcription running across CGIs, associated with specific chromatin modifications, is required for DNA methyltransferase 3B (DNMT3B)-mediated DNA methylation of many naturally occurring intragenic CGIs. Importantly, we also show that a subgroup of intragenic CGIs is not sensitive to this process of transcription-mediated methylation and that this correlates with their individual intrinsic capacity to initiate transcription in vivo. We propose a general model of how transcription could act as a primary determinant of the patterns of CGI methylation in normal development and differentiation, and in human disease.</p>',
'date' => '2017-09-05',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28827334',
'doi' => '',
'modified' => '2017-10-16 10:16:06',
'created' => '2017-10-16 10:16:06',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 23 => array(
'id' => '3240',
'name' => 'Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation',
'authors' => 'Pünzeler S. et al.',
'description' => '<p>Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA-based processes via poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel H2A.Z-nucleosome binder. PWWP2A is a functionally uncharacterized, vertebrate-specific protein that binds very tightly to chromatin through a concerted multivalent binding mode. Two internal protein regions mediate H2A.Z-specificity and nucleosome interaction, whereas the PWWP domain exhibits direct DNA binding. Genome-wide mapping reveals that PWWP2A binds selectively to H2A.Z-containing nucleosomes with strong preference for promoters of highly transcribed genes. In human cells, its depletion affects gene expression and impairs proliferation via a mitotic delay. While PWWP2A does not influence H2A.Z occupancy, the C-terminal tail of H2A.Z is one important mediator to recruit PWWP2A to chromatin. Knockdown of PWWP2A in <i>Xenopus</i> results in severe cranial facial defects, arising from neural crest cell differentiation and migration problems. Thus, PWWP2A is a novel H2A.Z-specific multivalent chromatin binder providing a surprising link between H2A.Z, chromosome segregation, and organ development.</p>',
'date' => '2017-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28645917',
'doi' => '',
'modified' => '2017-08-29 09:45:44',
'created' => '2017-08-29 09:45:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 24 => array(
'id' => '3216',
'name' => 'Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b',
'authors' => 'Kevin T. Ebata, Kathryn Mesh, Shichong Liu, Misha Bilenky, Alexander Fekete, Michael G. Acker, Martin Hirst, Benjamin A. Garcia and Miguel Ramalho-Santos',
'description' => '<section xmlns="" xmlns:fn="http://www.w3.org/2005/xpath-functions" xmlns:meta="http://www.springer.com/app/meta" class="Abstract" id="Abs1" lang="en">
<div class="js-CollapseSection">
<div xmlns:func="http://oscar.fig.bmc.com" xmlns="http://www.w3.org/1999/xhtml" class="AbstractSection" id="ASec1">
<h3 xmlns="" class="Heading">Background</h3>
<p id="Par1" class="Para">Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that vitamin C enhances the activity of Tet enzymes in embryonic stem (ES) cells, leading to DNA demethylation and activation of germline genes.</p>
</div>
<div xmlns:func="http://oscar.fig.bmc.com" xmlns="http://www.w3.org/1999/xhtml" class="AbstractSection" id="ASec2">
<h3 xmlns="" class="Heading">Results</h3>
<p id="Par2" class="Para">We report here that vitamin C induces a remarkably specific demethylation of histone H3 lysine 9 dimethylation (H3K9me2) in naïve ES cells. Vitamin C treatment reduces global levels of H3K9me2, but not other histone methylation marks analyzed, as measured by western blot, immunofluorescence and mass spectrometry. Vitamin C leads to widespread loss of H3K9me2 at large chromosomal domains as well as gene promoters and repeat elements. Vitamin C-induced loss of H3K9me2 occurs rapidly within 24 h and is reversible. Importantly, we found that the histone demethylases Kdm3a and Kdm3b are required for vitamin C-induced demethylation of H3K9me2. Moreover, we show that vitamin C-induced Kdm3a/b-mediated H3K9me2 demethylation and Tet-mediated DNA demethylation are independent processes at specific loci. Lastly, we document Kdm3a/b are partially required for the upregulation of germline genes by vitamin C.</p>
</div>
<div xmlns:func="http://oscar.fig.bmc.com" xmlns="http://www.w3.org/1999/xhtml" class="AbstractSection" id="ASec3">
<h3 xmlns="" class="Heading">Conclusions</h3>
<p id="Par3" class="Para">These results reveal a specific role for vitamin C in histone demethylation in ES cells and document that DNA methylation and H3K9me2 cooperate to silence germline genes in pluripotent cells.</p>
</div>
</div>
</section>',
'date' => '2017-07-12',
'pmid' => 'https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-017-0143-3',
'doi' => 'https://doi.org/10.1186/s13072-017-0143-3',
'modified' => '2017-08-23 14:47:51',
'created' => '2017-07-29 08:04:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 25 => array(
'id' => '3177',
'name' => 'Microinjection of Antibodies Targeting the Lamin A/C Histone-Binding Site Blocks Mitotic Entry and Reveals Separate Chromatin Interactions with HP1, CenpB and PML.',
'authors' => 'Dixon C.R. et al.',
'description' => '<p>Lamins form a scaffold lining the nucleus that binds chromatin and contributes to spatial genome organization; however, due to the many other functions of lamins, studies knocking out or altering the lamin polymer cannot clearly distinguish between direct and indirect effects. To overcome this obstacle, we specifically targeted the mapped histone-binding site of A/C lamins by microinjecting antibodies specific to this region predicting that this would make the genome more mobile. No increase in chromatin mobility was observed; however, interestingly, injected cells failed to go through mitosis, while control antibody-injected cells did. This effect was not due to crosslinking of the lamin polymer, as Fab fragments also blocked mitosis. The lack of genome mobility suggested other lamin-chromatin interactions. To determine what these might be, mini-lamin A constructs were expressed with or without the histone-binding site that assembled into independent intranuclear structures. HP1, CenpB and PML proteins accumulated at these structures for both constructs, indicating that other sites supporting chromatin interactions exist on lamin A. Together, these results indicate that lamin A-chromatin interactions are highly redundant and more diverse than generally acknowledged and highlight the importance of trying to experimentally separate their individual functions.</p>',
'date' => '2017-03-25',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28346356',
'doi' => '',
'modified' => '2017-05-17 10:39:58',
'created' => '2017-05-17 10:39:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 26 => array(
'id' => '3172',
'name' => 'Decoupling of DNA methylation and activity of intergenic LINE-1 promoters in colorectal cancer',
'authors' => 'Vafadar-Isfahani N. et al.',
'description' => '<p>Hypomethylation of LINE-1 repeats in cancer has been proposed as the main mechanism behind their activation; this assumption, however, was based on findings from early studies that were biased toward young and transpositionally active elements. Here, we investigate the relationship between methylation of 2 intergenic, transpositionally inactive LINE-1 elements and expression of the LINE-1 chimeric transcript (LCT) 13 and LCT14 driven by their antisense promoters (L1-ASP). Our data from DNA modification, expression, and 5'RACE analyses suggest that colorectal cancer methylation in the regions analyzed is not always associated with LCT repression. Consistent with this, in HCT116 colorectal cancer cells lacking DNA methyltransferases DNMT1 or DNMT3B, LCT13 expression decreases, while cells lacking both DNMTs or treated with the DNMT inhibitor 5-azacytidine (5-aza) show no change in LCT13 expression. Interestingly, levels of the H4K20me3 histone modification are inversely associated with LCT13 and LCT14 expression. Moreover, at these LINE-1s, H4K20me3 levels rather than DNA methylation seem to be good predictor of their sensitivity to 5-aza treatment. Therefore, by studying individual LINE-1 promoters we have shown that in some cases these promoters can be active without losing methylation; in addition, we provide evidence that other factors (e.g., H4K20me3 levels) play prominent roles in their regulation.</p>',
'date' => '2017-03-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28300471',
'doi' => '',
'modified' => '2017-05-10 16:26:24',
'created' => '2017-05-10 16:26:24',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 27 => array(
'id' => '3152',
'name' => 'H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements',
'authors' => 'Zink L.M. et al.',
'description' => '<p>Histone chaperones prevent promiscuous histone interactions before chromatin assembly. They guarantee faithful deposition of canonical histones and functionally specialized histone variants into chromatin in a spatial- and temporally-restricted manner. Here, we identify the binding partners of the primate-specific and H3.3-related histone variant H3.Y using several quantitative mass spectrometry approaches, and biochemical and cell biological assays. We find the HIRA, but not the DAXX/ATRX, complex to recognize H3.Y, explaining its presence in transcriptionally active euchromatic regions. Accordingly, H3.Y nucleosomes are enriched in the transcription-promoting FACT complex and depleted of repressive post-translational histone modifications. H3.Y mutational gain-of-function screens reveal an unexpected combinatorial amino acid sequence requirement for histone H3.3 interaction with DAXX but not HIRA, and for H3.3 recruitment to PML nuclear bodies. We demonstrate the importance and necessity of specific H3.3 core and C-terminal amino acids in discriminating between distinct chaperone complexes. Further, chromatin immunoprecipitation sequencing experiments reveal that in contrast to euchromatic HIRA-dependent deposition sites, human DAXX/ATRX-dependent regions of histone H3 variant incorporation are enriched in heterochromatic H3K9me3 and simple repeat sequences. These data demonstrate that H3.Y's unique amino acids allow a functional distinction between HIRA and DAXX binding and its consequent deposition into open chromatin.</p>',
'date' => '2017-02-21',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28334823',
'doi' => '',
'modified' => '2017-03-31 14:13:36',
'created' => '2017-03-31 14:13:36',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 28 => array(
'id' => '3100',
'name' => 'Muscle catabolic capacities and global hepatic epigenome are modified in juvenile rainbow trout fed different vitamin levels at first feeding',
'authors' => 'Panserat S. et al.',
'description' => '<p>Based on the concept of nutritional programming in mammals, we tested whether a short term hyper or hypo vitamin stimulus during first-feeding could induce long-lasting changes in nutrient metabolism in rainbow trout. Trout alevins received during the 4 first weeks of exogenous feeding a diet either without supplemental vitamins (NOSUP), a diet supplemented with a vitamin premix to satisfy the minimal requirement in all the vitamins (NRC) or a diet with a vitamin premix corresponding to an optimal vitamin nutrition (OVN). Following a common rearing period on the control diet, all three groups were then evaluated in terms of metabolic marker gene expressions at the end of the feeding period (day 119). Whereas no gene modifications for proteins involved in energy and lipid metabolism were observed in whole alevins (short-term effect), some of these genes showed a long-term molecular adaptation in the muscle of juveniles (long-term effect). Indeed, muscle of juveniles subjected at an early feeding of the OVN diet displayed up-regulated expression of markers of lipid catabolism (3-hydroxyacyl-CoA dehydrogenase – HOAD - enzyme) and mitochondrial energy metabolism (Citrate synthase - <em>cs</em>, Ubiquitinol cytochrome <em>c</em> reductase core protein 2 - QCR2, cytochrome oxidase 4 - COX4, ATP synthase form 5 - ATP5A) compared to fish fed the NOSUP diet. Moreover, some key enzymes involved in glucose catabolism (Muscle Pyruvate kinase - PKM) and amino acid catabolism (Glutamate dehydrogenase - GDH3) were also up regulated in muscle of juvenile fish fed with the OVN diet at first-feeding compared to fish fed the NOSUP diet. We researched if these permanently modified gene expressions could be related to global modifications of epigenetic marks (global DNA methylation and global histone acetylation and methylation). There was no variation of the epigenetic marks in muscle. However, we found changes in hepatic DNA methylation, global H3 acetylation and H3K4 methylation, dependent on the vitamin intake at early life. In summary, our data show, for the first time in fish, that a short-term vitamin-stimulus during early life may durably influence muscle energy and lipid metabolism as well as some hepatic epigenetic marks in rainbow trout.</p>',
'date' => '2017-02-01',
'pmid' => 'http://www.sciencedirect.com/science/article/pii/S0044848616309693',
'doi' => '',
'modified' => '2017-01-03 15:01:50',
'created' => '2017-01-03 15:01:50',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 29 => array(
'id' => '2825',
'name' => 'Oestrogen receptor β regulates epigenetic patterns at specific genomic loci through interaction with thymine DNA glycosylase.',
'authors' => 'Liu Y, Duong W, Krawczyk C, Bretschneider N, Borbély G, Varshney M, Zinser C, Schär P, Rüegg J.',
'description' => '<div class="">
<h4>BACKGROUND:</h4>
<p><abstracttext label="BACKGROUND" nlmcategory="BACKGROUND">DNA methylation is one way to encode epigenetic information and plays a crucial role in regulating gene expression during embryonic development. DNA methylation marks are established by the DNA methyltransferases and, recently, a mechanism for active DNA demethylation has emerged involving the ten-eleven translocator proteins and thymine DNA glycosylase (TDG). However, so far it is not clear how these enzymes are recruited to, and regulate DNA methylation at, specific genomic loci. A number of studies imply that sequence-specific transcription factors are involved in targeting DNA methylation and demethylation processes. Oestrogen receptor beta (ERβ) is a ligand-inducible transcription factor regulating gene expression in response to the female sex hormone oestrogen. Previously, we found that ERβ deficiency results in changes in DNA methylation patterns at two gene promoters, implicating an involvement of ERβ in DNA methylation. In this study, we set out to explore this involvement on a genome-wide level, and to investigate the underlying mechanisms of this function.</abstracttext></p>
<h4>RESULTS:</h4>
<p><abstracttext label="RESULTS" nlmcategory="RESULTS">Using reduced representation bisulfite sequencing, we compared genome-wide DNA methylation in mouse embryonic fibroblasts derived from wildtype and ERβ knock-out mice, and identified around 8000 differentially methylated positions (DMPs). Validation and further characterisation of selected DMPs showed that differences in methylation correlated with changes in expression of the nearest gene. Additionally, re-introduction of ERβ into the knock-out cells could reverse hypermethylation and reactivate expression of some of the genes. We also show that ERβ is recruited to regions around hypermethylated DMPs. Finally, we demonstrate here that ERβ interacts with TDG and that TDG binds ERβ-dependently to hypermethylated DMPs.</abstracttext></p>
<h4>CONCLUSION:</h4>
<p><abstracttext label="CONCLUSION" nlmcategory="CONCLUSIONS">We provide evidence that ERβ plays a role in regulating DNA methylation at specific genomic loci, likely as the result of its interaction with TDG at these regions. Our findings imply a novel function of ERβ, beyond direct transcriptional control, in regulating DNA methylation at target genes. Further, they shed light on the question how DNA methylation is regulated at specific genomic loci by supporting a concept in which sequence-specific transcription factors can target factors that regulate DNA methylation patterns.</abstracttext></p>
</div>',
'date' => '2016-02-16',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/26889208',
'doi' => '10.1186/s13072-016-0055-7.',
'modified' => '2016-02-22 10:05:14',
'created' => '2016-02-22 10:05:14',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 30 => array(
'id' => '2909',
'name' => 'Epigenetic priming of inflammatory response genes by high glucose in adipose progenitor cells',
'authors' => 'Rønningen T, Shah A, Reiner AH, Collas P, Moskaug JØ',
'description' => '<p>Cellular metabolism confers wide-spread epigenetic modifications required for regulation of transcriptional networks that determine cellular states. Mesenchymal stromal cells are responsive to metabolic cues including circulating glucose levels and modulate inflammatory responses. We show here that long term exposure of undifferentiated human adipose tissue stromal cells (ASCs) to high glucose upregulates a subset of inflammation response (IR) genes and alters their promoter histone methylation patterns in a manner consistent with transcriptional de-repression. Modeling of chromatin states from combinations of histone modifications in nearly 500 IR genes unveil three overarching chromatin configurations reflecting repressive, active, and potentially active states in promoter and enhancer elements. Accordingly, we show that adipogenic differentiation in high glucose predominantly upregulates IR genes. Our results indicate that elevated extracellular glucose levels sensitize in ASCs an IR gene expression program which is exacerbated during adipocyte differentiation. We propose that high glucose exposure conveys an epigenetic 'priming' of IR genes, favoring a transcriptional inflammatory response upon adipogenic stimulation. Chromatin alterations at IR genes by high glucose exposure may play a role in the etiology of metabolic diseases.</p>',
'date' => '2015-11-27',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/26462465',
'doi' => '10.1016/j.bbrc.2015.10.030',
'modified' => '2016-05-09 22:54:48',
'created' => '2016-05-09 22:54:48',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 31 => array(
'id' => '2874',
'name' => 'Polycomb RING1A- and RING1B-dependent histone H2A monoubiquitylation at pericentromeric regions promotes S-phase progression',
'authors' => 'Bravo M, Nicolini F, Starowicz K, Barroso S, Calés C, Aguilera A, Vidal M',
'description' => '<p>The functions of polycomb products extend beyond their well-known activity as transcriptional regulators to include genome duplication processes. Polycomb activities during DNA replication and DNA damage repair are unclear, particularly without induced replicative stress. We have used a cellular model of conditionally inactive polycomb E3 ligases (RING1A and RING1B), which monoubiquitylate lysine 119 of histone H2A (H2AK119Ub), to examine DNA replication in unperturbed cells. We identify slow elongation and fork stalling during DNA replication that is associated with the accumulation of mid and late S-phase cells. Signs of replicative stress and colocalisation of double-strand breaks with chromocenters, the sites of coalesced pericentromeric heterocromatic (PCH) domains, were enriched in cells at mid S-phase, the stage at which PCH is replicated. Altered replication was rescued by targeted monoubiquitylation of PCH through methyl-CpG binding domain protein 1. The acute senescence associated with the depletion of RING1 proteins, which is mediated by p21 (also known as CDKN1A) upregulation, could be uncoupled from a response to DNA damage. These findings link cell proliferation and the polycomb proteins RING1A and RING1B to S-phase progression through a specific function in PCH replication.</p>',
'date' => '2015-08-13',
'pmid' => 'http://jcs.biologists.org/content/128/19/3660',
'doi' => '10.1242/jcs.173021 ',
'modified' => '2016-03-29 16:29:38',
'created' => '2016-03-29 16:29:38',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 32 => array(
'id' => '2725',
'name' => 'Erosion of X Chromosome Inactivation in Human Pluripotent Cells Initiates with XACT Coating and Depends on a Specific Heterochromatin Landscape.',
'authors' => 'Vallot C, Ouimette JF, Makhlouf M, Féraud O, Pontis J, Côme J, Martinat C, Bennaceur-Griscelli A, Lalande M, Rougeulle C',
'description' => 'Human pluripotent stem cells (hPSCs) display extensive epigenetic instability, particularly on the X chromosome. In this study, we show that, in hPSCs, the inactive X chromosome has a specific heterochromatin landscape that predisposes it to erosion of X chromosome inactivation (XCI), a process that occurs spontaneously in hPSCs. Heterochromatin remodeling and gene reactivation occur in a non-random fashion and are confined to specific H3K27me3-enriched domains, leaving H3K9me3-marked regions unaffected. Using single-cell monitoring of XCI erosion, we show that this instability only occurs in pluripotent cells. We also provide evidence that loss of XIST expression is not the primary cause of XCI instability and that gene reactivation from the inactive X (Xi) precedes loss of XIST coating. Notably, expression and coating by the long non-coding RNA XACT are early events in XCI erosion and, therefore, may play a role in mediating this process.',
'date' => '2015-05-07',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25921272',
'doi' => '',
'modified' => '2015-07-24 15:39:05',
'created' => '2015-07-24 15:39:05',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 33 => array(
'id' => '2575',
'name' => 'Embryonic stem cell differentiation requires full length Chd1.',
'authors' => 'Piatti P, Lim CY, Nat R, Villunger A, Geley S, Shue YT, Soratroi C, Moser M, Lusser A',
'description' => 'The modulation of chromatin dynamics by ATP-dependent chromatin remodeling factors has been recognized as an important mechanism to regulate the balancing of self-renewal and pluripotency in embryonic stem cells (ESCs). Here we have studied the effects of a partial deletion of the gene encoding the chromatin remodeling factor Chd1 that generates an N-terminally truncated version of Chd1 in mouse ESCs in vitro as well as in vivo. We found that a previously uncharacterized serine-rich region (SRR) at the N-terminus is not required for chromatin assembly activity of Chd1 but that it is subject to phosphorylation. Expression of Chd1 lacking this region in ESCs resulted in aberrant differentiation properties of these cells. The self-renewal capacity and ESC chromatin structure, however, were not affected. Notably, we found that newly established ESCs derived from Chd1(Δ2/Δ2) mutant mice exhibited similar differentiation defects as in vitro generated mutant ESCs, even though the N-terminal truncation of Chd1 was fully compatible with embryogenesis and post-natal life in the mouse. These results underscore the importance of Chd1 for the regulation of pluripotency in ESCs and provide evidence for a hitherto unrecognized critical role of the phosphorylated N-terminal SRR for full functionality of Chd1.',
'date' => '2015-01-26',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25620209',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 34 => array(
'id' => '2513',
'name' => 'The histone demethylase enzyme KDM3A is a key estrogen receptor regulator in breast cancer.',
'authors' => 'Wade MA, Jones D, Wilson L, Stockley J, Coffey K, Robson CN, Gaughan L',
'description' => '<p>Endocrine therapy has successfully been used to treat estrogen receptor (ER)-positive breast cancer, but this invariably fails with cancers becoming refractory to treatment. Emerging evidence has suggested that fluctuations in ER co-regulatory protein expression may facilitate resistance to therapy and be involved in breast cancer progression. To date, a small number of enzymes that control methylation status of histones have been identified as co-regulators of ER signalling. We have identified the histone H3 lysine 9 mono- and di-methyl demethylase enzyme KDM3A as a positive regulator of ER activity. Here, we demonstrate that depletion of KDM3A by RNAi abrogates the recruitment of the ER to cis-regulatory elements within target gene promoters, thereby inhibiting estrogen-induced gene expression changes. Global gene expression analysis of KDM3A-depleted cells identified gene clusters associated with cell growth. Consistent with this, we show that knockdown of KDM3A reduces ER-positive cell proliferation and demonstrate that KDM3A is required for growth in a model of endocrine therapy-resistant disease. Crucially, we show that KDM3A catalytic activity is required for both ER-target gene expression and cell growth, demonstrating that developing compounds which target demethylase enzymatic activity may be efficacious in treating both ER-positive and endocrine therapy-resistant disease.</p>',
'date' => '2015-01-09',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25488809',
'doi' => '',
'modified' => '2016-05-03 11:59:18',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 35 => array(
'id' => '2502',
'name' => 'TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells.',
'authors' => 'Fasching L, Kapopoulou A, Sachdeva R, Petri R, Jönsson ME, Männe C, Turelli P, Jern P, Cammas F, Trono D, Jakobsson J',
'description' => '<p>TRIM28 is a corepressor that mediates transcriptional silencing by establishing local heterochromatin. Here, we show that deletion of TRIM28 in neural progenitor cells (NPCs) results in high-level expression of two groups of endogenous retroviruses (ERVs): IAP1 and MMERVK10C. We find that NPCs use TRIM28-mediated histone modifications to dynamically regulate transcription and silencing of ERVs, which is in contrast to other somatic cell types using DNA methylation. We also show that derepression of ERVs influences transcriptional dynamics in NPCs through the activation of nearby genes and the expression of long noncoding RNAs. These findings demonstrate a unique dynamic transcriptional regulation of ERVs in NPCs. Our results warrant future studies on the role of ERVs in the healthy and diseased brain.</p>',
'date' => '2015-01-06',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25543143',
'doi' => '',
'modified' => '2017-06-22 13:34:19',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 36 => array(
'id' => '2492',
'name' => 'Cryosectioning the intestinal crypt-villus axis: an ex vivo method to study the dynamics of epigenetic modifications from stem cells to differentiated cells',
'authors' => 'Vincent A, Kazmierczak C, Duchêne B, Jonckheere N, Leteurtre E, Van Seuningen I',
'description' => 'The intestinal epithelium is a particularly attractive biological adult model to study epigenetic mechanisms driving adult stem cell renewal and cell differentiation. Since epigenetic modifications are dynamic, we have developed an original ex vivo approach to study the expression and epigenetic profiles of key genes associated with either intestinal cell pluripotency or differentiation by isolating cryosections of the intestinal crypt-villus axis. Gene expression, DNA methylation and histone modifications were studied by qRT-PCR, Methylation Specific-PCR and micro-Chromatin Immunoprecipitation, respectively. Using this approach, it was possible to identify segment-specific methylation and chromatin profiles. We show that (i) expression of intestinal stem cell markers (Lgr5, Ascl2) exclusively in the crypt is associated with active histone marks, (ii) promoters of all pluripotency genes studied and transcription factors involved in intestinal cell fate (Cdx2) harbour a bivalent chromatin pattern in the crypts, (iii) expression of differentiation markers (Muc2, Sox9) along the crypt-villus axis is associated with DNA methylation. Hence, using an original model of cryosectioning along the crypt-villus axis that allows in situ detection of dynamic epigenetic modifications, we demonstrate that regulation of pluripotency and differentiation markers in healthy intestinal mucosa involves different and specific epigenetic mechanisms.',
'date' => '2014-12-27',
'pmid' => 'http://www.sciencedirect.com/science/article/pii/S1873506114001585',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 37 => array(
'id' => '2215',
'name' => 'Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation.',
'authors' => 'Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ',
'description' => 'Artificial transcription factors (ATFs) and genomic nucleases based on a DNA binding platform consisting of multiple zinc finger domains are currently being developed for clinical applications. However, no genome-wide investigations into their binding specificity have been performed. We have created six-finger ATFs to target two different 18 nt regions of the human SOX2 promoter; each ATF is constructed such that it contains or lacks a super KRAB domain (SKD) that interacts with a complex containing repressive histone methyltransferases. ChIP-seq analysis of the effector-free ATFs in MCF7 breast cancer cells identified thousands of binding sites, mostly in promoter regions; the addition of an SKD domain increased the number of binding sites ∼5-fold, with a majority of the new sites located outside of promoters. De novo motif analyses suggest that the lack of binding specificity is due to subsets of the finger domains being used for genomic interactions. Although the ATFs display widespread binding, few genes showed expression differences; genes repressed by the ATF-SKD have stronger binding sites and are more enriched for a 12 nt motif. Interestingly, epigenetic analyses indicate that the transcriptional repression caused by the ATF-SKD is not due to changes in active histone modifications.',
'date' => '2014-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25122745',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 38 => array(
'id' => '2664',
'name' => 'The PML-associated protein DEK regulates the balance of H3.3 loading on chromatin and is important for telomere integrity.',
'authors' => 'Ivanauskiene K, Delbarre E, McGhie JD, Küntziger T, Wong LH, Collas P',
'description' => 'Histone variant H3.3 is deposited in chromatin at active sites, telomeres, and pericentric heterochromatin by distinct chaperones, but the mechanisms of regulation and coordination of chaperone-mediated H3.3 loading remain largely unknown. We show here that the chromatin-associated oncoprotein DEK regulates differential HIRA- and DAAX/ATRX-dependent distribution of H3.3 on chromosomes in somatic cells and embryonic stem cells. Live cell imaging studies show that nonnucleosomal H3.3 normally destined to PML nuclear bodies is re-routed to chromatin after depletion of DEK. This results in HIRA-dependent widespread chromatin deposition of H3.3 and H3.3 incorporation in the foci of heterochromatin in a process requiring the DAXX/ATRX complex. In embryonic stem cells, loss of DEK leads to displacement of PML bodies and ATRX from telomeres, redistribution of H3.3 from telomeres to chromosome arms and pericentric heterochromatin, induction of a fragile telomere phenotype, and telomere dysfunction. Our results indicate that DEK is required for proper loading of ATRX and H3.3 on telomeres and for telomeric chromatin architecture. We propose that DEK acts as a "gatekeeper" of chromatin, controlling chromatin integrity by restricting broad access to H3.3 by dedicated chaperones. Our results also suggest that telomere stability relies on mechanisms ensuring proper histone supply and routing.',
'date' => '2014-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25049225',
'doi' => '',
'modified' => '2015-07-24 15:39:05',
'created' => '2015-07-24 15:39:05',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 39 => array(
'id' => '2338',
'name' => 'The specific alteration of histone methylation profiles by DZNep during early zebrafish development.',
'authors' => 'Ostrup O, Reiner AH, Aleström P, Collas P',
'description' => '<p>Early embryo development constitutes a unique opportunity to study acquisition of epigenetic marks, including histone methylation. This study investigates the in vivo function and specificity of 3-deazaneplanocin A (DZNep), a promising anti-cancer drug that targets polycomb complex genes. One- to two-cell stage embryos were cultured with DZNep, and subsequently evaluated at the post-mid blastula transition stage for H3K27me3, H3K4me3 and H3K9me3 occupancy and enrichment at promoters using ChIP-chip microarrays. DZNep affected promoter enrichment of H3K27me3 and H3K9me3, whereas H3K4me3 remained stable. Interestingly, DZNep induced a loss of H3K27me3 and H3K9me3 from a substantial number of promoters but did not prevent de novo acquisition of these marks on others, indicating gene-specific targeting of its action. Loss/gain of H3K27me3 on promoters did not result in changes in gene expression levels until 24h post-fertilization. In contrast, genes gaining H3K9me3 displayed strong and constant down-regulation upon DZNep treatment. H3K9me3 enrichment on these gene promoters was observed not only in the proximal area as expected, but also over the transcription start site. Altered H3K9me3 profiles were associated with severe neuronal and cranial phenotypes at day 4-5 post-fertilization. Thus, DZNep was shown to affect enrichment patterns of H3K27me3 and H3K9me3 at promoters in a gene-specific manner.</p>',
'date' => '2014-09-28',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25260724',
'doi' => '',
'modified' => '2016-04-08 09:43:32',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 40 => array(
'id' => '2226',
'name' => 'KMTase Set7/9 is a critical regulator of E2F1 activity upon genotoxic stress.',
'authors' => 'Lezina L, Aksenova V, Ivanova T, Purmessur N, Antonov AV, Tentler D, Fedorova O, Garabadgiu AV, Talianidis I, Melino G, Barlev NA',
'description' => 'During the recent years lysine methyltransferase Set7/9 ((Su(var)-3-9, Enhancer-of-Zeste, Trithorax) domain containing protein 7/9) has emerged as an important regulator of different transcription factors. In this study, we report a novel function for Set7/9 as a critical co-activator of E2 promoter-binding factor 1 (E2F1)-dependent transcription in response to DNA damage. By means of various biochemical, cell biology, and bioinformatics approaches, we uncovered that cell-cycle progression through the G1/S checkpoint of tumour cells upon DNA damage is defined by the threshold of expression of both E2F1 and Set7/9. The latter affects the activity of E2F1 by indirectly modulating histone modifications in the promoters of E2F1-dependent genes. Moreover, Set7/9 differentially affects E2F1 transcription targets: it promotes cell proliferation via expression of the CCNE1 gene and represses apoptosis by inhibiting the TP73 gene. Our biochemical screening of the panel of lung tumour cell lines suggests that these two factors are critically important for transcriptional upregulation of the CCNE1 gene product and hence successful progression through cell cycle. These findings identify Set7/9 as a potential biomarker in tumour cells with overexpressed E2F1 activity.Cell Death and Differentiation advance online publication, 15 August 2014; doi:10.1038/cdd.2014.108.',
'date' => '2014-08-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25124555',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 41 => array(
'id' => '2206',
'name' => 'The histone variant composition of centromeres is controlled by the pericentric heterochromatin state during the cell cycle.',
'authors' => 'Boyarchuk E, Filipescu D, Vassias I, Cantaloube S, Almouzni G',
'description' => 'Correct chromosome segregation requires a unique chromatin environment at centromeres and in their vicinity. Here, we address how the deposition of canonical H2A and H2A.Z histone variants is controlled at pericentric heterochromatin (PHC). Whereas in euchromatin newly synthesized H2A and H2A.Z are deposited throughout the cell cycle, we reveal two discrete waves of deposition at PHC - during mid to late S phase in a replication-dependent manner for H2A and during G1 phase for H2A.Z. This G1 cell cycle restriction is lost when heterochromatin features are altered, leading to the accumulation of H2A.Z at the domain. Interestingly, compromising PHC integrity also impacts upon neighboring centric chromatin, increasing the amount of centromeric CENP-A without changing the timing of its deposition. We conclude that the higher-order chromatin structure at the pericentric domain influences dynamics at the nucleosomal level within centromeric chromatin. The two different modes of rearrangement of the PHC during the cell cycle provide distinct opportunities to replenish one or the other H2A variant, highlighting PHC integrity as a potential signal to regulate the deposition timing and stoichiometry of histone variants at the centromere.',
'date' => '2014-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24906798',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 42 => array(
'id' => '2081',
'name' => 'RNAi-Mediated Gene silencing in Zebrafish Triggered by Convergent Transcription.',
'authors' => 'Andrews OE, Cha DJ, Wei C, Patton JG',
'description' => 'RNAi based strategies to induce gene silencing are commonly employed in numerous model organisms but have not been extensively used in zebrafish. We found that introduction of transgenes containing convergent transcription units in zebrafish embryos induced stable transcriptional gene silencing (TGS) in cis and trans for reporter (mCherry) and endogenous (One-Eyed Pinhead (OEP) and miR-27a/b) genes. Convergent transcription enabled detection of both sense and antisense transcripts and silencing was suppressed upon Dicer knockdown, indicating processing of double stranded RNA. By ChIP analyses, increased silencing was accompanied by enrichment of the heterochromatin mark H3K9me3 in the two convergently arranged promoters and in the intervening reading frame. Our work demonstrates that convergent transcription can induce gene silencing in zebrafish providing another tool to create specific temporal and spatial control of gene expression.',
'date' => '2014-06-09',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24909225',
'doi' => '',
'modified' => '2015-07-24 15:39:02',
'created' => '2015-07-24 15:39:02',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 43 => array(
'id' => '1888',
'name' => 'Transcriptional Derepression of the ERVWE1 Locus following Influenza A Virus Infection.',
'authors' => 'Li F, Nellåker C, Sabunciyan S, Yolken RH, Jones-Brando L, Johansson AS, Owe-Larsson B, Karlsson H',
'description' => 'UNLABELLED: Syncytin-1, a fusogenic protein encoded by a human endogenous retrovirus of the W family (HERV-W) element (ERVWE1), is expressed in the syncytiotrophoblast layer of the placenta. This locus is transcriptionally repressed in adult tissues through promoter CpG methylation and suppressive histone modifications. Whereas syncytin-1 appears to be crucial for the development and functioning of the human placenta, its ectopic expression has been associated with pathological conditions, such as multiple sclerosis and schizophrenia. We previously reported on the transactivation of HERV-W elements, including ERVWE1, during influenza A/WSN/33 virus infection in a range of human cell lines. Here we report the results of quantitative PCR analyses of transcripts encoding syncytin-1 in both cell lines and primary fibroblast cells. We observed that spliced ERVWE1 transcripts and those encoding the transcription factor glial cells missing 1 (GCM1), acting as an enhancer element upstream of ERVWE1, are prominently upregulated in response to influenza A/WSN/33 virus infection in nonplacental cells. Knockdown of GCM1 by small interfering RNA followed by infection suppressed the transactivation of ERVWE1. While the infection had no influence on CpG methylation in the ERVWE1 promoter, chromatin immunoprecipitation assays detected decreased H3K9 trimethylation (H3K9me3) and histone methyltransferase SETDB1 levels along with influenza virus proteins associated with ERVWE1 and other HERV-W loci in infected CCF-STTG1 cells. The present findings suggest that an exogenous influenza virus infection can transactivate ERVWE1 by increasing transcription of GCM1 and reducing H3K9me3 in this region and in other regions harboring HERV-W elements. IMPORTANCE: Syncytin-1, a protein encoded by the env gene in the HERV-W locus ERVWE1, appears to be crucial for the development and functioning of the human placenta and is transcriptionally repressed in nonplacental tissues. Nevertheless, its ectopic expression has been associated with pathological conditions, such as multiple sclerosis and schizophrenia. In the present paper, we report findings suggesting that an exogenous influenza A virus infection can transactivate ERVWE1 by increasing the transcription of GCM1 and reducing the repressive histone mark H3K9me3 in this region and in other regions harboring HERV-W elements. These observations have implications of potential relevance for viral pathogenesis and for conditions associated with the aberrant transcription of HERV-W loci.',
'date' => '2014-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24478419',
'doi' => '',
'modified' => '2015-07-24 15:39:02',
'created' => '2015-07-24 15:39:02',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 44 => array(
'id' => '1723',
'name' => 'HDAC inhibitor confers radiosensitivity to prostate stem-like cells.',
'authors' => 'Frame FM, Pellacani D, Collins AT, Simms MS, Mann VM, Jones G, Meuth M, Bristow RG, Maitland NJ',
'description' => 'Background:Radiotherapy can be an effective treatment for prostate cancer, but radiorecurrent tumours do develop. Considering prostate cancer heterogeneity, we hypothesised that primitive stem-like cells may constitute the radiation-resistant fraction.Methods:Primary cultures were derived from patients undergoing resection for prostate cancer or benign prostatic hyperplasia. After short-term culture, three populations of cells were sorted, reflecting the prostate epithelial hierarchy, namely stem-like cells (SCs, α2β1integrin(hi)/CD133(+)), transit-amplifying (TA, α2β1integrin(hi)/CD133(-)) and committed basal (CB, α2β1integrin(lo)) cells. Radiosensitivity was measured by colony-forming efficiency (CFE) and DNA damage by comet assay and DNA damage foci quantification. Immunofluorescence and flow cytometry were used to measure heterochromatin. The HDAC (histone deacetylase) inhibitor Trichostatin A was used as a radiosensitiser.Results:Stem-like cells had increased CFE post irradiation compared with the more differentiated cells (TA and CB). The SC population sustained fewer lethal double-strand breaks than either TA or CB cells, which correlated with SCs being less proliferative and having increased levels of heterochromatin. Finally, treatment with an HDAC inhibitor sensitised the SCs to radiation.Interpretation:Prostate SCs are more radioresistant than more differentiated cell populations. We suggest that the primitive cells survive radiation therapy and that pre-treatment with HDAC inhibitors may sensitise this resistant fraction.',
'date' => '2013-12-10',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24220693',
'doi' => '',
'modified' => '2015-07-24 15:39:01',
'created' => '2015-07-24 15:39:01',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 45 => array(
'id' => '1516',
'name' => 'Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes.',
'authors' => 'Lund E, Oldenburg AR, Delbarre E, Freberg CT, Duband-Goulet I, Eskeland R, Buendia B, Collas P',
'description' => 'The nuclear lamina is implicated in the organization of the eukaryotic nucleus. Association of nuclear lamins with the genome occurs through large chromatin domains including mostly, but not exclusively, repressed genes. How lamin interactions with regulatory elements modulate gene expression in different cellular contexts is unknown. We show here that in human adipose tissue stem cells, lamin A/C interacts with distinct spatially restricted subpromoter regions, both within and outside peripheral and intra-nuclear lamin-rich domains. These localized interactions are associated with distinct transcriptional outcomes in a manner dependent on local chromatin modifications. Down-regulation of lamin A/C leads to dissociation of lamin A/C from promoters and remodels repressive and permissive histone modifications by enhancing transcriptional permissiveness, but is not sufficient to elicit gene activation. Adipogenic differentiation resets a large number of lamin-genome associations globally and at subpromoter levels and redefines associated transcription outputs. We propose that lamin A/C acts as a modulator of local gene expression outcome through interaction with adjustable sites on promoters, and that these position-dependent transcriptional readouts may be reset upon differentiation.',
'date' => '2013-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23861385',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 46 => array(
'id' => '1595',
'name' => 'Long range epigenetic silencing is a trans-species mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells.',
'authors' => 'Forn M, Muñoz M, Tauriello DV, Merlos-Suárez A, Rodilla V, Bigas A, Batlle E, Jordà M, Peinado MA',
'description' => 'DNA methylation and chromatin remodeling are frequently implicated in the silencing of genes involved in carcinogenesis. Long Range Epigenetic Silencing (LRES) is a mechanism of gene inactivation that affects multiple contiguous CpG islands and has been described in different human cancer types. However, it is unknown whether there is a coordinated regulation of the genes embedded in these regions in normal cells and in early stages of tumor progression. To better characterize the molecular events associated with the regulation and remodeling of these regions we analyzed two regions undergoing LRES in human colon cancer in the mouse model. We demonstrate that LRES also occurs in murine cancer in vivo and mimics the molecular features of the human phenomenon, namely, downregulation of gene expression, acquisition of inactive histone marks, and DNA hypermethylation of specific CpG islands. The genes embedded in these regions showed a dynamic and autonomous regulation during mouse intestinal cell differentiation, indicating that, in the framework considered here, the coordinated regulation in LRES is restricted to cancer. Unexpectedly, benign adenomas in Apc(Min/+) mice showed overexpression of most of the genes affected by LRES in cancer, which suggests that the repressive remodeling of the region is a late event. Chromatin immunoprecipitation analysis of the transcriptional insulator CTCF in mouse colon cancer cells revealed disrupted chromatin domain boundaries as compared with normal cells. Malignant regression of cancer cells by in vitro differentiation resulted in partial reversion of LRES and gain of CTCF binding. We conclude that genes in LRES regions are plastically regulated in cell differentiation and hyperproliferation, but are constrained to a coordinated repression by abolishing boundaries and the autonomous regulation of chromatin domains in cancer cells.',
'date' => '2013-08-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24035705',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 47 => array(
'id' => '1486',
'name' => 'Transgene- and locus-dependent imprinting reveals allele-specific chromosome conformations.',
'authors' => 'Lonfat N, Montavon T, Jebb D, Tschopp P, Nguyen Huynh TH, Zakany J, Duboule D',
'description' => 'When positioned into the integrin α-6 gene, an Hoxd9lacZ reporter transgene displayed parental imprinting in mouse embryos. While the expression from the paternal allele was comparable with patterns seen for the same transgene when present at the neighboring HoxD locus, almost no signal was scored at this integration site when the transgene was inherited from the mother, although the Itga6 locus itself is not imprinted. The transgene exhibited maternal allele-specific DNA hypermethylation acquired during oogenesis, and its expression silencing was reversible on passage through the male germ line. Histone modifications also corresponded to profiles described at known imprinted loci. Chromosome conformation analyses revealed distinct chromatin microarchitectures, with a more compact structure characterizing the maternally inherited repressed allele. Such genetic analyses of well-characterized transgene insertions associated with a de novo-induced parental imprint may help us understand the molecular determinants of imprinting.',
'date' => '2013-07-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23818637',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 48 => array(
'id' => '1425',
'name' => 'Expression of a large LINE-1-driven antisense RNA is linked to epigenetic silencing of the metastasis suppressor gene TFPI-2 in cancer.',
'authors' => 'Cruickshanks HA, Vafadar-Isfahani N, Dunican DS, Lee A, Sproul D, Lund JN, Meehan RR, Tufarelli C',
'description' => 'LINE-1 retrotransposons are abundant repetitive elements of viral origin, which in normal cells are kept quiescent through epigenetic mechanisms. Activation of LINE-1 occurs frequently in cancer and can enable LINE-1 mobilization but also has retrotransposition-independent consequences. We previously reported that in cancer, aberrantly active LINE-1 promoters can drive transcription of flanking unique sequences giving rise to LINE-1 chimeric transcripts (LCTs). Here, we show that one such LCT, LCT13, is a large transcript (>300 kb) running antisense to the metastasis-suppressor gene TFPI-2. We have modelled antisense RNA expression at TFPI-2 in transgenic mouse embryonic stem (ES) cells and demonstrate that antisense RNA induces silencing and deposition of repressive histone modifications implying a causal link. Consistent with this, LCT13 expression in breast and colon cancer cell lines is associated with silencing and repressive chromatin at TFPI-2. Furthermore, we detected LCT13 transcripts in 56% of colorectal tumours exhibiting reduced TFPI-2 expression. Our findings implicate activation of LINE-1 elements in subsequent epigenetic remodelling of surrounding genes, thus hinting a novel retrotransposition-independent role for LINE-1 elements in malignancy.',
'date' => '2013-05-23',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23703216',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 49 => array(
'id' => '1497',
'name' => 'Histone lysine trimethylation or acetylation can be modulated by phytoestrogen, estrogen or anti-HDAC in breast cancer cell lines.',
'authors' => 'Dagdemir A, Durif J, Ngollo M, Bignon YJ, Bernard-Gallon D',
'description' => '<p>AIM: The isoflavones genistein, daidzein and equol (daidzein metabolite) have been reported to interact with epigenetic modifications, specifically hypermethylation of tumor suppressor genes. The objective of this study was to analyze and understand the mechanisms by which phytoestrogens act on chromatin in breast cancer cell lines. MATERIALS & METHODS: Two breast cancer cell lines, MCF-7 and MDA-MB 231, were treated with genistein (18.5 µM), daidzein (78.5 µM), equol (12.8 µM), 17β-estradiol (10 nM) and suberoylanilide hydroxamic acid (1 µM) for 48 h. A control with untreated cells was performed. 17β-estradiol and an anti-HDAC were used to compare their actions with phytoestrogens. The chromatin immunoprecipitation coupled with quantitative PCR was used to follow soy phytoestrogen effects on H3 and H4 histones on H3K27me3, H3K9me3, H3K4me3, H4K8ac and H3K4ac marks, and we selected six genes (EZH2, BRCA1, ERα, ERβ, SRC3 and P300) for analysis. RESULTS: Soy phytoestrogens induced a decrease in trimethylated marks and an increase in acetylating marks studied at six selected genes. CONCLUSION: We demonstrated that soy phytoestrogens tend to modify transcription through the demethylation and acetylation of histones in breast cancer cell lines.</p>',
'date' => '2013-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23414320',
'doi' => '',
'modified' => '2016-05-03 12:17:35',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 50 => array(
'id' => '1179',
'name' => 'Epigenetic Regulation of Nestin Expression During Neurogenic Differentiation of Adipose Tissue Stem Cells.',
'authors' => 'Boulland JL, Mastrangelopoulou M, Boquest AC, Jakobsen R, Noer A, Glover JC, Collas P.',
'description' => 'Adipose-tissue-derived stem cells (ASCs) have received considerable attention due to their easy access, expansion potential, and differentiation capacity. ASCs are believed to have the potential to differentiate into neurons. However, the mechanisms by which this may occur remain largely unknown. Here, we show that culturing ASCs under active proliferation conditions greatly improves their propensity to differentiate toward osteogenic, adipogenic, and neurogenic lineages. Neurogenic-induced ASCs express early neurogenic genes as well as markers of mature neurons, including voltage-gated ion channels. Nestin, highly expressed in neural progenitors, is upregulated by mitogenic stimulation of ASCs, and as in neural progenitors, then repressed during neurogenic differentiation. Nestin gene (NES) expression under these conditions appears to be regulated by epigenetic mechanisms. The neural-specific, but not muscle-specific, enhancer regions of NES are DNA demethylated by mitogenic stimulation, and remethylated upon neurogenic differentiation. We observe dynamic changes in histone H3K4, H3K9, and H3K27 methylation on the NES locus before and during neurogenic differentiation that are consistent with epigenetic processes involved in the regulation of NES expression. We suggest that ASCs are epigenetically prepatterned to differentiate toward a neural lineage and that this prepatterning is enhanced by demethylation of critical NES enhancer elements upon mitogenic stimulation preceding neurogenic differentiation. Our findings provide molecular evidence that the differentiation repertoire of ASCs may extend beyond mesodermal lineages.',
'date' => '2012-12-21',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/23140086',
'doi' => '',
'modified' => '2015-07-24 15:38:59',
'created' => '2015-07-24 15:38:59',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 51 => array(
'id' => '752',
'name' => 'The histone demethylase Kdm3a is essential to progression through differentiation.',
'authors' => 'Herzog M, Josseaux E, Dedeurwaerder S, Calonne E, Volkmar M, Fuks F',
'description' => 'Histone demethylation has important roles in regulating gene expression and forms part of the epigenetic memory system that regulates cell fate and identity by still poorly understood mechanisms. Here, we examined the role of histone demethylase Kdm3a during cell differentiation, showing that Kdm3a is essential for differentiation into parietal endoderm-like (PE) cells in the F9 mouse embryonal carcinoma model. We identified a number of target genes regulated by Kdm3a during endoderm differentiation; among the most dysregulated were the three developmental master regulators Dab2, Pdlim4 and FoxQ1. We show that dysregulation of the expression of these genes correlates with Kdm3a H3K9me2 demethylase activity. We further demonstrate that either Dab2 depletion or Kdm3a depletion prevents F9 cells from fully differentiating into PE cells, but that ectopic expression of Dab2 cannot compensate for Kdm3a knockdown; Dab2 is thus necessary, but insufficient on its own, to promote complete terminal differentiation. We conclude that Kdm3a plays a crucial role in progression through PE differentiation by regulating expression of a set of endoderm differentiation master genes. The emergence of Kdm3a as a key modulator of cell fate decision strengthens the view that histone demethylases are essential to cell differentiation.',
'date' => '2012-05-11',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22581778',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 52 => array(
'id' => '630',
'name' => 'Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.',
'authors' => 'Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B',
'description' => 'While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA hypomethylation in the cancer cell, primarily at partially methylated domains (PMDs) in normal breast cells. Unexpectedly, genes within these regions are largely silenced in cancer cells. The loss of DNA methylation in these regions is accompanied by formation of repressive chromatin, with a significant fraction displaying allelic DNA methylation where one allele is DNA methylated while the other allele is occupied by histone modifications H3K9me3 or H3K27me3. Our results show a mutually exclusive relationship between DNA methylation and H3K9me3 or H3K27me3. These results suggest that global DNA hypomethylation in breast cancer is tightly linked to the formation of repressive chromatin domains and gene silencing, thus identifying a potential epigenetic pathway for gene regulation in cancer cells.',
'date' => '2012-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22156296',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 53 => array(
'id' => '919',
'name' => 'Prepatterning of developmental gene expression by modified histones before zygotic genome activation.',
'authors' => 'Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Østrup O, Winata C, Mathavan S, Müller F, Aleström P, Collas P',
'description' => 'A hallmark of anamniote vertebrate development is a window of embryonic transcription-independent cell divisions before onset of zygotic genome activation (ZGA). Chromatin determinants of ZGA are unexplored; however, marking of developmental genes by modified histones in sperm suggests a predictive role of histone marks for ZGA. In zebrafish, pre-ZGA development for ten cell cycles provides an opportunity to examine whether genomic enrichment in modified histones is present before initiation of transcription. By profiling histone H3 trimethylation on all zebrafish promoters before and after ZGA, we demonstrate here an epigenetic prepatterning of developmental gene expression. This involves pre-ZGA marking of transcriptionally inactive genes involved in homeostatic and developmental regulation by permissive H3K4me3 with or without repressive H3K9me3 or H3K27me3. Our data suggest that histone modifications are instructive for the developmental gene expression program.',
'date' => '2011-12-13',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22137762',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 54 => array(
'id' => '637',
'name' => 'H3.5 is a novel hominid-specific histone H3 variant that is specifically expressed in the seminiferous tubules of human testes.',
'authors' => 'Schenk R, Jenke A, Zilbauer M, Wirth S, Postberg J',
'description' => 'The incorporation of histone variants into chromatin plays an important role for the establishment of particular chromatin states. Six human histone H3 variants are known to date, not counting CenH3 variants: H3.1, H3.2, H3.3 and the testis-specific H3.1t as well as the recently described variants H3.X and H3.Y. We report the discovery of H3.5, a novel non-CenH3 histone H3 variant. H3.5 is encoded on human chromosome 12p11.21 and probably evolved in a common ancestor of all recent great apes (Hominidae) as a consequence of H3F3B gene duplication by retrotransposition. H3.5 mRNA is specifically expressed in seminiferous tubules of human testis. Interestingly, H3.5 has two exact copies of ARKST motifs adjacent to lysine-9 or lysine-27, and lysine-79 is replaced by asparagine. In the Hek293 cell line, ectopically expressed H3.5 is assembled into chromatin and targeted by PTM. H3.5 preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes and can replace an essential function of RNAi-depleted H3.3 in cell growth.',
'date' => '2011-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21274551',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 55 => array(
'id' => '274',
'name' => 'Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability.',
'authors' => 'Cortázar D, Kunz C, Selfridge J, Lettieri T, Saito Y, MacDougall E, Wirz A, Schuermann D, Jacobs AL, Siegrist F, Steinacher R, Jiricny J, Bird A, Schär P',
'description' => 'Thymine DNA glycosylase (TDG) is a member of the uracil DNA glycosylase (UDG) superfamily of DNA repair enzymes. Owing to its ability to excise thymine when mispaired with guanine, it was proposed to act against the mutability of 5-methylcytosine (5-mC) deamination in mammalian DNA. However, TDG was also found to interact with transcription factors, histone acetyltransferases and de novo DNA methyltransferases, and it has been associated with DNA demethylation in gene promoters following activation of transcription, altogether implicating an engagement in gene regulation rather than DNA repair. Here we use a mouse genetic approach to determine the biological function of this multifaceted DNA repair enzyme. We find that, unlike other DNA glycosylases, TDG is essential for embryonic development, and that this phenotype is associated with epigenetic aberrations affecting the expression of developmental genes. Fibroblasts derived from Tdg null embryos (mouse embryonic fibroblasts, MEFs) show impaired gene regulation, coincident with imbalanced histone modification and CpG methylation at promoters of affected genes. TDG associates with the promoters of such genes both in fibroblasts and in embryonic stem cells (ESCs), but epigenetic aberrations only appear upon cell lineage commitment. We show that TDG contributes to the maintenance of active and bivalent chromatin throughout cell differentiation, facilitating a proper assembly of chromatin-modifying complexes and initiating base excision repair to counter aberrant de novo methylation. We thus conclude that TDG-dependent DNA repair has evolved to provide epigenetic stability in lineage committed cells.',
'date' => '2011-02-17',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21278727',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 56 => array(
'id' => '592',
'name' => 'Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.',
'authors' => 'Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ',
'description' => 'The H3K9me3 histone modification is often found at promoter regions, where it functions to repress transcription. However, we have previously shown that 3' exons of zinc finger genes (ZNFs) are marked by high levels of H3K9me3. We have now further investigated this unusual location for H3K9me3 in ZNF genes. Neither bioinformatic nor experimental approaches support the hypothesis that the 3' exons of ZNFs are promoters. We further characterized the histone modifications at the 3' ZNF exons and found that these regions also contain H3K36me3, a mark of transcriptional elongation. A genome-wide analysis of ChIP-seq data revealed that ZNFs constitute the majority of genes that have high levels of both H3K9me3 and H3K36me3. These results suggested the possibility that the ZNF genes may be imprinted, with one allele transcribed and one allele repressed. To test the hypothesis that the contradictory modifications are due to imprinting, we used a SNP analysis of RNA-seq data to demonstrate that both alleles of certain ZNF genes having H3K9me3 and H3K36me3 are transcribed. We next analyzed isolated ZNF 3' exons using stably integrated episomes. We found that although the H3K36me3 mark was lost when the 3' ZNF exon was removed from its natural genomic location, the isolated ZNF 3' exons retained the H3K9me3 mark. Thus, the H3K9me3 mark at ZNF 3' exons does not impede transcription and it is regulated independently of the H3K36me3 mark. Finally, we demonstrate a strong relationship between the number of tandemly repeated domains in the 3' exons and the H3K9me3 mark. We suggest that the H3K9me3 at ZNF 3' exons may function to protect the genome from inappropriate recombination rather than to regulate transcription.',
'date' => '2011-02-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21347206',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 57 => array(
'id' => '599',
'name' => 'ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes.',
'authors' => 'Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ',
'description' => 'Only a small percentage of human transcription factors (e.g. those associated with a specific differentiation program) are expressed in a given cell type. Thus, cell fate is mainly determined by cell type-specific silencing of transcription factors that drive different cellular lineages. Several histone modifications have been associated with gene silencing, including H3K27me3 and H3K9me3. We have previously shown that genes for the two largest classes of mammalian transcription factors are marked by distinct histone modifications; homeobox genes are marked by H3K27me3 and zinc finger genes are marked by H3K9me3. Several histone methyltransferases (e.g. G9a and SETDB1) may be involved in mediating the H3K9me3 silencing mark. We have used ChIP-chip and ChIP-seq to demonstrate that SETDB1, but not G9a, is associated with regions of the genome enriched for H3K9me3. One current model is that SETDB1 is recruited to specific genomic locations via interaction with the corepressor TRIM28 (KAP1), which is in turn recruited to the genome via interaction with zinc finger transcription factors that contain a Kruppel-associated box (KRAB) domain. However, specific KRAB-ZNFs that recruit TRIM28 (KAP1) and SETDB1 to the genome have not been identified. We now show that ZNF274 (a KRAB-ZNF that contains 5 C2H2 zinc finger domains), can interact with KAP1 both in vivo and in vitro and, using ChIP-seq, we show that ZNF274 binding sites co-localize with SETDB1, KAP1, and H3K9me3 at the 3' ends of zinc finger genes. Knockdown of ZNF274 with siRNAs reduced the levels of KAP1 and SETDB1 recruitment to the binding sites. These studies provide the first identification of a KRAB domain-containing ZNF that is involved in recruitment of the KAP1 and SETDB1 to specific regions of the human genome.',
'date' => '2010-12-08',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21170338',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 58 => array(
'id' => '74',
'name' => 'In vivo chromatin organization of mouse rod photoreceptors correlates with histone modifications.',
'authors' => 'Kizilyaprak C, Spehner D, Devys D, Schultz P',
'description' => 'BACKGROUND: The folding of genetic information into chromatin plays important regulatory roles in many nuclear processes and particularly in gene transcription. Post translational histone modifications are associated with specific chromatin condensation states and with distinct transcriptional activities. The peculiar chromatin organization of rod photoreceptor nuclei, with a large central domain of condensed chromatin surrounded by a thin border of extended chromatin was used as a model to correlate in vivo chromatin structure, histone modifications and transcriptional activity. METHODOLOGY: We investigated the functional relationships between chromatin compaction, distribution of histone modifications and location of RNA polymerase II in intact murine rod photoreceptors using cryo-preparation methods, electron tomography and immunogold labeling. Our results show that the characteristic central heterochromatin of rod nuclei is organized into concentric domains characterized by a progressive loosening of the chromatin architecture from inside towards outside and by specific combinations of silencing histone marks. The peripheral heterochromatin is formed by closely packed 30 nm fibers as revealed by a characteristic optical diffraction signal. Unexpectedly, the still highly condensed most external heterochromatin domain contains acetylated histones, which are usually associated with active transcription and decondensed chromatin. Histone acetylation is thus not sufficient in vivo for complete chromatin decondensation. The euchromatin domain contains several degrees of chromatin compaction and the histone tails are hyperacetylated, enriched in H3K4 monomethylation and hypo trimethylated on H3K9, H3K27 and H4K20. The transcriptionally active RNA polymerases II molecules are confined in the euchromatin domain and are preferentially located at the vicinity of the interface with heterochromatin. CONCLUSIONS: Our results show that transcription is located in the most decondensed and highly acetylated chromatin regions, but since acetylation is found associated with compact chromatin it is not sufficient to decondense chromatin in vivo. We also show that a combination of histone marks defines distinct concentric heterochromatin domains.',
'date' => '2010-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/20543957',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 59 => array(
'id' => '95',
'name' => 'MicroChIP--a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies.',
'authors' => 'Dahl JA, Collas P',
'description' => 'Chromatin immunoprecipitation (ChIP) is a powerful technique for studying protein-DNA interactions. Drawbacks of current ChIP assays however are a requirement for large cell numbers, which limits applicability of ChIP to rare cell samples, and/or lengthy procedures with limited applications. There are to date no protocols for fast and parallel ChIPs of post-translationally modified histones from small cell numbers or biopsies, and importantly, no protocol allowing for investigations of transcription factor binding in small cell numbers. We report here the development of a micro (micro) ChIP assay suitable for up to nine parallel quantitative ChIPs of modified histones or RNA polymerase II from a single batch of 1000 cells. MicroChIP can also be downscaled to monitor the association of one protein with multiple genomic sites in as few as 100 cells. MicroChIP is applicable to small fresh tissue biopsies, and a cross-link-while-thawing procedure makes the assay suitable for frozen biopsies. Using MicroChIP, we characterize transcriptionally permissive and repressive histone H3 modifications on developmentally regulated promoters in human embryonal carcinoma cells and in osteosarcoma biopsies. muChIP creates possibilities for multiple parallel and rapid transcription factor binding and epigenetic analyses of rare cell and tissue samples.',
'date' => '2008-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/18202078',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 60 => array(
'id' => '76',
'name' => 'A rapid micro chromatin immunoprecipitation assay (microChIP).',
'authors' => 'Dahl JA, Collas P',
'description' => 'Interactions of proteins with DNA mediate many critical nuclear functions. Chromatin immunoprecipitation (ChIP) is a robust technique for studying protein-DNA interactions. Current ChIP assays, however, either require large cell numbers, which prevent their application to rare cell samples or small-tissue biopsies, or involve lengthy procedures. We describe here a 1-day micro ChIP (microChIP) protocol suitable for up to eight parallel histone and/or transcription factor immunoprecipitations from a single batch of 1,000 cells. MicroChIP technique is also suitable for monitoring the association of one protein with multiple genomic sites in 100 cells. Alterations in cross-linking and chromatin preparation steps also make microChIP applicable to approximately 1-mm(3) fresh- or frozen-tissue biopsies. From cell fixation to PCR-ready DNA, the procedure takes approximately 8 h for 16 ChIPs.',
'date' => '2008-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/18536650',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 61 => array(
'id' => '75',
'name' => 'Fast genomic muChIP-chip from 1,000 cells',
'authors' => 'Dahl JA, Reiner AH, Collas P.',
'description' => 'Genome-wide location analysis of histone modifications and transcription factor binding relies on chromatin immunoprecipitation (ChIP) assays. These assays are, however, time-consuming and require large numbers of cells, hindering their application to the analysis of many interesting cell types. We report here a fast microChIP (μChIP) assay for 1,000 cells in combination with microarrays to produce genome-scale surveys of histone modifications. μChIP-chip reliably reproduces data obtained by large-scale assays: H3K9ac and H3K9m3 enrichment profiles are conserved and nucleosome-free regions are revealed.',
'date' => '0000-00-00',
'pmid' => '',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 62 => array(
'id' => '73',
'name' => 'Promoter DNA Methylation Patterns of Differentiated Cells Are Largely Programmed at the Progenitor Stage',
'authors' => 'Sørensen AL, Jacobsen BM, Reiner AH, Andersen IS, Collas P',
'description' => 'Mesenchymal stem cells (MSCs) isolated from various tissues share common phenotypic and functional properties. However, intrinsic molecular evidence supporting these observations has been lacking. Here, we unravel overlapping genome-wide promoter DNA methylation patterns between MSCs from adipose tissue, bone marrow, and skeletal muscle, whereas hematopoietic progenitors are more epigenetically distant from MSCs as a whole. Commonly hypermethylated genes are enriched in signaling, metabolic, and developmental functions, whereas genes hypermethylated only in MSCs are associated with early development functions. We find that most lineage-specification promoters are DNA hypomethylated and harbor a combination of trimethylated H3K4 and H3K27, whereas early developmental genes are DNA hypermethylated with or without H3K27 methylation. Promoter DNA methylation patterns of differentiated cells are largely established at the progenitor stage; yet, differentiation segregates a minor fraction of the commonly hypermethylated promoters, generating greater epigenetic divergence between differentiated cell types than between their undifferentiated counterparts. We also show an effect of promoter CpG content on methylation dynamics upon differentiation and distinct methylation profiles on transcriptionally active and inactive promoters. We infer that methylation state of lineage-specific promoters in MSCs is not a primary determinant of differentiation capacity. Our results support the view of a common origin of mesenchymal progenitors.',
'date' => '0000-00-00',
'pmid' => '',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 63 => array(
'id' => '72',
'name' => 'Chromatin Environment of Histone Variant H3.3 Revealed by Quantitative Imaging and Genome-scale Chromatin and DNA Immunoprecipitation',
'authors' => 'Delbarre E, Jacobsen BM, Reiner AH, Sørensen AL, Kuntziger T, Collas P',
'description' => 'In contrast to canonical histones, histone variant H3.3 is incorporated into chromatin in a replication-independent manner. Posttranslational modifications of H3.3 have been identified; however, the epigenetic environment of incorporated H3.3 is unclear. We have investigated the genomic distribution of epitope-tagged H3.3 in relation to histone modifications, DNA methylation, and transcription in mesenchymal stem cells. Quantitative imaging at the nucleus level shows that H3.3, relative to replicative H3.2 or canonical H2B, is enriched in chromatin domains marked by histone modifications of active or potentially active genes. Chromatin immunoprecipitation of epitope-tagged H3.3 and array hybridization identified 1649 H3.3-enriched promoters, a fraction of which is coenriched in H3K4me3 alone or together with H3K27me3, whereas H3K9me3 is excluded, corroborating nucleus-level imaging data. H3.3-enriched promoters are predominantly CpG-rich and preferentially DNA methylated, relative to the proportion of methylated RefSeq promoters in the genome. Most but not all H3.3-enriched promoters are transcriptionally active, and coenrichment of H3.3 with repressive H3K27me3 correlates with an enhanced proportion of expressed genes carrying this mark. H3.3-target genes are enriched in mesodermal differentiation and signaling functions. Our data suggest that in mesenchymal stem cells, H3.3 targets lineage-priming genes with a potential for activation facilitated by H3K4me3 in facultative association with H3K27me3.',
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'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 9 (H3K9me3)</strong>, using a KLH-conjugated synthetic peptide.</span></p>',
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<p><small> <strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022 ) on the SX-8G IP-Star automated system. A titration of the antibody consisting of 1, 2, 5, and 10 μg per ChIP experiment was analysed. IgG (2 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active c-fos and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " caption="false" width="432" height="214" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="432" height="61" /> <img src="https://www.diagenode.com/img/product/antibodies/C15410056-FigD.jpg" alt="H3K9me3 Antibody validated in ChIP-seq " caption="false" width="700" height="112" /></p>
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<p><small> <strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 0.5 μg of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) on sheared chromatin from 1 million HeLa cells using the “iDeal ChIP-seq” kit (Cat. No. C01010051). The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoter regions of the active GAPDH and EIF4A2 genes, for the coding region of the ZNF510 gene and for the Sat2 satellite repeat (figure 2A). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the BWA algorithm. Figure 2B shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2C and D show the enrichment at ZNF510 and ZNF12 on chromosome 9 and 7, respectively. These results clearly show an enrichment of H3K9me3 at ZNF repeat genes. </small></p>
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<p><small> <strong>Figure 3. Determination of the antibody titer</strong><br /> To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (Cat. No. C15410056), crude serum and flow through in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:60,000. </small></p>
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<p><small> <strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<p><small> <strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot analysis was performed on histone extracts from HeLa cells (15 μg, lane 1) and on recombinant H3 (1 μg, lane2) using the Diagenode antibody against H3K9me3 (Cat. No. C15410056). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left. </small></p>
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<p><small> <strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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<p><small> <strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022 ) on the SX-8G IP-Star automated system. A titration of the antibody consisting of 1, 2, 5, and 10 μg per ChIP experiment was analysed. IgG (2 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active c-fos and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="432" height="61" /> <img src="https://www.diagenode.com/img/product/antibodies/C15410056-FigD.jpg" alt="H3K9me3 Antibody validated in ChIP-seq " caption="false" width="700" height="112" /></p>
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<p><small> <strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 0.5 μg of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) on sheared chromatin from 1 million HeLa cells using the “iDeal ChIP-seq” kit (Cat. No. C01010051). The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoter regions of the active GAPDH and EIF4A2 genes, for the coding region of the ZNF510 gene and for the Sat2 satellite repeat (figure 2A). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the BWA algorithm. Figure 2B shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2C and D show the enrichment at ZNF510 and ZNF12 on chromosome 9 and 7, respectively. These results clearly show an enrichment of H3K9me3 at ZNF repeat genes. </small></p>
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<p><small> <strong>Figure 3. Determination of the antibody titer</strong><br /> To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (Cat. No. C15410056), crude serum and flow through in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:60,000. </small></p>
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<p><small> <strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<p><small> <strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot analysis was performed on histone extracts from HeLa cells (15 μg, lane 1) and on recombinant H3 (1 μg, lane2) using the Diagenode antibody against H3K9me3 (Cat. No. C15410056). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left. </small></p>
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<p><small> <strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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<p>将 <input name="data[Cart][quantity]" placeholder="1" value="1" min="1" style="width:60px;display:inline" type="number" id="CartQuantity" required="required"/> <strong> H3K27ac Antibody</strong> 添加至我的购物车。</p>
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'C15410196',
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$('#CartQuantity').val());" name="checkout" id="checkout" value="checkout" type="submit">结账</button> </div>
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'
$related = array(
'id' => '2270',
'antibody_id' => '109',
'name' => 'H3K27ac Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the acetylated lysine 27</strong> (<strong>H3K27ac</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation Data',
'info1' => '<div class="row">
<div class="small-6 columns">A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1a.png" width="356" /><br /> B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1b.png" width="356" /></div>
<div class="small-6 columns">
<p><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>Figure 1A ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196) and optimized PCR primer pairs for qPCR. ChIP was performed with the “Auto Histone ChIP-seq” kit on the IP-Star automated system, using sheared chromatin from 1,000,000 cells. A titration consisting of 1, 2, 5 and 10 µg of antibody per ChIP experiment was analyzed. IgG (2 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active EIF4A2 and ACTB genes, used as positive controls, and for the inactive TSH2B and MYT1 genes, used as negative controls.</p>
<p>Figure 1B ChIP assays were performed using human K562 cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196)and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 100,000 cells. A titration consisting of 0.2, 0.5, 1 and 2 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active GAPDH and EIF4A2 genes, used as positive controls, and for the coding regions of the inactive MB and MYT1 genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis)</p>
</div>
</div>
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<div class="row">
<div class="small-12 columns"><center>
<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2a.png" /></p>
</center><center>
<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2b.png" /></p>
</center><center>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2c.png" /></p>
</center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>ChIP was performed on sheared chromatin from 100,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) as described above. The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A shows the peak distribution along the complete human X-chromosome. Figure 2 B and C show the peak distribution in two regions surrounding the EIF4A2 and GAPDH positive control genes, respectively. The position of the PCR amplicon, used for validating the ChIP assay is indicated with an arrow.</p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-fig3.jpg" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (cat. No. C15410196) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions surrounding the EIF2S3 gene on the X-chromosome and the CCT5 gene on chromosome 5 (figure 3A and B, respectively).</p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-ELISA-Fig3.png" /></div>
<div class="small-6 columns">
<p><strong>Figure 4. Determination of the antibody titer</strong></p>
<p>To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:8,300.</p>
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<p><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27ac</strong><br />To test the cross reactivity of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>), a Dot Blot analysis was performed with peptides containing other histone modifications and the unmodified H3K27. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 5 shows a high specificity of the antibody for the modification of interest.</p>
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<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-WB-Fig5.png" /></center></div>
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<p><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27ac</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27ac (Cat. No. C1541196). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The marker (in kDa) is shown on the left.</p>
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<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-IF-Fig6.png" /></div>
<div class="small-8 columns">
<p><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27ac</strong></p>
<p>HeLa cells were stained with the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/ TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K27ac antibody (top) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown at the bottom.</p>
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'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 9 (H3K9me3)</strong>, using a KLH-conjugated synthetic peptide.</span></p>',
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<p><small> <strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022 ) on the SX-8G IP-Star automated system. A titration of the antibody consisting of 1, 2, 5, and 10 μg per ChIP experiment was analysed. IgG (2 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active c-fos and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " caption="false" width="432" height="214" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="432" height="61" /> <img src="https://www.diagenode.com/img/product/antibodies/C15410056-FigD.jpg" alt="H3K9me3 Antibody validated in ChIP-seq " caption="false" width="700" height="112" /></p>
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<p><small> <strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 0.5 μg of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) on sheared chromatin from 1 million HeLa cells using the “iDeal ChIP-seq” kit (Cat. No. C01010051). The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoter regions of the active GAPDH and EIF4A2 genes, for the coding region of the ZNF510 gene and for the Sat2 satellite repeat (figure 2A). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the BWA algorithm. Figure 2B shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2C and D show the enrichment at ZNF510 and ZNF12 on chromosome 9 and 7, respectively. These results clearly show an enrichment of H3K9me3 at ZNF repeat genes. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" caption="false" width="278" height="212" /></p>
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<p><small> <strong>Figure 3. Determination of the antibody titer</strong><br /> To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (Cat. No. C15410056), crude serum and flow through in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:60,000. </small></p>
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" caption="false" width="400" height="304" /></p>
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<div class="small-8 columns">
<p><small> <strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western Blot" caption="false" width="200" height="213" /></p>
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<div class="small-8 columns">
<p><small> <strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot analysis was performed on histone extracts from HeLa cells (15 μg, lane 1) and on recombinant H3 (1 μg, lane2) using the Diagenode antibody against H3K9me3 (Cat. No. C15410056). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left. </small></p>
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<p><small> <strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
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'description' => 'In contrast to canonical histones, histone variant H3.3 is incorporated into chromatin in a replication-independent manner. Posttranslational modifications of H3.3 have been identified; however, the epigenetic environment of incorporated H3.3 is unclear. We have investigated the genomic distribution of epitope-tagged H3.3 in relation to histone modifications, DNA methylation, and transcription in mesenchymal stem cells. Quantitative imaging at the nucleus level shows that H3.3, relative to replicative H3.2 or canonical H2B, is enriched in chromatin domains marked by histone modifications of active or potentially active genes. Chromatin immunoprecipitation of epitope-tagged H3.3 and array hybridization identified 1649 H3.3-enriched promoters, a fraction of which is coenriched in H3K4me3 alone or together with H3K27me3, whereas H3K9me3 is excluded, corroborating nucleus-level imaging data. H3.3-enriched promoters are predominantly CpG-rich and preferentially DNA methylated, relative to the proportion of methylated RefSeq promoters in the genome. Most but not all H3.3-enriched promoters are transcriptionally active, and coenrichment of H3.3 with repressive H3K27me3 correlates with an enhanced proportion of expressed genes carrying this mark. H3.3-target genes are enriched in mesodermal differentiation and signaling functions. Our data suggest that in mesenchymal stem cells, H3.3 targets lineage-priming genes with a potential for activation facilitated by H3K4me3 in facultative association with H3K27me3.',
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'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone H3 containing the trimethylated lysine 9 (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1 and 2 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control.<br /> <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for the ZNF510 gene and the Sat2 satellite repeat, used as positive controls, and for the EIF4A2 and GAPDH promoters, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).<br /> <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K9me1, H3K9me2, H3K9me3, H3K4me3, H3K27me3, H3K36me3, H4K20me3 modifications and the unmodified H3K9 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K9me3 modification when using 0.5 or 1 µg. With 2 µg of antibody, some recovery of the H3K27me3 nucleosome is observed.</small></p>
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<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " /></p>
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<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq4000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoom-in to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B and 2C show the enrichment along the ZNF510 positive control target and at the KCNQ1 imprinted gene.</small></p>
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<p><small><strong>Figure 3. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410056) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:198,000.</small></p>
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<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410056) with peptides containing other modifications of histone H3 and H4 and the unmodified sequence of histone H3. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 4 shows a high specificity of the antibody for the modification of interest.</small></p>
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<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot was performed on 40 µg whole cell extracts from HeLa cells (lane 1) and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K9me3 (cat. No. C15410056). The antibody was diluted 1:2,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right, the marker (in kDa) is shown on the left.</small></p>
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<td>Fig 1, 2</td>
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<td>1:2,000</td>
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'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone H3 containing the trimethylated lysine 9 (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_ChIP.jpg" alt="H3K9me3 Antibody ChIP Grade" /></p>
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1 and 2 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control.<br /> <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for the ZNF510 gene and the Sat2 satellite repeat, used as positive controls, and for the EIF4A2 and GAPDH promoters, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).<br /> <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K9me1, H3K9me2, H3K9me3, H3K4me3, H3K27me3, H3K36me3, H4K20me3 modifications and the unmodified H3K9 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K9me3 modification when using 0.5 or 1 µg. With 2 µg of antibody, some recovery of the H3K27me3 nucleosome is observed.</small></p>
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<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq Grade" /></p>
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<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " /></p>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" /></p>
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<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq4000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoom-in to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B and 2C show the enrichment along the ZNF510 positive control target and at the KCNQ1 imprinted gene.</small></p>
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<p><strong></strong></p>
<p><strong></strong></p>
<p><small><strong>Figure 3. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410056) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:198,000.</small></p>
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<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410056) with peptides containing other modifications of histone H3 and H4 and the unmodified sequence of histone H3. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 4 shows a high specificity of the antibody for the modification of interest.</small></p>
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<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot was performed on 40 µg whole cell extracts from HeLa cells (lane 1) and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K9me3 (cat. No. C15410056). The antibody was diluted 1:2,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right, the marker (in kDa) is shown on the left.</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_ChIP.jpg" alt="H3K9me3 Antibody ChIP Grade" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1 and 2 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control.<br /> <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for the ZNF510 gene and the Sat2 satellite repeat, used as positive controls, and for the EIF4A2 and GAPDH promoters, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).<br /> <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K9me1, H3K9me2, H3K9me3, H3K4me3, H3K27me3, H3K36me3, H4K20me3 modifications and the unmodified H3K9 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K9me3 modification when using 0.5 or 1 µg. With 2 µg of antibody, some recovery of the H3K27me3 nucleosome is observed.</small></p>
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<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq Grade" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " /></p>
<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" /></p>
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<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410056) on sheared chromatin from 500,000 K562 cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq4000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoom-in to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B and 2C show the enrichment along the ZNF510 positive control target and at the KCNQ1 imprinted gene.</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" /></p>
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<div class="small-6 columns">
<p><strong></strong></p>
<p><strong></strong></p>
<p><small><strong>Figure 3. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410056) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:198,000.</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410056) with peptides containing other modifications of histone H3 and H4 and the unmodified sequence of histone H3. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 4 shows a high specificity of the antibody for the modification of interest.</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western blot" /></p>
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<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot was performed on 40 µg whole cell extracts from HeLa cells (lane 1) and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K9me3 (cat. No. C15410056). The antibody was diluted 1:2,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right, the marker (in kDa) is shown on the left.</small></p>
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'meta_title' => 'H3K9me3 Antibody - ChIP-seq Grade (C15410056) | Diagenode',
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'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, ELISA, DB, WB and IF. Batch specific data available on the website.',
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'name' => 'iDeal ChIP-seq kit for Histones',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/ideal-chipseq-for-histones-complete-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>Don’t risk wasting your precious sequencing samples. Diagenode’s validated <strong>iDeal ChIP-seq kit for Histones</strong> has everything you need for a successful start-to-finish <strong>ChIP of histones prior to Next-Generation Sequencing</strong>. The complete kit contains all buffers and reagents for cell lysis, chromatin shearing, immunoprecipitation and DNA purification. In addition, unlike competing solutions, the kit contains positive and negative control antibodies (H3K4me3 and IgG, respectively) as well as positive and negative control PCR primers pairs (GAPDH TSS and Myoglobin exon 2, respectively) for your convenience and a guarantee of optimal results. The kit has been validated on multiple histone marks.</p>
<p> The iDeal ChIP-seq kit for Histones<strong> </strong>is perfect for <strong>cells</strong> (<strong>100,000 cells</strong> to <strong>1,000,000 cells</strong> per IP) and has been validated for <strong>tissues</strong> (<strong>1.5 mg</strong> to <strong>5 mg</strong> of tissue per IP).</p>
<p> The iDeal ChIP-seq kit is the only kit on the market validated for the major sequencing systems. Our expertise in ChIP-seq tools allows reproducible and efficient results every time.</p>
<p></p>
<p> <strong></strong></p>
<p></p>',
'label1' => 'Characteristics',
'info1' => '<ul style="list-style-type: disc;">
<li>Highly <strong>optimized</strong> protocol for ChIP-seq from cells and tissues</li>
<li><strong>Validated</strong> for ChIP-seq with multiple histones marks</li>
<li>Most <strong>complete</strong> kit available (covers all steps, including the control antibodies and primers)</li>
<li>Optimized chromatin preparation in combination with the Bioruptor ensuring the best <strong>epitope integrity</strong></li>
<li>Magnetic beads make ChIP easy, fast and more <strong>reproducible</strong></li>
<li>Combination with Diagenode ChIP-seq antibodies provides high yields with excellent <strong>specificity</strong> and <strong>sensitivity</strong></li>
<li>Purified DNA suitable for any downstream application</li>
<li>Easy-to-follow protocol</li>
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<p>Note: to obtain optimal results, this kit should be used in combination with the DiaMag1.5 - magnetic rack.</p>
<h3>ChIP-seq on cells</h3>
<p><img src="https://www.diagenode.com/img/product/kits/iDeal-kit-C01010053-figure-1.jpg" alt="Figure 1A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 1A. The high consistency of the iDeal ChIP-seq kit on the Ion Torrent™ PGM™ (Life Technologies) and GAIIx (Illumina<sup>®</sup>)</strong><br /> ChIP was performed on sheared chromatin from 1 million HelaS3 cells using the iDeal ChIP-seq kit and 1 µg of H3K4me3 positive control antibody. Two different biological samples have been analyzed using two different sequencers - GAIIx (Illumina<sup>®</sup>) and PGM™ (Ion Torrent™). The expected ChIP-seq profile for H3K4me3 on the GAPDH promoter region has been obtained.<br /> Image A shows a several hundred bp along chr12 with high similarity of read distribution despite the radically different sequencers. Image B is a close capture focusing on the GAPDH that shows that even the peak structure is similar.</p>
<p class="text-center"><strong>Perfect match between ChIP-seq data obtained with the iDeal ChIP-seq workflow and reference dataset</strong></p>
<p><img src="https://www.diagenode.com/img/product/kits/perfect-match-between-chipseq-data.png" alt="Figure 1B" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 1B.</strong> The ChIP-seq dataset from this experiment has been compared with a reference dataset from the Broad Institute. We observed a perfect match between the top 40% of Diagenode peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>
<p><img src="https://www.diagenode.com/img/product/kits/iDeal-kit-C01010053-figure-2.jpg" alt="Figure 2" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 2. Efficient and easy chromatin shearing using the Bioruptor<sup>®</sup> and Shearing buffer iS1 from the iDeal ChIP-seq kit</strong><br /> Chromatin from 1 million of Hela cells was sheared using the Bioruptor<sup>®</sup> combined with the Bioruptor<sup>®</sup> Water cooler (Cat No. BioAcc-cool) during 3 rounds of 10 cycles of 30 seconds “ON” / 30 seconds “OFF” at HIGH power setting (position H). Diagenode 1.5 ml TPX tubes (Cat No. M-50001) were used for chromatin shearing. Samples were gently vortexed before and after performing each sonication round (rounds of 10 cycles), followed by a short centrifugation at 4°C to recover the sample volume at the bottom of the tube. The sheared chromatin was then decross-linked as described in the kit manual and analyzed by agarose gel electrophoresis.</p>
<p><img src="https://www.diagenode.com/img/product/kits/iDeal-kit-C01010053-figure-3.jpg" alt="Figure 3" style="display: block; margin-left: auto; margin-right: auto;" width="264" height="320" /></p>
<p><strong>Figure 3. Validation of ChIP by qPCR: reliable results using Diagenode’s ChIP-seq grade H3K4me3 antibody, isotype control and sets of validated primers</strong><br /> Specific enrichment on positive loci (GAPDH, EIF4A2, c-fos promoter regions) comparing to no enrichment on negative loci (TSH2B promoter region and Myoglobin exon 2) was detected by qPCR. Samples were prepared using the Diagenode iDeal ChIP-seq kit. Diagenode ChIP-seq grade antibody against H3K4me3 and the corresponding isotype control IgG were used for immunoprecipitation. qPCR amplification was performed with sets of validated primers.</p>
<h3>ChIP-seq on tissue</h3>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-figure-h3k4me3.jpg" alt="Figure 4A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure 4A.</strong> Chromatin Immunoprecipitation has been performed using chromatin from mouse liver tissue, the iDeal ChIP-seq kit for Histones and the Diagenode ChIP-seq-grade H3K4me3 (Cat. No. C15410003) antibody. The IP'd DNA was subsequently analysed on an Illumina® HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. This figure shows the peak distribution in a region surrounding the GAPDH positive control gene.</p>
<p><img src="https://www.diagenode.com/img/product/kits/match-of-the-top40-peaks-2.png" alt="Figure 4B" caption="false" style="display: block; margin-left: auto; margin-right: auto;" width="700" height="280" /></p>
<p><strong>Figure 4B.</strong> The ChIP-seq dataset from this experiment has been compared with a reference dataset from the Broad Institute. We observed a perfect match between the top 40% of Diagenode peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>',
'label2' => 'Species, cell lines, tissues tested',
'info2' => '<p>The iDeal ChIP-seq Kit for Histones is compatible with a broad variety of cell lines, tissues and species - some examples are shown below. Other species / cell lines / tissues can be used with this kit.</p>
<p><u>Cell lines:</u></p>
<p>Human: A549, A673, CD8+ T, Blood vascular endothelial cells, Lymphatic endothelial cells, fibroblasts, K562, MDA-MB231</p>
<p>Pig: Alveolar macrophages</p>
<p>Mouse: C2C12, primary HSPC, synovial fibroblasts, HeLa-S3, FACS sorted cells from embryonic kidneys, macrophages, mesodermal cells, myoblasts, NPC, salivary glands, spermatids, spermatocytes, skeletal muscle stem cells, stem cells, Th2</p>
<p>Hamster: CHO</p>
<p>Other cell lines / species: compatible, not tested</p>
<p><u>Tissues</u></p>
<p>Bee – brain</p>
<p>Daphnia – whole animal</p>
<p>Horse – brain, heart, lamina, liver, lung, skeletal muscles, ovary</p>
<p>Human – Erwing sarcoma tumor samples</p>
<p>Other tissues: compatible, not tested</p>
<p>Did you use the iDeal ChIP-seq for Histones Kit on other cell line / tissue / species? <a href="mailto:agnieszka.zelisko@diagenode.com?subject=Species, cell lines, tissues tested with the iDeal ChIP-seq Kit for TF&body=Dear Customer,%0D%0A%0D%0APlease, leave below your feedback about the iDeal ChIP-seq for Transcription Factors (cell / tissue type, species, other information...).%0D%0A%0D%0AThank you for sharing with us your experience !%0D%0A%0D%0ABest regards,%0D%0A%0D%0AAgnieszka Zelisko-Schmidt, PhD">Let us know!</a></p>',
'label3' => ' Additional solutions compatible with iDeal ChIP-seq Kit for Histones',
'info3' => '<p><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin EasyShear Kit - Ultra Low SDS </a>optimizes chromatin shearing, a critical step for ChIP.</p>
<p> The <a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq">MicroPlex Library Preparation Kit </a>provides easy and optimal library preparation of ChIPed samples.</p>
<p><a href="../categories/chip-seq-grade-antibodies">ChIP-seq grade anti-histone antibodies</a> provide high yields with excellent specificity and sensitivity.</p>
<p> Plus, for our IP-Star Automation users for automated ChIP, check out our <a href="../p/auto-ideal-chip-seq-kit-for-histones-x24-24-rxns">automated</a> version of this kit.</p>',
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'name' => 'True MicroChIP-seq Kit',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/truemicrochipseq-kit-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>The <b>True </b><b>MicroChIP-seq</b><b> kit </b>provides a robust ChIP protocol suitable for the investigation of histone modifications within chromatin from as few as <b>10 000 cells</b>, including <b>FACS sorted cells</b>. The kit can be used for chromatin preparation for downstream ChIP-qPCR or ChIP-seq analysis. The <b>complete kit</b> contains everything you need for start-to-finish ChIP including all validated buffers and reagents for chromatin shearing, immunoprecipitation and DNA purification for exceptional <strong>ChIP-qPCR</strong> or <strong>ChIP-seq</strong> results. In addition, positive control antibodies and negative control PCR primers are included for your convenience and assurance of result sensitivity and specificity.</p>
<p>The True MicroChIP-seq kit offers unique benefits:</p>
<ul>
<li>An <b>optimized chromatin preparation </b>protocol compatible with low number of cells (<b>10.000</b>) in combination with the Bioruptor™ shearing device</li>
<li>Most <b>complete kit </b>available (covers all steps and includes control antibodies and primers)</li>
<li><b>Magnetic beads </b>make ChIP easy, fast, and more reproducible</li>
<li>MicroChIP DiaPure columns (included in the kit) enable the <b>maximum recovery </b>of immunoprecipitation DNA suitable for any downstream application</li>
<li><b>Excellent </b><b>ChIP</b><b>-seq </b>result when combined with <a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq">MicroPlex</a><a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq"> Library Preparation kit </a>adapted for low input</li>
</ul>
<p>For fast ChIP-seq on low input – check out Diagenode’s <a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns">µ</a><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns">ChIPmentation</a><a href="https://www.diagenode.com/en/p/uchipmentation-for-histones-24-rxns"> for histones</a>.</p>
<p><sub>The True MicroChIP-seq kit, Cat. No. C01010132 is an upgraded version of the kit True MicroChIP, Cat. No. C01010130, with the new validated protocols (e.g. FACS sorted cells) and MicroChIP DiaPure columns included in the kit.</sub></p>',
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<li><b>Revolutionary:</b> Only 10,000 cells needed for complete ChIP-seq procedure</li>
<li><b>Validated on</b> studies for histone marks</li>
<li><b>Automated protocol </b>for the IP-Star<sup>®</sup> Compact Automated Platform available</li>
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<p>The True MicroChIP-seq kit protocol has been optimized for the use of 10,000 - 100,000 cells per immunoprecipitation reaction. Regarding chromatin immunoprecipitation, three protocol variants have been optimized:<br />starting with a batch, starting with an individual sample and starting with the FACS-sorted cells.</p>
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<h3>High efficiency ChIP on 10,000 cells</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><img src="https://www.diagenode.com/img/product/kits/true-micro-chip-histone-results.png" width="800px" /></div>
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<p><small><strong>Figure 1. </strong>ChIP efficiency on 10,000 cells. ChIP was performed on human Hela cells using the Diagenode antibodies <a href="https://www.diagenode.com/en/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">H3K4me3</a> (Cat. No. C15410003), <a href="https://www.diagenode.com/en/p/h3k27ac-polyclonal-antibody-classic-50-mg-42-ml">H3K27ac</a> (C15410174), <a href="https://www.diagenode.com/en/p/h3k9me3-polyclonal-antibody-classic-50-ug">H3K9me3</a> (C15410056) and <a href="https://www.diagenode.com/en/p/h3k27me3-polyclonal-antibody-classic-50-mg-34-ml">H3K27me3</a> (C15410069). Sheared chromatin from 10,000 cells and 0.1 µg (H3K27ac), 0.25 µg (H3K4me3 and H3K27me3) or 0.5 µg (H3K9me3) of the antibody were used per IP. Corresponding amount of IgG was used as control. Quantitative PCR was performed with primers for corresponding positive and negative loci. Figure shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
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<h3>True MicroChIP-seq protocol in a combination with MicroPlex library preparation kit results in reliable and accurate sequencing data</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><img src="https://www.diagenode.com/img/product/kits/fig2-truemicro.jpg" alt="True MicroChip results" width="800px" /></div>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center>
<p><small><strong>Figure 2.</strong> Integrative genomics viewer (IGV) visualization of ChIP-seq experiments using 50.000 of K562 cells. ChIP has been performed accordingly to True MicroChIP protocol followed by the library preparation using MicroPlex Library Preparation Kit (C05010001). The above figure shows the peaks from ChIP-seq experiments using the following antibodies: H3K4me1 (C15410194), H3K9/14ac (C15410200), H3K27ac (C15410196) and H3K36me3 (C15410192).</small></p>
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<h3>Successful chromatin profiling from 10.000 of FACS-sorted cells</h3>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><img src="https://www.diagenode.com/img/product/kits/fig3ab-truemicro.jpg" alt="small non coding RNA" width="800px" /></div>
<div class="large-10 small-12 medium-10 large-centered medium-centered small-centered columns"><center>
<p><small><strong>Figure 3.</strong> (A) Integrative genomics viewer (IGV) visualization of ChIP-seq experiments and heatmap 3kb upstream and downstream of the TSS (B) for H3K4me3. ChIP has been performed using 10.000 of FACS-sorted cells (K562) and H3K4me3 antibody (C15410003) accordingly to True MicroChIP protocol followed by the library preparation using MicroPlex Library Preparation Kit (C05010001). Data were compared to ENCODE standards.</small></p>
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'label2' => 'Additional solutions compatible with the True MicroChIP-seq Kit',
'info2' => '<p><span style="font-weight: 400;">The <a href="https://www.diagenode.com/en/p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin EasyShear Kit – High SDS</a></span><span style="font-weight: 400;"> Recommended for the optimizing chromatin shearing.</span></p>
<p><a href="https://www.diagenode.com/en/categories/chip-seq-grade-antibodies"><span style="font-weight: 400;">ChIP-seq grade antibodies</span></a><span style="font-weight: 400;"> for high yields, specificity, and sensitivity.</span></p>
<p><span style="font-weight: 400;">Check the list of available </span><a href="https://www.diagenode.com/en/categories/primer-pairs"><span style="font-weight: 400;">primer pairs</span></a><span style="font-weight: 400;"> designed for high specificity to specific genomic regions.</span></p>
<p><span style="font-weight: 400;">For library preparation of immunoprecipitated samples we recommend to use the </span><b> </b><a href="https://www.diagenode.com/en/categories/library-preparation-for-ChIP-seq"><span style="font-weight: 400;">MicroPlex Library Preparation Kit</span></a><span style="font-weight: 400;"> - validated for library preparation from picogram inputs.</span></p>
<p><span style="font-weight: 400;">For IP-Star Automation users, check out the </span><a href="https://www.diagenode.com/en/p/auto-true-microchip-kit-16-rxns"><span style="font-weight: 400;">automated version</span></a><span style="font-weight: 400;"> of this kit.</span></p>
<p><span style="font-weight: 400;">Application note: </span><a href="https://www.diagenode.com/files/application_notes/Diagenode_AATI_Joint.pdf"><span style="font-weight: 400;">Best Workflow Practices for ChIP-seq Analysis with Small Samples</span></a></p>
<p></p>',
'label3' => 'Species, cell lines, tissues tested',
'info3' => '<p>The True MicroChIP-seq kit is compatible with a broad variety of cell lines, tissues and species - some examples are shown below. Other species / cell lines / tissues can be used with this kit.</p>
<p><strong>Cell lines:</strong></p>
<p>Bovine: blastocysts,<br />Drosophila: embryos, salivary glands<br />Human: EndoC-ẞH1 cells, HeLa cells, PBMC, urothelial cells<br />Mouse: adipocytes, B cells, blastocysts, pre-B cells, BMDM cells, chondrocytes, embryonic stem cells, KH2 cells, LSK cells, macrophages, MEP cells, microglia, NK cells, oocytes, pancreatic cells, P19Cl6 cells, RPE cells,</p>
<p>Other cell lines / species: compatible, not tested</p>
<p><strong>Tissues:</strong></p>
<p>Horse: adipose tissue</p>
<p>Mice: intestine tissue</p>
<p>Other tissues: not tested</p>',
'format' => '20 rxns',
'catalog_number' => 'C01010132',
'old_catalog_number' => 'C01010130',
'sf_code' => 'C01010132-',
'type' => 'RFR',
'search_order' => '04-undefined',
'price_EUR' => '625',
'price_USD' => '680',
'price_GBP' => '575',
'price_JPY' => '97905',
'price_CNY' => '',
'price_AUD' => '1700',
'country' => 'ALL',
'except_countries' => 'None',
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'slug' => 'true-microchip-kit-x16-16-rxns',
'meta_title' => 'True MicroChIP-seq Kit | Diagenode C01010132',
'meta_keywords' => '',
'meta_description' => 'True MicroChIP-seq Kit provides a robust ChIP protocol suitable for the investigation of histone modifications within chromatin from as few as 10 000 cells, including FACS sorted cells. Compatible with ChIP-qPCR as well as ChIP-seq.',
'modified' => '2023-04-20 16:06:10',
'created' => '2015-06-29 14:08:20',
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'id' => '1927',
'antibody_id' => null,
'name' => 'MicroPlex Library Preparation Kit v2 (12 indexes)',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/MicroPlex-Libary-Prep-Kit-v2-manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p><span><strong>Specifically optimized for ChIP-seq</strong></span><br /><br /><span>The MicroPlex Library Preparation™ kit is the only kit on the market which is validated for ChIP-seq and which allows the preparation of indexed libraries from just picogram inputs. In combination with the </span><a href="./true-microchip-kit-x16-16-rxns">True MicroChIP kit</a><span>, it allows for performing ChIP-seq on as few as 10,000 cells. Less input, fewer steps, fewer supplies, faster time to results! </span></p>
<p>The MicroPlex v2 kit (Cat. No. C05010012) contains all necessary reagents including single indexes for multiplexing up to 12 samples using single barcoding. For higher multiplexing (using dual indexes) check <a href="https://www.diagenode.com/en/p/microplex-lib-prep-kit-v3-48-rxns">MicroPlex Library Preparation Kits v3</a>.</p>',
'label1' => 'Characteristics',
'info1' => '<ul>
<li><strong>1 tube, 2 hours, 3 steps</strong> protocol</li>
<li><strong>Input: </strong>50 pg – 50 ng</li>
<li><strong>Reduce potential bias</strong> - few PCR amplification cycles needed</li>
<li><strong>High sensitivity ChIP-seq</strong> - low PCR duplication rate</li>
<li><strong>Great multiplexing flexibility</strong> with 12 barcodes (8 nt) included</li>
<li><strong>Validated with the <a href="https://www.diagenode.com/p/sx-8g-ip-star-compact-automated-system-1-unit" title="IP-Star Automated System">IP-Star<sup>®</sup> Automated Platform</a></strong></li>
</ul>
<h3>How it works</h3>
<center><img src="https://www.diagenode.com/img/product/kits/microplex-method-overview-v2.png" /></center>
<p style="margin-bottom: 0;"><small><strong>Microplex workflow - protocol with single indexes</strong><br />An input of 50 pg to 50 ng of fragmented dsDNA is converted into sequencing-ready libraries for Illumina® NGS platforms using a fast and simple 3-step protocol</small></p>
<ul class="accordion" data-accordion="" id="readmore" style="margin-left: 0;">
<li class="accordion-navigation"><a href="#first" style="background: #ffffff; padding: 0rem; margin: 0rem; color: #13b2a2;"><small>Read more about MicroPlex workflow</small></a>
<div id="first" class="content">
<p><small><strong>Step 1. Template Preparation</strong> provides efficient repair of the fragmented double-stranded DNA input.</small></p>
<p><small>In this step, the DNA is repaired and yields molecules with blunt ends.</small></p>
<p><small><strong>Step 2. Library Synthesis.</strong> enables ligation of MicroPlex patented stem- loop adapters.</small></p>
<p><small>In the next step, stem-loop adaptors with blocked 5’ ends are ligated with high efficiency to the 5’ end of the genomic DNA, leaving a nick at the 3’ end. The adaptors cannot ligate to each other and do not have single- strand tails, both of which contribute to non-specific background found with many other NGS preparations.</small></p>
<p><small><strong>Step 3. Library Amplification</strong> enables extension of the template, cleavage of the stem-loop adaptors, and amplification of the library. Illumina- compatible indexes are also introduced using a high-fidelity, highly- processive, low-bias DNA polymerase.</small></p>
<p><small>In the final step, the 3’ ends of the genomic DNA are extended to complete library synthesis and Illumina-compatible indexes are added through a high-fidelity amplification. Any remaining free adaptors are destroyed. Hands-on time and the risk of contamination are minimized by using a single tube and eliminating intermediate purifications.</small></p>
<p><small>Obtained libraries are purified, quantified and sized. The libraries pooling can be performed as well before sequencing.</small></p>
</div>
</li>
</ul>
<p></p>
<h3>Reliable detection of enrichments in ChIP-seq</h3>
<p><img src="https://www.diagenode.com/img/product/kits/microplex-library-prep-kit-figure-a.png" alt="Reliable detection of enrichments in ChIP-seq figure 1" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure A.</strong> ChIP has been peformed with H3K4me3 antibody, amplification of 17 pg of DNA ChIP'd from 10.000 cells and amplification of 35 pg of DNA ChIP'd from 100.000 cells (control experiment). The IP'd DNA was amplified and transformed into a sequencing-ready preparation for the Illumina plateform with the MicroPlex Library Preparation kit. The library was then analysed on an Illumina<sup>®</sup> Genome Analyzer. Cluster generation and sequencing were performed according to the manufacturer's instructions.</p>
<p><img src="https://www.diagenode.com/img/product/kits/microplex-library-prep-kit-figure-b.png" alt="Reliable detection of enrichments in ChIP-seq figure 2" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><strong>Figure B.</strong> We observed a perfect match between the top 40% of True MicroChIP peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.</p>',
'label2' => '',
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'info3' => '',
'format' => '12 rxns',
'catalog_number' => 'C05010012',
'old_catalog_number' => 'C05010010',
'sf_code' => 'C05010012-',
'type' => 'FRE',
'search_order' => '04-undefined',
'price_EUR' => '935',
'price_USD' => '1215',
'price_GBP' => '835',
'price_JPY' => '146470',
'price_CNY' => '',
'price_AUD' => '3038',
'country' => 'ALL',
'except_countries' => 'None',
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'slug' => 'microplex-library-preparation-kit-v2-x12-12-indices-12-rxns',
'meta_title' => 'MicroPlex Library Preparation Kit v2 x12 (12 indices)',
'meta_keywords' => '',
'meta_description' => 'MicroPlex Library Preparation Kit v2 x12 (12 indices)',
'modified' => '2023-04-20 15:01:16',
'created' => '2015-06-29 14:08:20',
'ProductsRelated' => array(
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(int) 3 => array(
'id' => '2264',
'antibody_id' => '121',
'name' => 'H3K9me3 Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone<strong> H3 containing the trimethylated lysine 9</strong> (<strong>H3K9me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation Data',
'info1' => '<div class="row">
<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig1.png" /></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (cat. No. C15410193) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). A titration of the antibody consisting of 0.5, 1, 2, and 5 µg per ChIP experiment was analysed. IgG (1 µg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2a.png" width="700" /></center><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2b.png" width="700" /></center><center>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2c.png" width="700" /></center><center>D.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-ChIP-Fig2d.png" width="700" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br />ChIP was performed with 0.5 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410193) on sheared chromatin from 1,000,000 HeLa cells using the “iDeal ChIP-seq” kit as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq 2000. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. The arrows indicate two satellite repeat regions which exhibit a stronger signal. Figures 2B, 2C and 2D show the enrichment along the ZNF510 positive control target and at the H19 and KCNQ1 imprinted genes.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-CT-Fig3a.png" width="700" /></center><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410193-CT-Fig3b.png" width="700" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K9me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K9me3 (cat. No. C15410193) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in a genomic regions on chromosome 1 containing several ZNF repeat genes and in a genomic region surrounding the KCNQ1 imprinting control gene on chromosome 11 (figure 3A and B, respectively).</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-Elisa-Fig4.png" /></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (cat. No. C15410193) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:87,000.</small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-DB-Fig5.png" /></center></div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (cat. No. C15410193) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 5 shows a high specificity of the antibody for the modification of interest.</small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-WB-Fig6.png" /></center></div>
<div class="small-8 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K9me3 (cat. No. C15410193). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410193-IF-Fig7.png" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br />HeLa cells were stained with the Diagenode antibody against H3K9me3 (cat. No. C15410193) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (middle) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The left panel shows staining of the nuclei with DAPI. A merge of both stainings is shown on the right.</small></p>
</div>
</div>',
'label2' => 'Target Description',
'info2' => '<p>Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Trimethylation of histone H3K9 is associated with inactive genomic regions, satellite repeats and ZNF gene repeats.</p>',
'label3' => '',
'info3' => '',
'format' => '50 μg',
'catalog_number' => 'C15410193',
'old_catalog_number' => 'pAb-193-050',
'sf_code' => 'C15410193-D001-000581',
'type' => 'FRE',
'search_order' => '03-Antibody',
'price_EUR' => '480',
'price_USD' => '470',
'price_GBP' => '430',
'price_JPY' => '75190',
'price_CNY' => '0',
'price_AUD' => '1175',
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'slug' => 'h3k9me3-polyclonal-antibody-premium-50-mg',
'meta_title' => 'H3K9me3 Antibody - ChIP-seq Grade (C15410193) | Diagenode',
'meta_keywords' => '',
'meta_description' => 'H3K9me3 (Histone H3 trimethylated at lysine 9) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, CUT&Tag, ELISA, DB, WB and IF. Specificity confirmed by Peptide array assay. Batch-specific data available on the website. Sample size available.',
'modified' => '2021-10-20 09:55:53',
'created' => '2015-06-29 14:08:20',
'ProductsRelated' => array(
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(int) 4 => array(
'id' => '2173',
'antibody_id' => '115',
'name' => 'H3K4me3 Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 4</strong> (<strong>H3K4me3</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation data',
'info1' => '<div class="row">
<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" /></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me3</strong><br />ChIP assays were performed using human K562 cells, the Diagenode antibody against H3K4me3 (cat. No. C15410003) and optimized PCR primer pairs for qPCR. ChIP was performed with the iDeal ChIP-seq kit (cat. No. C01010051), using sheared chromatin from 500,000 cells. A titration consisting of 0.5, 1, 2 and 5 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers specific for the promoter of the active genes GAPDH and EIF4A2, used as positive controls, and for the inactive MYOD1 gene and the Sat2 satellite repeat, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
</div>
</div>
<p></p>
<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2a-ChIP-seq.jpg" width="800" /></center><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2b-ChIP-seq.jpg" width="800" /></center><center>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2c-ChIP-seq.jpg" width="800" /></center><center>D.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig2d-ChIP-seq.jpg" width="800" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me3</strong><br />ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using 1 µg of the Diagenode antibody against H3K4me3 (cat. No. C15410003) as described above. The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2 shows the peak distribution along the complete sequence and a 600 kb region of the X-chromosome (figure 2A and B) and in two regions surrounding the GAPDH and EIF4A2 positive control genes, respectively (figure 2C and D). These results clearly show an enrichment of the H3K4 trimethylation at the promoters of active genes.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-cuttag-a.png" width="800" /></center></div>
<div class="small-12 columns"><center>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410003-cuttag-b.png" width="800" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K4me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 0.5 µg of the Diagenode antibody against H3K4me3 (cat. No. C15410003) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions surrounding the FOS gene on chromosome 14 and the ACTB gene on chromosome 7 (figure 3A and B, respectively).</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig3-ELISA.jpg" width="350" /></center><center></center><center></center><center></center><center></center></div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody against H3K4me3 (cat. No. C15410003). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:11,000.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig4-DB.jpg" /></div>
<div class="small-6 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K4me3</strong><br />To test the cross reactivity of the Diagenode antibody against H3K4me3 (cat. No. C15410003), a Dot Blot analysis was performed with peptides containing other histone modifications and the unmodified H3K4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:2,000. Figure 5A shows a high specificity of the antibody for the modification of interest.</small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig5-WB.jpg" /></div>
<div class="small-8 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K4me3</strong><br />Western blot was performed on whole cell extracts (40 µg, lane 1) from HeLa cells, and on 1 µg of recombinant histone H3 (lane 2) using the Diagenode antibody against H3K4me3 (cat. No. C15410003). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig6-if.jpg" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K4me3</strong><br />HeLa cells were stained with the Diagenode antibody against H3K4me3 (cat. No. C15410003) and with DAPI. Cells were fixed with 4% formaldehyde for 20’ and blocked with PBS/TX-100 containing 5% normal goat serum. The cells were immunofluorescently labelled with the H3K4me3 antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa568 or with DAPI (middle), which specifically labels DNA. The right picture shows a merge of both stainings.</small></p>
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'meta_description' => 'H3K4me3 (Histone H3 trimethylated at lysine 4) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, CUT&Tag, ELISA, DB, WB and IF. Specificity confirmed by Peptide array. Batch-specific data available on the website. Sample size available.',
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'description' => '<p>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 27</strong> (<strong>H3K27me3</strong>), using a KLH-conjugated synthetic peptide.</p>',
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<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig1.png" alt="H3K27me3 Antibody ChIP Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2.png" alt="H3K27me3 Antibody for ChIP" /></p>
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 1 million cells. The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation. A titration consisting of 0.5, 1, 2 and 5 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control.</small></p>
<p><small><strong>Figure 1A.</strong> Quantitative PCR was performed with primers specific for the promoter of the active GAPDH and EIF4A2 genes, used as negative controls, and for the inactive TSH2B and MYT1 genes, used as positive controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
<p><small><strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K27me1, H3K27me2, H3K27me3, H3K4me3, H3K9me3 and H3K36me3 modifications and the unmodified H3K27 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K27me3 modification.</small></p>
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<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2a.png" alt="H3K27me3 Antibody ChIP-seq Grade" /></p>
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<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2b.png" alt="H3K27me3 Antibody for ChIP-seq" /></p>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2c.png" alt="H3K27me3 Antibody for ChIP-seq assay" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2d.png" alt="H3K27me3 Antibody validated in ChIP-seq" /></p>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP was performed on sheared chromatin from 1 million HeLa cells using 1 µg of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2 shows the enrichment in genomic regions of chromosome 6 and 20, surrounding the TSH2B and MYT1 positive control genes (fig 2A and 2B, respectively), and in two genomic regions of chromosome 1 and X (figure 2C and D).</small></p>
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<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3A.png" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3B.png" /></p>
</div>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27me3 (cat. No. C15410195) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions on chromosome and 13 and 20 (figure 3A and B, respectively).</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-ELISA-Fig4.png" alt="H3K27me3 Antibody ELISA Validation " /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K27me3 (Cat. No. C15410195). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:3,000.</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-DB-Fig5a.png" alt="H3K27me3 Antibody Dot Blot Validation " /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) with peptides containing other modifications of histone H3 and H4 and the unmodified H3K27 sequence. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:5,000. Figure 5 shows a high specificity of the antibody for the modification of interest. Please note that the antibody also recognizes the modification if S28 is phosphorylated.</small></p>
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<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-WB-Fig6.png" alt="H3K27me3 Antibody validated in Western Blot" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27me3</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27me3 (cat. No. C15410195) diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-IF-Fig7.png" alt="H3K27me3 Antibody validated for Immunofluorescence" /></p>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27me3</strong><br />Human HeLa cells were stained with the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K27me3 antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.</small></p>
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'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the acetylated lysine 27</strong> (<strong>H3K27ac</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<div class="small-6 columns">A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1a.png" width="356" /><br /> B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1b.png" width="356" /></div>
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<p><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>Figure 1A ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196) and optimized PCR primer pairs for qPCR. ChIP was performed with the “Auto Histone ChIP-seq” kit on the IP-Star automated system, using sheared chromatin from 1,000,000 cells. A titration consisting of 1, 2, 5 and 10 µg of antibody per ChIP experiment was analyzed. IgG (2 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active EIF4A2 and ACTB genes, used as positive controls, and for the inactive TSH2B and MYT1 genes, used as negative controls.</p>
<p>Figure 1B ChIP assays were performed using human K562 cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196)and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 100,000 cells. A titration consisting of 0.2, 0.5, 1 and 2 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active GAPDH and EIF4A2 genes, used as positive controls, and for the coding regions of the inactive MB and MYT1 genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis)</p>
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<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2a.png" /></p>
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<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2b.png" /></p>
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<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2c.png" /></p>
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<div class="row">
<div class="small-12 columns">
<p><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>ChIP was performed on sheared chromatin from 100,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) as described above. The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A shows the peak distribution along the complete human X-chromosome. Figure 2 B and C show the peak distribution in two regions surrounding the EIF4A2 and GAPDH positive control genes, respectively. The position of the PCR amplicon, used for validating the ChIP assay is indicated with an arrow.</p>
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<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-fig3.jpg" /></center></div>
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<div class="row">
<div class="small-12 columns">
<p><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (cat. No. C15410196) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions surrounding the EIF2S3 gene on the X-chromosome and the CCT5 gene on chromosome 5 (figure 3A and B, respectively).</p>
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<div class="row">
<div class="small-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-ELISA-Fig3.png" /></div>
<div class="small-6 columns">
<p><strong>Figure 4. Determination of the antibody titer</strong></p>
<p>To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:8,300.</p>
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<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-DB-Fig4.png" /></center></div>
<div class="small-8 columns">
<p><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27ac</strong><br />To test the cross reactivity of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>), a Dot Blot analysis was performed with peptides containing other histone modifications and the unmodified H3K27. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 5 shows a high specificity of the antibody for the modification of interest.</p>
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<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-WB-Fig5.png" /></center></div>
<div class="small-8 columns">
<p><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27ac</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27ac (Cat. No. C1541196). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The marker (in kDa) is shown on the left.</p>
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<div class="row">
<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-IF-Fig6.png" /></div>
<div class="small-8 columns">
<p><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27ac</strong></p>
<p>HeLa cells were stained with the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/ TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K27ac antibody (top) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown at the bottom.</p>
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'description' => '<p><strong>Western blot</strong> : The quality of antibodies used in this technique is crucial for correct and specific protein identification. Diagenode offers huge selection of highly sensitive and specific western blot-validated antibodies.</p>
<p>Learn more about: <a href="https://www.diagenode.com/applications/western-blot">Loading control, MW marker visualization</a><em>. <br /></em></p>
<p><em></em>Check our selection of antibodies validated in Western blot.</p>',
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'description' => '<p><b>Unparalleled ChIP-Seq results with the most rigorously validated antibodies</b></p>
<p><span style="font-weight: 400;">Diagenode provides leading solutions for epigenetic research. Because ChIP-seq is a widely-used technique, we validate our antibodies in ChIP and ChIP-seq experiments (in addition to conventional methods like Western blot, Dot blot, ELISA, and immunofluorescence) to provide the highest quality antibody. We standardize our validation and production to guarantee high product quality without technical bias. Diagenode guarantees ChIP-seq grade antibody performance under our suggested conditions.</span></p>
<div class="row">
<div class="small-12 medium-9 large-9 columns">
<p><strong>ChIP-seq profile</strong> of active (H3K4me3 and H3K36me3) and inactive (H3K27me3) marks using Diagenode antibodies.</p>
<img src="https://www.diagenode.com/img/categories/antibodies/chip-seq-grade-antibodies.png" /></div>
<div class="small-12 medium-3 large-3 columns">
<p><small> ChIP was performed on sheared chromatin from 100,000 K562 cells using iDeal ChIP-seq kit for Histones (cat. No. C01010051) with 1 µg of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 µg of the antibody against H3K36me3 (cat. No. C15410192). The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. The figure shows the signal distribution along the complete sequence of human chromosome 3, a zoomin to a 10 Mb region and a further zoomin to a 1.5 Mb region. </small></p>
</div>
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<p>Diagenode’s highly validated antibodies:</p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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'description' => '<p>Histones are the main protein components of chromatin involved in the compaction of DNA into nucleosomes, the basic units of chromatin. A <strong>nucleosome</strong> consists of one pair of each of the core histones (<strong>H2A</strong>, <strong>H2B</strong>, <strong>H3</strong> and <strong>H4</strong>) forming an octameric structure wrapped by 146 base pairs of DNA. The different nucleosomes are linked by the linker histone<strong> H1, </strong>allowing for further condensation of chromatin.</p>
<p>The core histones have a globular structure with large unstructured N-terminal tails protruding from the nucleosome. They can undergo to multiple post-translational modifications (PTM), mainly at the N-terminal tails. These <strong>post-translational modifications </strong>include methylation, acetylation, phosphorylation, ubiquitinylation, citrullination, sumoylation, deamination and crotonylation. The most well characterized PTMs are <strong>methylation,</strong> <strong>acetylation and phosphorylation</strong>. Histone methylation occurs mainly on lysine (K) residues, which can be mono-, di- or tri-methylated, and on arginines (R), which can be mono-methylated and symmetrically or asymmetrically di-methylated. Histone acetylation occurs on lysines and histone phosphorylation mainly on serines (S), threonines (T) and tyrosines (Y).</p>
<p>The PTMs of the different residues are involved in numerous processes such as DNA repair, DNA replication and chromosome condensation. They influence the chromatin organization and can be positively or negatively associated with gene expression. Trimethylation of H3K4, H3K36 and H3K79, and lysine acetylation generally result in an open chromatin configuration (figure below) and are therefore associated with <strong>euchromatin</strong> and gene activation. Trimethylation of H3K9, K3K27 and H4K20, on the other hand, is enriched in <strong>heterochromatin </strong>and associated with gene silencing. The combination of different histone modifications is called the "<strong>histone code</strong>”, analogous to the genetic code.</p>
<p><img src="https://www.diagenode.com/img/categories/antibodies/histone-marks-illustration.png" /></p>
<p>Diagenode is proud to offer a large range of antibodies against histones and histone modifications. Our antibodies are highly specific and have been validated in many applications, including <strong>ChIP</strong> and <strong>ChIP-seq</strong>.</p>
<p>Diagenode’s collection includes antibodies recognizing:</p>
<ul>
<li><strong>Histone H1 variants</strong></li>
<li><strong>Histone H2A, H2A variants and histone H2A</strong> <strong>modifications</strong> (serine phosphorylation, lysine acetylation, lysine ubiquitinylation)</li>
<li><strong>Histone H2B and H2B</strong> <strong>modifications </strong>(serine phosphorylation, lysine acetylation)</li>
<li><strong>Histone H3 and H3 modifications </strong>(lysine methylation (mono-, di- and tri-methylated), lysine acetylation, serine phosphorylation, threonine phosphorylation, arginine methylation (mono-methylated, symmetrically and asymmetrically di-methylated))</li>
<li><strong>Histone H4 and H4 modifications (</strong>lysine methylation (mono-, di- and tri-methylated), lysine acetylation, arginine methylation (mono-methylated and symmetrically di-methylated), serine phosphorylation )</li>
</ul>
<p><span style="font-weight: 400;"><strong>HDAC's HAT's, HMT's and other</strong> <strong>enzymes</strong> which modify histones can be found in the category <a href="../categories/chromatin-modifying-proteins-histone-transferase">Histone modifying enzymes</a><br /></span></p>
<p><span style="font-weight: 400;"> Diagenode’s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> Expert technical support</span></li>
<li><span style="font-weight: 400;"> Sample sizes available</span></li>
<li><span style="font-weight: 400;"> 100% satisfaction guarantee</span></li>
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'description' => '<p><span style="font-weight: 400;">All Diagenode’s antibodies are listed below. Please, use our Quick search field to find the antibody of interest by target name, application, purity.</span></p>
<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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'name' => 'ChIP-grade antibodies',
'description' => '<div class="row">
<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
<p></p>
</div>
</div>
<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
<div class="row">
<div class="small-12 medium-6 large-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" alt="" width="400" height="315" /> </div>
<div class="small-12 medium-6 large-6 columns">
<p></p>
<p></p>
<p></p>
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<p></p>
<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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'meta_description' => 'Diagenode Offers Extensively Validated ChIP-Grade Antibodies, Confirmed for their Specificity, and high level of Performance in Chromatin Immunoprecipitation ChIP',
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'description' => '<p>More than in any other immuoprecipitation assays, quality antibodies are critical tools in many epigenetics experiments. Since 10 years, Diagenode has developed the most stringent quality production available on the market for antibodies exclusively focused on epigenetic uses. All our antibodies have been qualified to work in epigenetic applications.</p>',
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'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
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'name' => 'SMYD3 represses tumor-intrinsic interferon response in HPV-negativesquamous cell carcinoma of the head and neck.',
'authors' => 'Nigam N. et al.',
'description' => '<p>Cancers often display immune escape, but the mechanisms are incompletely understood. Herein, we identify SMYD3 as a mediator of immune escape in human papilloma virus (HPV)-negative head and neck squamous cell carcinoma (HNSCC), an aggressive disease with poor response to immunotherapy with pembrolizumab. SMYD3 depletion induces upregulation of multiple type I interferon (IFN) response and antigen presentation machinery genes in HNSCC cells. Mechanistically, SMYD3 binds to and regulates the transcription of UHRF1, encoding for a reader of H3K9me3, which binds to H3K9me3-enriched promoters of key immune-related genes, recruits DNMT1, and silences their expression. SMYD3 further maintains the repression of immune-related genes through intragenic deposition of H4K20me3. In vivo, Smyd3 depletion induces influx of CD8 T cells and increases sensitivity to anti-programmed death 1 (PD-1) therapy. SMYD3 overexpression is associated with decreased CD8 T cell infiltration and poor response to neoadjuvant pembrolizumab. These data support combining SMYD3 depletion strategies with checkpoint blockade to overcome anti-PD-1 resistance in HPV-negative HNSCC.</p>',
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'description' => '<p><span>Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including </span><em>MYC, DTX1, HES4, IL7R,</em><span><span> </span>and<span> </span></span><em>NOTCH3</em><span>. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.</span></p>',
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'name' => 'Gene Regulatory Interactions at Lamina-Associated Domains',
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'description' => '<p>The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are inactive, over ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to interact with regulatory elements remain unclear. Here, we integrate publicly available enhancer-capture Hi-C data with our own chromatin state and transcriptomic datasets to show that inferred enhancers of active genes in LADs are able to form connections with other enhancers within LADs and outside LADs. Fluorescence in situ hybridization analyses show proximity changes between differentially expressed genes in LADs and distant enhancers upon the induction of adipogenic differentiation. We also provide evidence of involvement of lamin A/C, but not lamin B1, in repressing genes at the border of an in-LAD active region within a topological domain. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with gene expression in this dynamic nuclear compartment.</p>',
'date' => '2023-01-01',
'pmid' => 'https://doi.org/10.3390%2Fgenes14020334',
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'name' => 'Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing.',
'authors' => 'O'Geen H.et al.',
'description' => '<p>Precision epigenome editing has gained significant attention as a method to modulate gene expression without altering genetic information. However, a major limiting factor has been that the gene expression changes are often transient, unlike the life-long epigenetic changes that occur frequently in nature. Here, we systematically interrogate the ability of CRISPR/dCas9-based epigenome editors (Epi-dCas9) to engineer persistent epigenetic silencing. We elucidated cis regulatory features that contribute to the differential stability of epigenetic reprogramming, such as the active transcription histone marks H3K36me3 and H3K27ac strongly correlating with resistance to short-term repression and resistance to long-term silencing, respectively. H3K27ac inversely correlates with increased DNA methylation. Interestingly, the dependance on H3K27ac was only observed when a combination of KRAB-dCas9 and targetable DNA methyltransferases (DNMT3A-dCas9 + DNMT3L) was used, but not when KRAB was replaced with the targetable H3K27 histone methyltransferase Ezh2. In addition, programmable Ezh2/DNMT3A + L treatment demonstrated enhanced engineering of localized DNA methylation and was not sensitive to a divergent chromatin state. Our results highlight the importance of local chromatin features for heritability of programmable silencing and the differential response to KRAB- and Ezh2-based epigenetic editing platforms. The information gained in this study provides fundamental insights into understanding contextual cues to more predictably engineer persistent silencing.</p>',
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'name' => 'The prolyl-isomerase PIN1 is essential for nuclear Lamin-Bstructure and function and protects heterochromatin under mechanicalstress.',
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'description' => '<p>Chromatin organization plays a crucial role in tissue homeostasis. Heterochromatin relaxation and consequent unscheduled mobilization of transposable elements (TEs) are emerging as key contributors of aging and aging-related pathologies, including Alzheimer's disease (AD) and cancer. However, the mechanisms governing heterochromatin maintenance or its relaxation in pathological conditions remain poorly understood. Here we show that PIN1, the only phosphorylation-specific cis/trans prolyl isomerase, whose loss is associated with premature aging and AD, is essential to preserve heterochromatin. We demonstrate that this PIN1 function is conserved from Drosophila to humans and prevents TE mobilization-dependent neurodegeneration and cognitive defects. Mechanistically, PIN1 maintains nuclear type-B Lamin structure and anchoring function for heterochromatin protein 1α (HP1α). This mechanism prevents nuclear envelope alterations and heterochromatin relaxation under mechanical stress, which is a key contributor to aging-related pathologies.</p>',
'date' => '2021-09-01',
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'name' => 'Dynamic association of the H3K64 trimethylation mark with genes encodingexported proteins in Plasmodium falciparum.',
'authors' => 'Jabeena, C A et al.',
'description' => '<p>Epigenetic modifications have emerged as critical regulators of virulence genes and stage-specific gene expression in Plasmodium falciparum. However, the specific roles of histone core epigenetic modifications in regulating the stage-specific gene expression are not well understood. In this study, we report an unconventional trimethylation at lysine 64 on histone 3 (H3K64me3) and characterize its functional relevance in P. falciparum. We show that PfSET4 and PfSET5 proteins of P. falciparum methylate H3K64 and that they prefer the nucleosome as a substrate over free histone 3 proteins. Structural analysis of PfSET5 revealed that it interacts with the nucleosome as a dimer. The H3K64me3 mark is dynamic, being enriched in the ring and trophozoite stages and drastically reduced in schizont stages. Stage-specific global ChIP-sequencing analysis of the H3K64me3 mark revealed the selective enrichment of this methyl mark on the genes of exported family proteins in the ring and trophozoite stages, and a significant reduction of the same in the schizont stages. Collectively, our data identify a novel epigenetic mark that are associated with the subset of genes encoding for exported proteins which may regulate their expression in different stages of P. falciparum.</p>',
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'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33839154',
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(int) 6 => array(
'id' => '4149',
'name' => 'Restricted nucleation and piRNA-mediated establishment of heterochromatinduring embryogenesis in Drosophila miranda',
'authors' => 'Wei, K. et al.',
'description' => '<p>Heterochromatin is a key architectural feature of eukaryotic genomes, crucial for silencing of repetitive elements and maintaining genome stability. Heterochromatin shows stereotypical enrichment patterns around centromeres and repetitive sequences, but the molecular details of how heterochromatin is established during embryogenesis are poorly understood. Here, we map the genome-wide distribution of H3K9me3-dependent heterochromatin in individual embryos of D. miranda at precisely staged developmental time points. We find that canonical H3K9me3 enrichment patterns are established early on before cellularization, and mature into stable and broad heterochromatin domains through development. Intriguingly, initial nucleation sites of H3K9me3 enrichment appear as early as embryonic stage3 (nuclear cycle 9) over transposable elements (TE) and progressively broaden, consistent with spreading to neighboring nucleosomes. The earliest nucleation sites are limited to specific regions of a small number of TE families and often appear over promoter regions, while late nucleation develops broadly across most TEs. Early nucleating TEs are highly targeted by maternal piRNAs and show early zygotic transcription, consistent with a model of co-transcriptional silencing of TEs by small RNAs. Interestingly, truncated TE insertions lacking nucleation sites show significantly reduced enrichment across development, suggesting that the underlying sequences play an important role in recruiting histone methyltransferases for heterochromatin</p>',
'date' => '2021-02-01',
'pmid' => 'https://doi.org/10.1101%2F2021.02.16.431328',
'doi' => '10.1101/2021.02.16.431328',
'modified' => '2021-12-14 09:28:27',
'created' => '2021-12-06 15:53:19',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'id' => '3995',
'name' => 'Epigenetic, transcriptional and phenotypic responses in Daphnia magna exposed to low-level ionizing radiation',
'authors' => 'Thaulow Jens, Song You, Lindeman Leif C., Kamstra Jorke H., Lee YeonKyeong, Xie Li, Aleström Peter, Salbu Brit, Tollefsen Knut Erik',
'description' => '<p>Ionizing radiation is known to induce oxidative stress and DNA damage as well as epigenetic effects in aquatic organisms. Epigenetic changes can be part of the adaptive responses to protect organisms from radiation-induced damage, or act as drivers of toxicity pathways leading to adverse effects. To investigate the potential roles of epigenetic mechanisms in low-dose ionizing radiation-induced stress responses, an ecologically relevant crustacean, adult Daphnia magna were chronically exposed to low and medium level external 60Co gamma radiation ranging from 0.4, 1, 4, 10, and 40 mGy/h for seven days. Biological effects at the molecular (global DNA methylation, histone modification, gene expression), cellular (reactive oxygen species formation), tissue/organ (ovary, gut and epidermal histology) and organismal (fecundity) levels were investigated using a suite of effect assessment tools. The results showed an increase in global DNA methylation associated with loci-specific alterations of histone H3K9 methylation and acetylation, and downregulation of genes involved in DNA methylation, one-carbon metabolism, antioxidant defense, DNA repair, apoptosis, calcium signaling and endocrine regulation of development and reproduction. Temporal changes of reactive oxygen species (ROS) formation were also observed with an apparent transition from ROS suppression to induction from 2-7 days after gamma exposure. The cumulative fecundity, however, was not significantly changed by the gamma exposure. On the basis of the new experimental evidence and existing knowledge, a hypothetical model was proposed to provide in-depth mechanistic understanding of the roles of epigenetic mechanisms in low dose ionizing radiation induced stress responses in D. magna.</p>',
'date' => '2020-07-18',
'pmid' => 'https://www.sciencedirect.com/science/article/pii/S0013935120308252',
'doi' => '10.1016/j.envres.2020.109930',
'modified' => '2020-09-01 14:51:16',
'created' => '2020-08-21 16:41:39',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 8 => array(
'id' => '3964',
'name' => 'The 20S proteasome activator PA28γ controls the compaction of chromatin',
'authors' => 'Didier Fesquet, David Llères, Cristina Viganò, Francisca Méchali, Séverine Boulon, Robert Feil, Olivier Coux, Catherine Bonne-Andrea, Véronique Baldin',
'description' => '<p>The nuclear PA28γ is known to activate the 20S proteasome, but its precise cellular functions remains unclear. Here, we identify PA28γ as a key factor that structures heterochromatin. We find that in human cells, a fraction of PA28γ-20S proteasome complexes localizes within HP1-linked heterochromatin foci. Our biochemical studies show that PA28γ interacts with HP1 proteins, particularly HP1β, which recruits the PA28γ-20S proteasome complexes to heterochromatin. Loss of PA28γ does not modify the localization of HP1β, its mobility within nuclear foci, or the level of H3K9 tri-methylation, but reduces H4K20 mono- and tri-methylation, modifications involved in heterochromatin establishment. Concordantly, using a quantitative FRET-based microscopy assay to monitor nanometer-scale proximity between nucleosomes in living cells, we find that PA28γ regulates nucleosome proximity within heterochromatin, and thereby controls its compaction. This function of PA28γ is independent of the 20S proteasome. Importantly, HP1β on its own is unable to drive heterochromatin compaction without PA28γ. Combined, our data reveal an unexpected chromatin structural role of PA28γ, and provide new insights into the mechanism that controls HP1β-mediated heterochromatin compaction.</p>',
'date' => '2020-05-28',
'pmid' => 'https://www.biorxiv.org/content/10.1101/716332v1.article-info',
'doi' => 'https://doi.org/10.1101/716332',
'modified' => '2020-08-12 09:44:09',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'id' => '3965',
'name' => 'Histone post-translational modifications in Silene latifolia X and Y chromosomes suggest a mammal-like dosage compensation system',
'authors' => 'Luis Rodríguez Lorenzo José, Hubinský Marcel, Vyskot Boris, Hobza Roman',
'description' => '<p>Silene latifolia is a model organism to study evolutionary young heteromorphic sex chromosome evolution in plants. Previous research indicates a Y-allele gene degeneration and a dosage compensation system already operating. Here, we propose an epigenetic approach based on analysis of several histone post-translational modifications (PTMs) to find the first epigenetic hints of the X:Y sex chromosome system regulation in S. latifolia. Through chromatin immunoprecipitation we interrogated six genes from X and Y alleles. Several histone PTMS linked to DNA methylation and transcriptional repression (H3K27me3, H3K23me, H3K9me2 and H3K9me3) and to transcriptional activation (H3K4me3 and H4K5, 8, 12, 16ac) were used. DNA enrichment (Immunoprecipitated DNA/input DNA) was analyzed and showed three main results: i) promoters of the Y allele are associated with heterochromatin marks, ii) promoters of the X allele in males are associated with activation of transcription marks and finally, iii) promoters of X alleles in females are associated with active and repressive marks. Our finding indicates a transcription activation of X allele and transcription repression of Y allele in males. In females we found a possible differential regulation (up X1, down X2) of each female X allele. These results agree with the mammal-like epigenetic dosage compensation regulation.</p>',
'date' => '2020-05-24',
'pmid' => 'https://www.sciencedirect.com/science/article/abs/pii/S0168945220301333',
'doi' => '10.1016/j.plantsci.2020.110528',
'modified' => '2020-08-12 09:42:21',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 10 => array(
'id' => '3943',
'name' => 'SETDB2 promoted breast cancer stem cell maintenance by interaction with and stabilization of ΔNp63α protein',
'authors' => 'Ying Liu, Fei Xie, Jialun Li, Jianpeng Xiao, Jie Wang, Zhaolin Mei, Hongjia Fan, Huan Fang, Sha Li, Qiuju Wu, Lin Yuan, Cuicui Liu, You Peng, Weiwei Zhao, Lulu Wang, Jiemin Wong, Jing Li, Jing Feng',
'description' => '<p>The histone H3K9 methyltransferase SETDB2 is involved in cell cycle dysregulation in acute leukemia and has oncogenic roles in gastric cancer. In our study, we found that SETDB2 plays essential roles in breast cancer stem cell maintenance. Depleted SETDB2 significantly decreased the breast cancer stem cell population and mammosphere formation in vitro and also inhibited breast tumor initiation and growth in vivo. Restoring SETDB2 expression rescued the defect in breast cancer stem cell maintenance. A mechanistic analysis showed that SETDB2 upregulated the transcription of the ΔNp63α downstream Hedgehog pathway gene. SETDB2 also interacted with and methylated ΔNp63α, and stabilized ΔNp63α protein. Restoring ΔNp63α expression rescued the breast cancer stem cell maintenance defect which mediated by SETDB2 knockdown. In conclusion, our study reveals a novel function of SETDB2 in cancer stem cell maintenance in breast cancer.</p>',
'date' => '2020-04-28',
'pmid' => 'https://www.ijbs.com/v16p2180',
'doi' => '10.7150/ijbs.43611',
'modified' => '2020-08-17 10:17:33',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 11 => array(
'id' => '3762',
'name' => 'Transit amplifying cells coordinate mouse incisor mesenchymal stem cell activation.',
'authors' => 'Walker JV, Zhuang H, Singer D, Illsley CS, Kok WL, Sivaraj KK, Gao Y, Bolton C, Liu Y, Zhao M, Grayson PRC, Wang S, Karbanová J, Lee T, Ardu S, Lai Q, Liu J, Kassem M, Chen S, Yang K, Bai Y, Tredwin C, Zambon AC, Corbeil D, Adams R, Abdallah BM, Hu B',
'description' => '<p>Stem cells (SCs) receive inductive cues from the surrounding microenvironment and cells. Limited molecular evidence has connected tissue-specific mesenchymal stem cells (MSCs) with mesenchymal transit amplifying cells (MTACs). Using mouse incisor as the model, we discover a population of MSCs neibouring to the MTACs and epithelial SCs. With Notch signaling as the key regulator, we disclose molecular proof and lineage tracing evidence showing the distinct MSCs contribute to incisor MTACs and the other mesenchymal cell lineages. MTACs can feedback and regulate the homeostasis and activation of CL-MSCs through Delta-like 1 homolog (Dlk1), which balances MSCs-MTACs number and the lineage differentiation. Dlk1's function on SCs priming and self-renewal depends on its biological forms and its gene expression is under dynamic epigenetic control. Our findings can be validated in clinical samples and applied to accelerate tooth wound healing, providing an intriguing insight of how to direct SCs towards tissue regeneration.</p>',
'date' => '2019-08-09',
'pmid' => 'http://www.pubmed.gov/31399601',
'doi' => '10.1038/s41467-019-11611-0',
'modified' => '2019-10-03 10:03:31',
'created' => '2019-10-02 16:16:55',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 12 => array(
'id' => '3715',
'name' => 'Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner.',
'authors' => 'O'Geen H, Bates SL, Carter SS, Nisson KA, Halmai J, Fink KD, Rhie SK, Farnham PJ, Segal DJ',
'description' => '<p>BACKGROUND: Rewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve in a predictable manner using targeted systems. RESULTS: Here, we report that persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). We demonstrate that the histone methyltransferase requirement can be locus specific. Co-targeting Ezh2-dCas9, but not KRAB-dCas9, with DNMT3A-dCas9 and DNMT3L induced long-term HER2 repression over at least 50 days (approximately 57 cell divisions) and triggered an epigenetic switch to a heterochromatic environment. An increase in H3K27 trimethylation and DNA methylation was stably maintained and accompanied by a sustained loss of H3K27 acetylation. Interestingly, substitution of Ezh2-dCas9 with KRAB-dCas9 enabled long-term repression at some target genes (e.g., SNURF) but not at HER2, at which H3K9me3 and DNA methylation were transiently acquired and subsequently lost. Off-target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the off-target loci tested. Conversely, robust hypermethylation was observed at HER2. We further demonstrated that Ezh2-dCas9 required full-length DNMT3L for maximal activity and that co-targeting DNMT3L was sufficient for persistent repression by Ezh2-dCas9 or KRAB-dCas9. CONCLUSIONS: These data demonstrate that targeting different combinations of histone and DNA methyltransferases is required to achieve maximal repression at different loci. Fine-tuning of targeting tools is a necessity to engineer epigenetic memory at any given locus in any given cell type.</p>',
'date' => '2019-05-03',
'pmid' => 'http://www.pubmed.gov/31053162',
'doi' => '10.1186/s13072-019-0275-8',
'modified' => '2019-07-05 13:15:49',
'created' => '2019-07-04 10:42:34',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 13 => array(
'id' => '3709',
'name' => 'Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation.',
'authors' => 'Paulsen J, Liyakat Ali TM, Nekrasov M, Delbarre E, Baudement MO, Kurscheid S, Tremethick D, Collas P',
'description' => '<p>Genomic information is selectively used to direct spatial and temporal gene expression during differentiation. Interactions between topologically associating domains (TADs) and between chromatin and the nuclear lamina organize and position chromosomes in the nucleus. However, how these genomic organizers together shape genome architecture is unclear. Here, using a dual-lineage differentiation system, we report long-range TAD-TAD interactions that form constitutive and variable TAD cliques. A differentiation-coupled relationship between TAD cliques and lamina-associated domains suggests that TAD cliques stabilize heterochromatin at the nuclear periphery. We also provide evidence of dynamic TAD cliques during mouse embryonic stem-cell differentiation and somatic cell reprogramming and of inter-TAD associations in single-cell high-resolution chromosome conformation capture (Hi-C) data. TAD cliques represent a level of four-dimensional genome conformation that reinforces the silencing of repressed developmental genes.</p>',
'date' => '2019-05-01',
'pmid' => 'http://www.pubmed.gov/31011212',
'doi' => '10.1038/s41588-019-0392-0',
'modified' => '2019-07-05 14:33:38',
'created' => '2019-07-04 10:42:34',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 14 => array(
'id' => '3692',
'name' => 'PML modulates H3.3 targeting to telomeric and centromeric repeats in mouse fibroblasts.',
'authors' => 'Spirkoski J, Shah A, Reiner AH, Collas P, Delbarre E',
'description' => '<p>Targeted deposition of histone variant H3.3 into chromatin is paramount for proper regulation of chromatin integrity, particularly in heterochromatic regions including repeats. We have recently shown that the promyelocytic leukemia (PML) protein prevents H3.3 from being deposited in large heterochromatic PML-associated domains (PADs). However, to what extent PML modulates H3.3 loading on chromatin in other areas of the genome remains unexplored. Here, we examined the impact of PML on targeting of H3.3 to genes and repeat regions that reside outside PADs. We show that loss of PML increases H3.3 deposition in subtelomeric, telomeric, pericentric and centromeric repeats in mouse embryonic fibroblasts, while other repeat classes are not affected. Expression of major satellite, minor satellite and telomeric non-coding transcripts is altered in Pml-null cells. In particular, telomeric Terra transcripts are strongly upregulated, in concordance with a marked reduction in H4K20me3 at these sites. Lastly, for most genes H3.3 enrichment or gene expression outcomes are independent of PML. Our data argue towards the importance of a PML-H3.3 axis in preserving a heterochromatin state at centromeres and telomeres.</p>',
'date' => '2019-04-16',
'pmid' => 'http://www.pubmed.gov/30850162',
'doi' => '10.1016/j.bbrc.2019.02.087',
'modified' => '2019-06-28 13:50:40',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 15 => array(
'id' => '3644',
'name' => 'Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs.',
'authors' => 'Pontis J, Planet E, Offner S, Turelli P, Duc J, Coudray A, Theunissen TW, Jaenisch R, Trono D',
'description' => '<p>Expansion of transposable elements (TEs) coincides with evolutionary shifts in gene expression. TEs frequently harbor binding sites for transcriptional regulators, thus enabling coordinated genome-wide activation of species- and context-specific gene expression programs, but such regulation must be balanced against their genotoxic potential. Here, we show that Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) control the timely and pleiotropic activation of TE-derived transcriptional cis regulators during early embryogenesis. Evolutionarily recent SVA, HERVK, and HERVH TE subgroups contribute significantly to chromatin opening during human embryonic genome activation and are KLF-stimulated enhancers in naive human embryonic stem cells (hESCs). KZFPs of corresponding evolutionary ages are simultaneously induced and repress the transcriptional activity of these TEs. Finally, the same KZFP-controlled TE-based enhancers later serve as developmental and tissue-specific enhancers. Thus, by controlling the transcriptional impact of TEs during embryogenesis, KZFPs facilitate their genome-wide incorporation into transcriptional networks, thereby contributing to human genome regulation.</p>',
'date' => '2019-03-27',
'pmid' => 'http://www.pubmed.gov/31006620',
'doi' => '10.1016/j.stem.2019.03.012',
'modified' => '2019-06-07 10:16:36',
'created' => '2019-06-06 12:11:18',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 16 => array(
'id' => '3686',
'name' => 'Gamma radiation induces locus specific changes to histone modification enrichment in zebrafish and Atlantic salmon.',
'authors' => 'Lindeman LC, Kamstra JH, Ballangby J, Hurem S, Martín LM, Brede DA, Teien HC, Oughton DH, Salbu B, Lyche JL, Aleström P',
'description' => '<p>Ionizing radiation is a recognized genotoxic agent, however, little is known about the role of the functional form of DNA in these processes. Post translational modifications on histone proteins control the organization of chromatin and hence control transcriptional responses that ultimately affect the phenotype. The purpose of this study was to investigate effects on chromatin caused by ionizing radiation in fish. Direct exposure of zebrafish (Danio rerio) embryos to gamma radiation (10.9 mGy/h for 3h) induced hyper-enrichment of H3K4me3 at the genes hnf4a, gmnn and vegfab. A similar relative hyper-enrichment was seen at the hnf4a loci of irradiated Atlantic salmon (Salmo salar) embryos (30 mGy/h for 10 days). At the selected genes in ovaries of adult zebrafish irradiated during gametogenesis (8.7 and 53 mGy/h for 27 days), a reduced enrichment of H3K4me3 was observed, which was correlated with reduced levels of histone H3 was observed. F1 embryos of the exposed parents showed hyper-methylation of H3K4me3, H3K9me3 and H3K27me3 on the same three loci, while these differences were almost negligible in F2 embryos. Our results from three selected loci suggest that ionizing radiation can affect chromatin structure and organization, and that these changes can be detected in F1 offspring, but not in subsequent generations.</p>',
'date' => '2019-01-01',
'pmid' => 'http://www.pubmed.gov/30759148',
'doi' => '10.1371/journal.pone.0212123',
'modified' => '2019-06-28 13:57:39',
'created' => '2019-06-21 14:55:31',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 17 => array(
'id' => '3635',
'name' => 'TIP60: an actor in acetylation of H3K4 and tumor development in breast cancer.',
'authors' => 'Judes G, Dubois L, Rifaï K, Idrissou M, Mishellany F, Pajon A, Besse S, Daures M, Degoul F, Bignon YJ, Penault-Llorca F, Bernard-Gallon D',
'description' => '<p>AIM: The acetyltransferase TIP60 is reported to be downregulated in several cancers, in particular breast cancer, but the molecular mechanisms resulting from its alteration are still unclear. MATERIALS & METHODS: In breast tumors, H3K4ac enrichment and its link with TIP60 were evaluated by chromatin immunoprecipitation-qPCR and re-chromatin immunoprecipitation techniques. To assess the biological roles of TIP60 in breast cancer, two cell lines of breast cancer, MDA-MB-231 (ER-) and MCF-7 (ER+) were transfected with shRNA specifically targeting TIP60 and injected to athymic Balb-c mice. RESULTS: We identified a potential target of TIP60, H3K4. We show that an underexpression of TIP60 could contribute to a reduction of H3K4 acetylation in breast cancer. An increase in tumor development was noted in sh-TIP60 MDA-MB-231 xenografts and a slowdown of tumor growth in sh-TIP60 MCF-7 xenografts. CONCLUSION: This is evidence that the underexpression of TIP60 observed in breast cancer can promote the tumorigenesis of ER-negative tumors.</p>',
'date' => '2018-11-01',
'pmid' => 'http://www.pubmed.gov/30324811',
'doi' => '10.2217/epi-2018-0004',
'modified' => '2019-06-07 10:29:04',
'created' => '2019-06-06 12:11:18',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 18 => array(
'id' => '3556',
'name' => 'PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex.',
'authors' => 'Link S, Spitzer RMM, Sana M, Torrado M, Völker-Albert MC, Keilhauer EC, Burgold T, Pünzeler S, Low JKK, Lindström I, Nist A, Regnard C, Stiewe T, Hendrich B, Imhof A, Mann M, Mackay JP, Bartkuhn M, Hake SB',
'description' => '<p>Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified that PWWP2A tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial-facial development. Here, using in vitro assays, we show that distinct domains of PWWP2A mediate binding to free linker DNA as well as H3K36me3 nucleosomes. In vivo, PWWP2A strongly recognizes H2A.Z-containing regulatory regions and weakly binds H3K36me3-containing gene bodies. Further, PWWP2A binds to an MTA1-specific subcomplex of the NuRD complex (M1HR), which consists solely of MTA1, HDAC1, and RBBP4/7, and excludes CHD, GATAD2 and MBD proteins. Depletion of PWWP2A leads to an increase of acetylation levels on H3K27 as well as H2A.Z, presumably by impaired chromatin recruitment of M1HR. Thus, this study identifies PWWP2A as a complex chromatin-binding protein that serves to direct the deacetylase complex M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels.</p>',
'date' => '2018-10-16',
'pmid' => 'http://www.pubmed.gov/30327463',
'doi' => '10.1038/s41467-018-06665-5',
'modified' => '2019-07-22 09:17:39',
'created' => '2019-03-21 14:12:08',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 19 => array(
'id' => '3551',
'name' => 'HIV-2/SIV viral protein X counteracts HUSH repressor complex.',
'authors' => 'Ghina Chougui, Soundasse Munir-Matloob, Roy Matkovic, Michaël M Martin, Marina Morel, Hichem Lahouassa, Marjorie Leduc, Bertha Cecilia Ramirez, Lucie Etienne and Florence Margottin-Goguet',
'description' => '<p>To evade host immune defences, human immunodeficiency viruses 1 and 2 (HIV-1 and HIV-2) have evolved auxiliary proteins that target cell restriction factors. Viral protein X (Vpx) from the HIV-2/SIVsmm lineage enhances viral infection by antagonizing SAMHD1 (refs ), but this antagonism is not sufficient to explain all Vpx phenotypes. Here, through a proteomic screen, we identified another Vpx target-HUSH (TASOR, MPP8 and periphilin)-a complex involved in position-effect variegation. HUSH downregulation by Vpx is observed in primary cells and HIV-2-infected cells. Vpx binds HUSH and induces its proteasomal degradation through the recruitment of the DCAF1 ubiquitin ligase adaptor, independently from SAMHD1 antagonism. As a consequence, Vpx is able to reactivate HIV latent proviruses, unlike Vpx mutants, which are unable to induce HUSH degradation. Although antagonism of human HUSH is not conserved among all lentiviral lineages including HIV-1, it is a feature of viral protein R (Vpr) from simian immunodeficiency viruses (SIVs) of African green monkeys and from the divergent SIV of l'Hoest's monkey, arguing in favour of an ancient lentiviral species-specific vpx/vpr gene function. Altogether, our results suggest the HUSH complex as a restriction factor, active in primary CD4 T cells and counteracted by Vpx, therefore providing a molecular link between intrinsic immunity and epigenetic control.</p>',
'date' => '2018-08-01',
'pmid' => 'http://www.pubmed.gov/29891865',
'doi' => '10.1038/s41564-018-0179-6',
'modified' => '2019-02-28 10:20:23',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 20 => array(
'id' => '3470',
'name' => 'Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes.',
'authors' => 'Lomberk G, Blum Y, Nicolle R, Nair A, Gaonkar KS, Marisa L, Mathison A, Sun Z, Yan H, Elarouci N, Armenoult L, Ayadi M, Ordog T, Lee JH, Oliver G, Klee E, Moutardier V, Gayet O, Bian B, Duconseil P, Gilabert M, Bigonnet M, Garcia S, Turrini O, Delpero JR,',
'description' => '<p>Recent studies have offered ample insight into genome-wide expression patterns to define pancreatic ductal adenocarcinoma (PDAC) subtypes, although there remains a lack of knowledge regarding the underlying epigenomics of PDAC. Here we perform multi-parametric integrative analyses of chromatin immunoprecipitation-sequencing (ChIP-seq) on multiple histone modifications, RNA-sequencing (RNA-seq), and DNA methylation to define epigenomic landscapes for PDAC subtypes, which can predict their relative aggressiveness and survival. Moreover, we describe the state of promoters, enhancers, super-enhancers, euchromatic, and heterochromatic regions for each subtype. Further analyses indicate that the distinct epigenomic landscapes are regulated by different membrane-to-nucleus pathways. Inactivation of a basal-specific super-enhancer associated pathway reveals the existence of plasticity between subtypes. Thus, our study provides new insight into the epigenetic landscapes associated with the heterogeneity of PDAC, thereby increasing our mechanistic understanding of this disease, as well as offering potential new markers and therapeutic targets.</p>',
'date' => '2018-05-17',
'pmid' => 'http://www.pubmed.gov/29773832',
'doi' => '10.1038/s41467-018-04383-6',
'modified' => '2019-02-15 21:08:07',
'created' => '2019-02-14 15:01:22',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 21 => array(
'id' => '3536',
'name' => 'PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites.',
'authors' => 'Diagouraga B, Clément JAJ, Duret L, Kadlec J, de Massy B, Baudat F',
'description' => '<p>The programmed formation of hundreds of DNA double-strand breaks (DSBs) is essential for proper meiosis and fertility. In mice and humans, the location of these breaks is determined by the meiosis-specific protein PRDM9, through the DNA-binding specificity of its zinc-finger domain. PRDM9 also has methyltransferase activity. Here, we show that this activity is required for H3K4me3 and H3K36me3 deposition and for DSB formation at PRDM9-binding sites. By analyzing mice that express two PRDM9 variants with distinct DNA-binding specificities, we show that each variant generates its own set of H3K4me3 marks independently from the other variant. Altogether, we reveal several basic principles of PRDM9-dependent DSB site determination, in which an excess of sites are designated through PRDM9 binding and subsequent histone methylation, from which a subset is selected for DSB formation.</p>',
'date' => '2018-03-01',
'pmid' => 'http://www.pubmed.gov/29478809',
'doi' => '10.1016/j.molcel.2018.01.033',
'modified' => '2019-02-28 10:51:44',
'created' => '2019-02-27 12:54:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 22 => array(
'id' => '3276',
'name' => 'DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease',
'authors' => 'Jeziorska D.M. et al.',
'description' => '<p>The human genome contains ∼30,000 CpG islands (CGIs). While CGIs associated with promoters nearly always remain unmethylated, many of the ∼9,000 CGIs lying within gene bodies become methylated during development and differentiation. Both promoter and intragenic CGIs may also become abnormally methylated as a result of genome rearrangements and in malignancy. The epigenetic mechanisms by which some CGIs become methylated but others, in the same cell, remain unmethylated in these situations are poorly understood. Analyzing specific loci and using a genome-wide analysis, we show that transcription running across CGIs, associated with specific chromatin modifications, is required for DNA methyltransferase 3B (DNMT3B)-mediated DNA methylation of many naturally occurring intragenic CGIs. Importantly, we also show that a subgroup of intragenic CGIs is not sensitive to this process of transcription-mediated methylation and that this correlates with their individual intrinsic capacity to initiate transcription in vivo. We propose a general model of how transcription could act as a primary determinant of the patterns of CGI methylation in normal development and differentiation, and in human disease.</p>',
'date' => '2017-09-05',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28827334',
'doi' => '',
'modified' => '2017-10-16 10:16:06',
'created' => '2017-10-16 10:16:06',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 23 => array(
'id' => '3240',
'name' => 'Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation',
'authors' => 'Pünzeler S. et al.',
'description' => '<p>Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA-based processes via poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel H2A.Z-nucleosome binder. PWWP2A is a functionally uncharacterized, vertebrate-specific protein that binds very tightly to chromatin through a concerted multivalent binding mode. Two internal protein regions mediate H2A.Z-specificity and nucleosome interaction, whereas the PWWP domain exhibits direct DNA binding. Genome-wide mapping reveals that PWWP2A binds selectively to H2A.Z-containing nucleosomes with strong preference for promoters of highly transcribed genes. In human cells, its depletion affects gene expression and impairs proliferation via a mitotic delay. While PWWP2A does not influence H2A.Z occupancy, the C-terminal tail of H2A.Z is one important mediator to recruit PWWP2A to chromatin. Knockdown of PWWP2A in <i>Xenopus</i> results in severe cranial facial defects, arising from neural crest cell differentiation and migration problems. Thus, PWWP2A is a novel H2A.Z-specific multivalent chromatin binder providing a surprising link between H2A.Z, chromosome segregation, and organ development.</p>',
'date' => '2017-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28645917',
'doi' => '',
'modified' => '2017-08-29 09:45:44',
'created' => '2017-08-29 09:45:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 24 => array(
'id' => '3216',
'name' => 'Vitamin C induces specific demethylation of H3K9me2 in mouse embryonic stem cells via Kdm3a/b',
'authors' => 'Kevin T. Ebata, Kathryn Mesh, Shichong Liu, Misha Bilenky, Alexander Fekete, Michael G. Acker, Martin Hirst, Benjamin A. Garcia and Miguel Ramalho-Santos',
'description' => '<section xmlns="" xmlns:fn="http://www.w3.org/2005/xpath-functions" xmlns:meta="http://www.springer.com/app/meta" class="Abstract" id="Abs1" lang="en">
<div class="js-CollapseSection">
<div xmlns:func="http://oscar.fig.bmc.com" xmlns="http://www.w3.org/1999/xhtml" class="AbstractSection" id="ASec1">
<h3 xmlns="" class="Heading">Background</h3>
<p id="Par1" class="Para">Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that vitamin C enhances the activity of Tet enzymes in embryonic stem (ES) cells, leading to DNA demethylation and activation of germline genes.</p>
</div>
<div xmlns:func="http://oscar.fig.bmc.com" xmlns="http://www.w3.org/1999/xhtml" class="AbstractSection" id="ASec2">
<h3 xmlns="" class="Heading">Results</h3>
<p id="Par2" class="Para">We report here that vitamin C induces a remarkably specific demethylation of histone H3 lysine 9 dimethylation (H3K9me2) in naïve ES cells. Vitamin C treatment reduces global levels of H3K9me2, but not other histone methylation marks analyzed, as measured by western blot, immunofluorescence and mass spectrometry. Vitamin C leads to widespread loss of H3K9me2 at large chromosomal domains as well as gene promoters and repeat elements. Vitamin C-induced loss of H3K9me2 occurs rapidly within 24 h and is reversible. Importantly, we found that the histone demethylases Kdm3a and Kdm3b are required for vitamin C-induced demethylation of H3K9me2. Moreover, we show that vitamin C-induced Kdm3a/b-mediated H3K9me2 demethylation and Tet-mediated DNA demethylation are independent processes at specific loci. Lastly, we document Kdm3a/b are partially required for the upregulation of germline genes by vitamin C.</p>
</div>
<div xmlns:func="http://oscar.fig.bmc.com" xmlns="http://www.w3.org/1999/xhtml" class="AbstractSection" id="ASec3">
<h3 xmlns="" class="Heading">Conclusions</h3>
<p id="Par3" class="Para">These results reveal a specific role for vitamin C in histone demethylation in ES cells and document that DNA methylation and H3K9me2 cooperate to silence germline genes in pluripotent cells.</p>
</div>
</div>
</section>',
'date' => '2017-07-12',
'pmid' => 'https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-017-0143-3',
'doi' => 'https://doi.org/10.1186/s13072-017-0143-3',
'modified' => '2017-08-23 14:47:51',
'created' => '2017-07-29 08:04:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 25 => array(
'id' => '3177',
'name' => 'Microinjection of Antibodies Targeting the Lamin A/C Histone-Binding Site Blocks Mitotic Entry and Reveals Separate Chromatin Interactions with HP1, CenpB and PML.',
'authors' => 'Dixon C.R. et al.',
'description' => '<p>Lamins form a scaffold lining the nucleus that binds chromatin and contributes to spatial genome organization; however, due to the many other functions of lamins, studies knocking out or altering the lamin polymer cannot clearly distinguish between direct and indirect effects. To overcome this obstacle, we specifically targeted the mapped histone-binding site of A/C lamins by microinjecting antibodies specific to this region predicting that this would make the genome more mobile. No increase in chromatin mobility was observed; however, interestingly, injected cells failed to go through mitosis, while control antibody-injected cells did. This effect was not due to crosslinking of the lamin polymer, as Fab fragments also blocked mitosis. The lack of genome mobility suggested other lamin-chromatin interactions. To determine what these might be, mini-lamin A constructs were expressed with or without the histone-binding site that assembled into independent intranuclear structures. HP1, CenpB and PML proteins accumulated at these structures for both constructs, indicating that other sites supporting chromatin interactions exist on lamin A. Together, these results indicate that lamin A-chromatin interactions are highly redundant and more diverse than generally acknowledged and highlight the importance of trying to experimentally separate their individual functions.</p>',
'date' => '2017-03-25',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28346356',
'doi' => '',
'modified' => '2017-05-17 10:39:58',
'created' => '2017-05-17 10:39:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 26 => array(
'id' => '3172',
'name' => 'Decoupling of DNA methylation and activity of intergenic LINE-1 promoters in colorectal cancer',
'authors' => 'Vafadar-Isfahani N. et al.',
'description' => '<p>Hypomethylation of LINE-1 repeats in cancer has been proposed as the main mechanism behind their activation; this assumption, however, was based on findings from early studies that were biased toward young and transpositionally active elements. Here, we investigate the relationship between methylation of 2 intergenic, transpositionally inactive LINE-1 elements and expression of the LINE-1 chimeric transcript (LCT) 13 and LCT14 driven by their antisense promoters (L1-ASP). Our data from DNA modification, expression, and 5'RACE analyses suggest that colorectal cancer methylation in the regions analyzed is not always associated with LCT repression. Consistent with this, in HCT116 colorectal cancer cells lacking DNA methyltransferases DNMT1 or DNMT3B, LCT13 expression decreases, while cells lacking both DNMTs or treated with the DNMT inhibitor 5-azacytidine (5-aza) show no change in LCT13 expression. Interestingly, levels of the H4K20me3 histone modification are inversely associated with LCT13 and LCT14 expression. Moreover, at these LINE-1s, H4K20me3 levels rather than DNA methylation seem to be good predictor of their sensitivity to 5-aza treatment. Therefore, by studying individual LINE-1 promoters we have shown that in some cases these promoters can be active without losing methylation; in addition, we provide evidence that other factors (e.g., H4K20me3 levels) play prominent roles in their regulation.</p>',
'date' => '2017-03-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28300471',
'doi' => '',
'modified' => '2017-05-10 16:26:24',
'created' => '2017-05-10 16:26:24',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 27 => array(
'id' => '3152',
'name' => 'H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements',
'authors' => 'Zink L.M. et al.',
'description' => '<p>Histone chaperones prevent promiscuous histone interactions before chromatin assembly. They guarantee faithful deposition of canonical histones and functionally specialized histone variants into chromatin in a spatial- and temporally-restricted manner. Here, we identify the binding partners of the primate-specific and H3.3-related histone variant H3.Y using several quantitative mass spectrometry approaches, and biochemical and cell biological assays. We find the HIRA, but not the DAXX/ATRX, complex to recognize H3.Y, explaining its presence in transcriptionally active euchromatic regions. Accordingly, H3.Y nucleosomes are enriched in the transcription-promoting FACT complex and depleted of repressive post-translational histone modifications. H3.Y mutational gain-of-function screens reveal an unexpected combinatorial amino acid sequence requirement for histone H3.3 interaction with DAXX but not HIRA, and for H3.3 recruitment to PML nuclear bodies. We demonstrate the importance and necessity of specific H3.3 core and C-terminal amino acids in discriminating between distinct chaperone complexes. Further, chromatin immunoprecipitation sequencing experiments reveal that in contrast to euchromatic HIRA-dependent deposition sites, human DAXX/ATRX-dependent regions of histone H3 variant incorporation are enriched in heterochromatic H3K9me3 and simple repeat sequences. These data demonstrate that H3.Y's unique amino acids allow a functional distinction between HIRA and DAXX binding and its consequent deposition into open chromatin.</p>',
'date' => '2017-02-21',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28334823',
'doi' => '',
'modified' => '2017-03-31 14:13:36',
'created' => '2017-03-31 14:13:36',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 28 => array(
'id' => '3100',
'name' => 'Muscle catabolic capacities and global hepatic epigenome are modified in juvenile rainbow trout fed different vitamin levels at first feeding',
'authors' => 'Panserat S. et al.',
'description' => '<p>Based on the concept of nutritional programming in mammals, we tested whether a short term hyper or hypo vitamin stimulus during first-feeding could induce long-lasting changes in nutrient metabolism in rainbow trout. Trout alevins received during the 4 first weeks of exogenous feeding a diet either without supplemental vitamins (NOSUP), a diet supplemented with a vitamin premix to satisfy the minimal requirement in all the vitamins (NRC) or a diet with a vitamin premix corresponding to an optimal vitamin nutrition (OVN). Following a common rearing period on the control diet, all three groups were then evaluated in terms of metabolic marker gene expressions at the end of the feeding period (day 119). Whereas no gene modifications for proteins involved in energy and lipid metabolism were observed in whole alevins (short-term effect), some of these genes showed a long-term molecular adaptation in the muscle of juveniles (long-term effect). Indeed, muscle of juveniles subjected at an early feeding of the OVN diet displayed up-regulated expression of markers of lipid catabolism (3-hydroxyacyl-CoA dehydrogenase – HOAD - enzyme) and mitochondrial energy metabolism (Citrate synthase - <em>cs</em>, Ubiquitinol cytochrome <em>c</em> reductase core protein 2 - QCR2, cytochrome oxidase 4 - COX4, ATP synthase form 5 - ATP5A) compared to fish fed the NOSUP diet. Moreover, some key enzymes involved in glucose catabolism (Muscle Pyruvate kinase - PKM) and amino acid catabolism (Glutamate dehydrogenase - GDH3) were also up regulated in muscle of juvenile fish fed with the OVN diet at first-feeding compared to fish fed the NOSUP diet. We researched if these permanently modified gene expressions could be related to global modifications of epigenetic marks (global DNA methylation and global histone acetylation and methylation). There was no variation of the epigenetic marks in muscle. However, we found changes in hepatic DNA methylation, global H3 acetylation and H3K4 methylation, dependent on the vitamin intake at early life. In summary, our data show, for the first time in fish, that a short-term vitamin-stimulus during early life may durably influence muscle energy and lipid metabolism as well as some hepatic epigenetic marks in rainbow trout.</p>',
'date' => '2017-02-01',
'pmid' => 'http://www.sciencedirect.com/science/article/pii/S0044848616309693',
'doi' => '',
'modified' => '2017-01-03 15:01:50',
'created' => '2017-01-03 15:01:50',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 29 => array(
'id' => '2825',
'name' => 'Oestrogen receptor β regulates epigenetic patterns at specific genomic loci through interaction with thymine DNA glycosylase.',
'authors' => 'Liu Y, Duong W, Krawczyk C, Bretschneider N, Borbély G, Varshney M, Zinser C, Schär P, Rüegg J.',
'description' => '<div class="">
<h4>BACKGROUND:</h4>
<p><abstracttext label="BACKGROUND" nlmcategory="BACKGROUND">DNA methylation is one way to encode epigenetic information and plays a crucial role in regulating gene expression during embryonic development. DNA methylation marks are established by the DNA methyltransferases and, recently, a mechanism for active DNA demethylation has emerged involving the ten-eleven translocator proteins and thymine DNA glycosylase (TDG). However, so far it is not clear how these enzymes are recruited to, and regulate DNA methylation at, specific genomic loci. A number of studies imply that sequence-specific transcription factors are involved in targeting DNA methylation and demethylation processes. Oestrogen receptor beta (ERβ) is a ligand-inducible transcription factor regulating gene expression in response to the female sex hormone oestrogen. Previously, we found that ERβ deficiency results in changes in DNA methylation patterns at two gene promoters, implicating an involvement of ERβ in DNA methylation. In this study, we set out to explore this involvement on a genome-wide level, and to investigate the underlying mechanisms of this function.</abstracttext></p>
<h4>RESULTS:</h4>
<p><abstracttext label="RESULTS" nlmcategory="RESULTS">Using reduced representation bisulfite sequencing, we compared genome-wide DNA methylation in mouse embryonic fibroblasts derived from wildtype and ERβ knock-out mice, and identified around 8000 differentially methylated positions (DMPs). Validation and further characterisation of selected DMPs showed that differences in methylation correlated with changes in expression of the nearest gene. Additionally, re-introduction of ERβ into the knock-out cells could reverse hypermethylation and reactivate expression of some of the genes. We also show that ERβ is recruited to regions around hypermethylated DMPs. Finally, we demonstrate here that ERβ interacts with TDG and that TDG binds ERβ-dependently to hypermethylated DMPs.</abstracttext></p>
<h4>CONCLUSION:</h4>
<p><abstracttext label="CONCLUSION" nlmcategory="CONCLUSIONS">We provide evidence that ERβ plays a role in regulating DNA methylation at specific genomic loci, likely as the result of its interaction with TDG at these regions. Our findings imply a novel function of ERβ, beyond direct transcriptional control, in regulating DNA methylation at target genes. Further, they shed light on the question how DNA methylation is regulated at specific genomic loci by supporting a concept in which sequence-specific transcription factors can target factors that regulate DNA methylation patterns.</abstracttext></p>
</div>',
'date' => '2016-02-16',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/26889208',
'doi' => '10.1186/s13072-016-0055-7.',
'modified' => '2016-02-22 10:05:14',
'created' => '2016-02-22 10:05:14',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 30 => array(
'id' => '2909',
'name' => 'Epigenetic priming of inflammatory response genes by high glucose in adipose progenitor cells',
'authors' => 'Rønningen T, Shah A, Reiner AH, Collas P, Moskaug JØ',
'description' => '<p>Cellular metabolism confers wide-spread epigenetic modifications required for regulation of transcriptional networks that determine cellular states. Mesenchymal stromal cells are responsive to metabolic cues including circulating glucose levels and modulate inflammatory responses. We show here that long term exposure of undifferentiated human adipose tissue stromal cells (ASCs) to high glucose upregulates a subset of inflammation response (IR) genes and alters their promoter histone methylation patterns in a manner consistent with transcriptional de-repression. Modeling of chromatin states from combinations of histone modifications in nearly 500 IR genes unveil three overarching chromatin configurations reflecting repressive, active, and potentially active states in promoter and enhancer elements. Accordingly, we show that adipogenic differentiation in high glucose predominantly upregulates IR genes. Our results indicate that elevated extracellular glucose levels sensitize in ASCs an IR gene expression program which is exacerbated during adipocyte differentiation. We propose that high glucose exposure conveys an epigenetic 'priming' of IR genes, favoring a transcriptional inflammatory response upon adipogenic stimulation. Chromatin alterations at IR genes by high glucose exposure may play a role in the etiology of metabolic diseases.</p>',
'date' => '2015-11-27',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/26462465',
'doi' => '10.1016/j.bbrc.2015.10.030',
'modified' => '2016-05-09 22:54:48',
'created' => '2016-05-09 22:54:48',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 31 => array(
'id' => '2874',
'name' => 'Polycomb RING1A- and RING1B-dependent histone H2A monoubiquitylation at pericentromeric regions promotes S-phase progression',
'authors' => 'Bravo M, Nicolini F, Starowicz K, Barroso S, Calés C, Aguilera A, Vidal M',
'description' => '<p>The functions of polycomb products extend beyond their well-known activity as transcriptional regulators to include genome duplication processes. Polycomb activities during DNA replication and DNA damage repair are unclear, particularly without induced replicative stress. We have used a cellular model of conditionally inactive polycomb E3 ligases (RING1A and RING1B), which monoubiquitylate lysine 119 of histone H2A (H2AK119Ub), to examine DNA replication in unperturbed cells. We identify slow elongation and fork stalling during DNA replication that is associated with the accumulation of mid and late S-phase cells. Signs of replicative stress and colocalisation of double-strand breaks with chromocenters, the sites of coalesced pericentromeric heterocromatic (PCH) domains, were enriched in cells at mid S-phase, the stage at which PCH is replicated. Altered replication was rescued by targeted monoubiquitylation of PCH through methyl-CpG binding domain protein 1. The acute senescence associated with the depletion of RING1 proteins, which is mediated by p21 (also known as CDKN1A) upregulation, could be uncoupled from a response to DNA damage. These findings link cell proliferation and the polycomb proteins RING1A and RING1B to S-phase progression through a specific function in PCH replication.</p>',
'date' => '2015-08-13',
'pmid' => 'http://jcs.biologists.org/content/128/19/3660',
'doi' => '10.1242/jcs.173021 ',
'modified' => '2016-03-29 16:29:38',
'created' => '2016-03-29 16:29:38',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 32 => array(
'id' => '2725',
'name' => 'Erosion of X Chromosome Inactivation in Human Pluripotent Cells Initiates with XACT Coating and Depends on a Specific Heterochromatin Landscape.',
'authors' => 'Vallot C, Ouimette JF, Makhlouf M, Féraud O, Pontis J, Côme J, Martinat C, Bennaceur-Griscelli A, Lalande M, Rougeulle C',
'description' => 'Human pluripotent stem cells (hPSCs) display extensive epigenetic instability, particularly on the X chromosome. In this study, we show that, in hPSCs, the inactive X chromosome has a specific heterochromatin landscape that predisposes it to erosion of X chromosome inactivation (XCI), a process that occurs spontaneously in hPSCs. Heterochromatin remodeling and gene reactivation occur in a non-random fashion and are confined to specific H3K27me3-enriched domains, leaving H3K9me3-marked regions unaffected. Using single-cell monitoring of XCI erosion, we show that this instability only occurs in pluripotent cells. We also provide evidence that loss of XIST expression is not the primary cause of XCI instability and that gene reactivation from the inactive X (Xi) precedes loss of XIST coating. Notably, expression and coating by the long non-coding RNA XACT are early events in XCI erosion and, therefore, may play a role in mediating this process.',
'date' => '2015-05-07',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25921272',
'doi' => '',
'modified' => '2015-07-24 15:39:05',
'created' => '2015-07-24 15:39:05',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 33 => array(
'id' => '2575',
'name' => 'Embryonic stem cell differentiation requires full length Chd1.',
'authors' => 'Piatti P, Lim CY, Nat R, Villunger A, Geley S, Shue YT, Soratroi C, Moser M, Lusser A',
'description' => 'The modulation of chromatin dynamics by ATP-dependent chromatin remodeling factors has been recognized as an important mechanism to regulate the balancing of self-renewal and pluripotency in embryonic stem cells (ESCs). Here we have studied the effects of a partial deletion of the gene encoding the chromatin remodeling factor Chd1 that generates an N-terminally truncated version of Chd1 in mouse ESCs in vitro as well as in vivo. We found that a previously uncharacterized serine-rich region (SRR) at the N-terminus is not required for chromatin assembly activity of Chd1 but that it is subject to phosphorylation. Expression of Chd1 lacking this region in ESCs resulted in aberrant differentiation properties of these cells. The self-renewal capacity and ESC chromatin structure, however, were not affected. Notably, we found that newly established ESCs derived from Chd1(Δ2/Δ2) mutant mice exhibited similar differentiation defects as in vitro generated mutant ESCs, even though the N-terminal truncation of Chd1 was fully compatible with embryogenesis and post-natal life in the mouse. These results underscore the importance of Chd1 for the regulation of pluripotency in ESCs and provide evidence for a hitherto unrecognized critical role of the phosphorylated N-terminal SRR for full functionality of Chd1.',
'date' => '2015-01-26',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25620209',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 34 => array(
'id' => '2513',
'name' => 'The histone demethylase enzyme KDM3A is a key estrogen receptor regulator in breast cancer.',
'authors' => 'Wade MA, Jones D, Wilson L, Stockley J, Coffey K, Robson CN, Gaughan L',
'description' => '<p>Endocrine therapy has successfully been used to treat estrogen receptor (ER)-positive breast cancer, but this invariably fails with cancers becoming refractory to treatment. Emerging evidence has suggested that fluctuations in ER co-regulatory protein expression may facilitate resistance to therapy and be involved in breast cancer progression. To date, a small number of enzymes that control methylation status of histones have been identified as co-regulators of ER signalling. We have identified the histone H3 lysine 9 mono- and di-methyl demethylase enzyme KDM3A as a positive regulator of ER activity. Here, we demonstrate that depletion of KDM3A by RNAi abrogates the recruitment of the ER to cis-regulatory elements within target gene promoters, thereby inhibiting estrogen-induced gene expression changes. Global gene expression analysis of KDM3A-depleted cells identified gene clusters associated with cell growth. Consistent with this, we show that knockdown of KDM3A reduces ER-positive cell proliferation and demonstrate that KDM3A is required for growth in a model of endocrine therapy-resistant disease. Crucially, we show that KDM3A catalytic activity is required for both ER-target gene expression and cell growth, demonstrating that developing compounds which target demethylase enzymatic activity may be efficacious in treating both ER-positive and endocrine therapy-resistant disease.</p>',
'date' => '2015-01-09',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25488809',
'doi' => '',
'modified' => '2016-05-03 11:59:18',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 35 => array(
'id' => '2502',
'name' => 'TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells.',
'authors' => 'Fasching L, Kapopoulou A, Sachdeva R, Petri R, Jönsson ME, Männe C, Turelli P, Jern P, Cammas F, Trono D, Jakobsson J',
'description' => '<p>TRIM28 is a corepressor that mediates transcriptional silencing by establishing local heterochromatin. Here, we show that deletion of TRIM28 in neural progenitor cells (NPCs) results in high-level expression of two groups of endogenous retroviruses (ERVs): IAP1 and MMERVK10C. We find that NPCs use TRIM28-mediated histone modifications to dynamically regulate transcription and silencing of ERVs, which is in contrast to other somatic cell types using DNA methylation. We also show that derepression of ERVs influences transcriptional dynamics in NPCs through the activation of nearby genes and the expression of long noncoding RNAs. These findings demonstrate a unique dynamic transcriptional regulation of ERVs in NPCs. Our results warrant future studies on the role of ERVs in the healthy and diseased brain.</p>',
'date' => '2015-01-06',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25543143',
'doi' => '',
'modified' => '2017-06-22 13:34:19',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 36 => array(
'id' => '2492',
'name' => 'Cryosectioning the intestinal crypt-villus axis: an ex vivo method to study the dynamics of epigenetic modifications from stem cells to differentiated cells',
'authors' => 'Vincent A, Kazmierczak C, Duchêne B, Jonckheere N, Leteurtre E, Van Seuningen I',
'description' => 'The intestinal epithelium is a particularly attractive biological adult model to study epigenetic mechanisms driving adult stem cell renewal and cell differentiation. Since epigenetic modifications are dynamic, we have developed an original ex vivo approach to study the expression and epigenetic profiles of key genes associated with either intestinal cell pluripotency or differentiation by isolating cryosections of the intestinal crypt-villus axis. Gene expression, DNA methylation and histone modifications were studied by qRT-PCR, Methylation Specific-PCR and micro-Chromatin Immunoprecipitation, respectively. Using this approach, it was possible to identify segment-specific methylation and chromatin profiles. We show that (i) expression of intestinal stem cell markers (Lgr5, Ascl2) exclusively in the crypt is associated with active histone marks, (ii) promoters of all pluripotency genes studied and transcription factors involved in intestinal cell fate (Cdx2) harbour a bivalent chromatin pattern in the crypts, (iii) expression of differentiation markers (Muc2, Sox9) along the crypt-villus axis is associated with DNA methylation. Hence, using an original model of cryosectioning along the crypt-villus axis that allows in situ detection of dynamic epigenetic modifications, we demonstrate that regulation of pluripotency and differentiation markers in healthy intestinal mucosa involves different and specific epigenetic mechanisms.',
'date' => '2014-12-27',
'pmid' => 'http://www.sciencedirect.com/science/article/pii/S1873506114001585',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 37 => array(
'id' => '2215',
'name' => 'Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation.',
'authors' => 'Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ',
'description' => 'Artificial transcription factors (ATFs) and genomic nucleases based on a DNA binding platform consisting of multiple zinc finger domains are currently being developed for clinical applications. However, no genome-wide investigations into their binding specificity have been performed. We have created six-finger ATFs to target two different 18 nt regions of the human SOX2 promoter; each ATF is constructed such that it contains or lacks a super KRAB domain (SKD) that interacts with a complex containing repressive histone methyltransferases. ChIP-seq analysis of the effector-free ATFs in MCF7 breast cancer cells identified thousands of binding sites, mostly in promoter regions; the addition of an SKD domain increased the number of binding sites ∼5-fold, with a majority of the new sites located outside of promoters. De novo motif analyses suggest that the lack of binding specificity is due to subsets of the finger domains being used for genomic interactions. Although the ATFs display widespread binding, few genes showed expression differences; genes repressed by the ATF-SKD have stronger binding sites and are more enriched for a 12 nt motif. Interestingly, epigenetic analyses indicate that the transcriptional repression caused by the ATF-SKD is not due to changes in active histone modifications.',
'date' => '2014-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25122745',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 38 => array(
'id' => '2664',
'name' => 'The PML-associated protein DEK regulates the balance of H3.3 loading on chromatin and is important for telomere integrity.',
'authors' => 'Ivanauskiene K, Delbarre E, McGhie JD, Küntziger T, Wong LH, Collas P',
'description' => 'Histone variant H3.3 is deposited in chromatin at active sites, telomeres, and pericentric heterochromatin by distinct chaperones, but the mechanisms of regulation and coordination of chaperone-mediated H3.3 loading remain largely unknown. We show here that the chromatin-associated oncoprotein DEK regulates differential HIRA- and DAAX/ATRX-dependent distribution of H3.3 on chromosomes in somatic cells and embryonic stem cells. Live cell imaging studies show that nonnucleosomal H3.3 normally destined to PML nuclear bodies is re-routed to chromatin after depletion of DEK. This results in HIRA-dependent widespread chromatin deposition of H3.3 and H3.3 incorporation in the foci of heterochromatin in a process requiring the DAXX/ATRX complex. In embryonic stem cells, loss of DEK leads to displacement of PML bodies and ATRX from telomeres, redistribution of H3.3 from telomeres to chromosome arms and pericentric heterochromatin, induction of a fragile telomere phenotype, and telomere dysfunction. Our results indicate that DEK is required for proper loading of ATRX and H3.3 on telomeres and for telomeric chromatin architecture. We propose that DEK acts as a "gatekeeper" of chromatin, controlling chromatin integrity by restricting broad access to H3.3 by dedicated chaperones. Our results also suggest that telomere stability relies on mechanisms ensuring proper histone supply and routing.',
'date' => '2014-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25049225',
'doi' => '',
'modified' => '2015-07-24 15:39:05',
'created' => '2015-07-24 15:39:05',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 39 => array(
'id' => '2338',
'name' => 'The specific alteration of histone methylation profiles by DZNep during early zebrafish development.',
'authors' => 'Ostrup O, Reiner AH, Aleström P, Collas P',
'description' => '<p>Early embryo development constitutes a unique opportunity to study acquisition of epigenetic marks, including histone methylation. This study investigates the in vivo function and specificity of 3-deazaneplanocin A (DZNep), a promising anti-cancer drug that targets polycomb complex genes. One- to two-cell stage embryos were cultured with DZNep, and subsequently evaluated at the post-mid blastula transition stage for H3K27me3, H3K4me3 and H3K9me3 occupancy and enrichment at promoters using ChIP-chip microarrays. DZNep affected promoter enrichment of H3K27me3 and H3K9me3, whereas H3K4me3 remained stable. Interestingly, DZNep induced a loss of H3K27me3 and H3K9me3 from a substantial number of promoters but did not prevent de novo acquisition of these marks on others, indicating gene-specific targeting of its action. Loss/gain of H3K27me3 on promoters did not result in changes in gene expression levels until 24h post-fertilization. In contrast, genes gaining H3K9me3 displayed strong and constant down-regulation upon DZNep treatment. H3K9me3 enrichment on these gene promoters was observed not only in the proximal area as expected, but also over the transcription start site. Altered H3K9me3 profiles were associated with severe neuronal and cranial phenotypes at day 4-5 post-fertilization. Thus, DZNep was shown to affect enrichment patterns of H3K27me3 and H3K9me3 at promoters in a gene-specific manner.</p>',
'date' => '2014-09-28',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25260724',
'doi' => '',
'modified' => '2016-04-08 09:43:32',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 40 => array(
'id' => '2226',
'name' => 'KMTase Set7/9 is a critical regulator of E2F1 activity upon genotoxic stress.',
'authors' => 'Lezina L, Aksenova V, Ivanova T, Purmessur N, Antonov AV, Tentler D, Fedorova O, Garabadgiu AV, Talianidis I, Melino G, Barlev NA',
'description' => 'During the recent years lysine methyltransferase Set7/9 ((Su(var)-3-9, Enhancer-of-Zeste, Trithorax) domain containing protein 7/9) has emerged as an important regulator of different transcription factors. In this study, we report a novel function for Set7/9 as a critical co-activator of E2 promoter-binding factor 1 (E2F1)-dependent transcription in response to DNA damage. By means of various biochemical, cell biology, and bioinformatics approaches, we uncovered that cell-cycle progression through the G1/S checkpoint of tumour cells upon DNA damage is defined by the threshold of expression of both E2F1 and Set7/9. The latter affects the activity of E2F1 by indirectly modulating histone modifications in the promoters of E2F1-dependent genes. Moreover, Set7/9 differentially affects E2F1 transcription targets: it promotes cell proliferation via expression of the CCNE1 gene and represses apoptosis by inhibiting the TP73 gene. Our biochemical screening of the panel of lung tumour cell lines suggests that these two factors are critically important for transcriptional upregulation of the CCNE1 gene product and hence successful progression through cell cycle. These findings identify Set7/9 as a potential biomarker in tumour cells with overexpressed E2F1 activity.Cell Death and Differentiation advance online publication, 15 August 2014; doi:10.1038/cdd.2014.108.',
'date' => '2014-08-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25124555',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 41 => array(
'id' => '2206',
'name' => 'The histone variant composition of centromeres is controlled by the pericentric heterochromatin state during the cell cycle.',
'authors' => 'Boyarchuk E, Filipescu D, Vassias I, Cantaloube S, Almouzni G',
'description' => 'Correct chromosome segregation requires a unique chromatin environment at centromeres and in their vicinity. Here, we address how the deposition of canonical H2A and H2A.Z histone variants is controlled at pericentric heterochromatin (PHC). Whereas in euchromatin newly synthesized H2A and H2A.Z are deposited throughout the cell cycle, we reveal two discrete waves of deposition at PHC - during mid to late S phase in a replication-dependent manner for H2A and during G1 phase for H2A.Z. This G1 cell cycle restriction is lost when heterochromatin features are altered, leading to the accumulation of H2A.Z at the domain. Interestingly, compromising PHC integrity also impacts upon neighboring centric chromatin, increasing the amount of centromeric CENP-A without changing the timing of its deposition. We conclude that the higher-order chromatin structure at the pericentric domain influences dynamics at the nucleosomal level within centromeric chromatin. The two different modes of rearrangement of the PHC during the cell cycle provide distinct opportunities to replenish one or the other H2A variant, highlighting PHC integrity as a potential signal to regulate the deposition timing and stoichiometry of histone variants at the centromere.',
'date' => '2014-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24906798',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 42 => array(
'id' => '2081',
'name' => 'RNAi-Mediated Gene silencing in Zebrafish Triggered by Convergent Transcription.',
'authors' => 'Andrews OE, Cha DJ, Wei C, Patton JG',
'description' => 'RNAi based strategies to induce gene silencing are commonly employed in numerous model organisms but have not been extensively used in zebrafish. We found that introduction of transgenes containing convergent transcription units in zebrafish embryos induced stable transcriptional gene silencing (TGS) in cis and trans for reporter (mCherry) and endogenous (One-Eyed Pinhead (OEP) and miR-27a/b) genes. Convergent transcription enabled detection of both sense and antisense transcripts and silencing was suppressed upon Dicer knockdown, indicating processing of double stranded RNA. By ChIP analyses, increased silencing was accompanied by enrichment of the heterochromatin mark H3K9me3 in the two convergently arranged promoters and in the intervening reading frame. Our work demonstrates that convergent transcription can induce gene silencing in zebrafish providing another tool to create specific temporal and spatial control of gene expression.',
'date' => '2014-06-09',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24909225',
'doi' => '',
'modified' => '2015-07-24 15:39:02',
'created' => '2015-07-24 15:39:02',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 43 => array(
'id' => '1888',
'name' => 'Transcriptional Derepression of the ERVWE1 Locus following Influenza A Virus Infection.',
'authors' => 'Li F, Nellåker C, Sabunciyan S, Yolken RH, Jones-Brando L, Johansson AS, Owe-Larsson B, Karlsson H',
'description' => 'UNLABELLED: Syncytin-1, a fusogenic protein encoded by a human endogenous retrovirus of the W family (HERV-W) element (ERVWE1), is expressed in the syncytiotrophoblast layer of the placenta. This locus is transcriptionally repressed in adult tissues through promoter CpG methylation and suppressive histone modifications. Whereas syncytin-1 appears to be crucial for the development and functioning of the human placenta, its ectopic expression has been associated with pathological conditions, such as multiple sclerosis and schizophrenia. We previously reported on the transactivation of HERV-W elements, including ERVWE1, during influenza A/WSN/33 virus infection in a range of human cell lines. Here we report the results of quantitative PCR analyses of transcripts encoding syncytin-1 in both cell lines and primary fibroblast cells. We observed that spliced ERVWE1 transcripts and those encoding the transcription factor glial cells missing 1 (GCM1), acting as an enhancer element upstream of ERVWE1, are prominently upregulated in response to influenza A/WSN/33 virus infection in nonplacental cells. Knockdown of GCM1 by small interfering RNA followed by infection suppressed the transactivation of ERVWE1. While the infection had no influence on CpG methylation in the ERVWE1 promoter, chromatin immunoprecipitation assays detected decreased H3K9 trimethylation (H3K9me3) and histone methyltransferase SETDB1 levels along with influenza virus proteins associated with ERVWE1 and other HERV-W loci in infected CCF-STTG1 cells. The present findings suggest that an exogenous influenza virus infection can transactivate ERVWE1 by increasing transcription of GCM1 and reducing H3K9me3 in this region and in other regions harboring HERV-W elements. IMPORTANCE: Syncytin-1, a protein encoded by the env gene in the HERV-W locus ERVWE1, appears to be crucial for the development and functioning of the human placenta and is transcriptionally repressed in nonplacental tissues. Nevertheless, its ectopic expression has been associated with pathological conditions, such as multiple sclerosis and schizophrenia. In the present paper, we report findings suggesting that an exogenous influenza A virus infection can transactivate ERVWE1 by increasing the transcription of GCM1 and reducing the repressive histone mark H3K9me3 in this region and in other regions harboring HERV-W elements. These observations have implications of potential relevance for viral pathogenesis and for conditions associated with the aberrant transcription of HERV-W loci.',
'date' => '2014-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24478419',
'doi' => '',
'modified' => '2015-07-24 15:39:02',
'created' => '2015-07-24 15:39:02',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 44 => array(
'id' => '1723',
'name' => 'HDAC inhibitor confers radiosensitivity to prostate stem-like cells.',
'authors' => 'Frame FM, Pellacani D, Collins AT, Simms MS, Mann VM, Jones G, Meuth M, Bristow RG, Maitland NJ',
'description' => 'Background:Radiotherapy can be an effective treatment for prostate cancer, but radiorecurrent tumours do develop. Considering prostate cancer heterogeneity, we hypothesised that primitive stem-like cells may constitute the radiation-resistant fraction.Methods:Primary cultures were derived from patients undergoing resection for prostate cancer or benign prostatic hyperplasia. After short-term culture, three populations of cells were sorted, reflecting the prostate epithelial hierarchy, namely stem-like cells (SCs, α2β1integrin(hi)/CD133(+)), transit-amplifying (TA, α2β1integrin(hi)/CD133(-)) and committed basal (CB, α2β1integrin(lo)) cells. Radiosensitivity was measured by colony-forming efficiency (CFE) and DNA damage by comet assay and DNA damage foci quantification. Immunofluorescence and flow cytometry were used to measure heterochromatin. The HDAC (histone deacetylase) inhibitor Trichostatin A was used as a radiosensitiser.Results:Stem-like cells had increased CFE post irradiation compared with the more differentiated cells (TA and CB). The SC population sustained fewer lethal double-strand breaks than either TA or CB cells, which correlated with SCs being less proliferative and having increased levels of heterochromatin. Finally, treatment with an HDAC inhibitor sensitised the SCs to radiation.Interpretation:Prostate SCs are more radioresistant than more differentiated cell populations. We suggest that the primitive cells survive radiation therapy and that pre-treatment with HDAC inhibitors may sensitise this resistant fraction.',
'date' => '2013-12-10',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24220693',
'doi' => '',
'modified' => '2015-07-24 15:39:01',
'created' => '2015-07-24 15:39:01',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 45 => array(
'id' => '1516',
'name' => 'Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes.',
'authors' => 'Lund E, Oldenburg AR, Delbarre E, Freberg CT, Duband-Goulet I, Eskeland R, Buendia B, Collas P',
'description' => 'The nuclear lamina is implicated in the organization of the eukaryotic nucleus. Association of nuclear lamins with the genome occurs through large chromatin domains including mostly, but not exclusively, repressed genes. How lamin interactions with regulatory elements modulate gene expression in different cellular contexts is unknown. We show here that in human adipose tissue stem cells, lamin A/C interacts with distinct spatially restricted subpromoter regions, both within and outside peripheral and intra-nuclear lamin-rich domains. These localized interactions are associated with distinct transcriptional outcomes in a manner dependent on local chromatin modifications. Down-regulation of lamin A/C leads to dissociation of lamin A/C from promoters and remodels repressive and permissive histone modifications by enhancing transcriptional permissiveness, but is not sufficient to elicit gene activation. Adipogenic differentiation resets a large number of lamin-genome associations globally and at subpromoter levels and redefines associated transcription outputs. We propose that lamin A/C acts as a modulator of local gene expression outcome through interaction with adjustable sites on promoters, and that these position-dependent transcriptional readouts may be reset upon differentiation.',
'date' => '2013-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23861385',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 46 => array(
'id' => '1595',
'name' => 'Long range epigenetic silencing is a trans-species mechanism that results in cancer specific deregulation by overriding the chromatin domains of normal cells.',
'authors' => 'Forn M, Muñoz M, Tauriello DV, Merlos-Suárez A, Rodilla V, Bigas A, Batlle E, Jordà M, Peinado MA',
'description' => 'DNA methylation and chromatin remodeling are frequently implicated in the silencing of genes involved in carcinogenesis. Long Range Epigenetic Silencing (LRES) is a mechanism of gene inactivation that affects multiple contiguous CpG islands and has been described in different human cancer types. However, it is unknown whether there is a coordinated regulation of the genes embedded in these regions in normal cells and in early stages of tumor progression. To better characterize the molecular events associated with the regulation and remodeling of these regions we analyzed two regions undergoing LRES in human colon cancer in the mouse model. We demonstrate that LRES also occurs in murine cancer in vivo and mimics the molecular features of the human phenomenon, namely, downregulation of gene expression, acquisition of inactive histone marks, and DNA hypermethylation of specific CpG islands. The genes embedded in these regions showed a dynamic and autonomous regulation during mouse intestinal cell differentiation, indicating that, in the framework considered here, the coordinated regulation in LRES is restricted to cancer. Unexpectedly, benign adenomas in Apc(Min/+) mice showed overexpression of most of the genes affected by LRES in cancer, which suggests that the repressive remodeling of the region is a late event. Chromatin immunoprecipitation analysis of the transcriptional insulator CTCF in mouse colon cancer cells revealed disrupted chromatin domain boundaries as compared with normal cells. Malignant regression of cancer cells by in vitro differentiation resulted in partial reversion of LRES and gain of CTCF binding. We conclude that genes in LRES regions are plastically regulated in cell differentiation and hyperproliferation, but are constrained to a coordinated repression by abolishing boundaries and the autonomous regulation of chromatin domains in cancer cells.',
'date' => '2013-08-30',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24035705',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 47 => array(
'id' => '1486',
'name' => 'Transgene- and locus-dependent imprinting reveals allele-specific chromosome conformations.',
'authors' => 'Lonfat N, Montavon T, Jebb D, Tschopp P, Nguyen Huynh TH, Zakany J, Duboule D',
'description' => 'When positioned into the integrin α-6 gene, an Hoxd9lacZ reporter transgene displayed parental imprinting in mouse embryos. While the expression from the paternal allele was comparable with patterns seen for the same transgene when present at the neighboring HoxD locus, almost no signal was scored at this integration site when the transgene was inherited from the mother, although the Itga6 locus itself is not imprinted. The transgene exhibited maternal allele-specific DNA hypermethylation acquired during oogenesis, and its expression silencing was reversible on passage through the male germ line. Histone modifications also corresponded to profiles described at known imprinted loci. Chromosome conformation analyses revealed distinct chromatin microarchitectures, with a more compact structure characterizing the maternally inherited repressed allele. Such genetic analyses of well-characterized transgene insertions associated with a de novo-induced parental imprint may help us understand the molecular determinants of imprinting.',
'date' => '2013-07-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23818637',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 48 => array(
'id' => '1425',
'name' => 'Expression of a large LINE-1-driven antisense RNA is linked to epigenetic silencing of the metastasis suppressor gene TFPI-2 in cancer.',
'authors' => 'Cruickshanks HA, Vafadar-Isfahani N, Dunican DS, Lee A, Sproul D, Lund JN, Meehan RR, Tufarelli C',
'description' => 'LINE-1 retrotransposons are abundant repetitive elements of viral origin, which in normal cells are kept quiescent through epigenetic mechanisms. Activation of LINE-1 occurs frequently in cancer and can enable LINE-1 mobilization but also has retrotransposition-independent consequences. We previously reported that in cancer, aberrantly active LINE-1 promoters can drive transcription of flanking unique sequences giving rise to LINE-1 chimeric transcripts (LCTs). Here, we show that one such LCT, LCT13, is a large transcript (>300 kb) running antisense to the metastasis-suppressor gene TFPI-2. We have modelled antisense RNA expression at TFPI-2 in transgenic mouse embryonic stem (ES) cells and demonstrate that antisense RNA induces silencing and deposition of repressive histone modifications implying a causal link. Consistent with this, LCT13 expression in breast and colon cancer cell lines is associated with silencing and repressive chromatin at TFPI-2. Furthermore, we detected LCT13 transcripts in 56% of colorectal tumours exhibiting reduced TFPI-2 expression. Our findings implicate activation of LINE-1 elements in subsequent epigenetic remodelling of surrounding genes, thus hinting a novel retrotransposition-independent role for LINE-1 elements in malignancy.',
'date' => '2013-05-23',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23703216',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 49 => array(
'id' => '1497',
'name' => 'Histone lysine trimethylation or acetylation can be modulated by phytoestrogen, estrogen or anti-HDAC in breast cancer cell lines.',
'authors' => 'Dagdemir A, Durif J, Ngollo M, Bignon YJ, Bernard-Gallon D',
'description' => '<p>AIM: The isoflavones genistein, daidzein and equol (daidzein metabolite) have been reported to interact with epigenetic modifications, specifically hypermethylation of tumor suppressor genes. The objective of this study was to analyze and understand the mechanisms by which phytoestrogens act on chromatin in breast cancer cell lines. MATERIALS & METHODS: Two breast cancer cell lines, MCF-7 and MDA-MB 231, were treated with genistein (18.5 µM), daidzein (78.5 µM), equol (12.8 µM), 17β-estradiol (10 nM) and suberoylanilide hydroxamic acid (1 µM) for 48 h. A control with untreated cells was performed. 17β-estradiol and an anti-HDAC were used to compare their actions with phytoestrogens. The chromatin immunoprecipitation coupled with quantitative PCR was used to follow soy phytoestrogen effects on H3 and H4 histones on H3K27me3, H3K9me3, H3K4me3, H4K8ac and H3K4ac marks, and we selected six genes (EZH2, BRCA1, ERα, ERβ, SRC3 and P300) for analysis. RESULTS: Soy phytoestrogens induced a decrease in trimethylated marks and an increase in acetylating marks studied at six selected genes. CONCLUSION: We demonstrated that soy phytoestrogens tend to modify transcription through the demethylation and acetylation of histones in breast cancer cell lines.</p>',
'date' => '2013-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23414320',
'doi' => '',
'modified' => '2016-05-03 12:17:35',
'created' => '2015-07-24 15:39:00',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 50 => array(
'id' => '1179',
'name' => 'Epigenetic Regulation of Nestin Expression During Neurogenic Differentiation of Adipose Tissue Stem Cells.',
'authors' => 'Boulland JL, Mastrangelopoulou M, Boquest AC, Jakobsen R, Noer A, Glover JC, Collas P.',
'description' => 'Adipose-tissue-derived stem cells (ASCs) have received considerable attention due to their easy access, expansion potential, and differentiation capacity. ASCs are believed to have the potential to differentiate into neurons. However, the mechanisms by which this may occur remain largely unknown. Here, we show that culturing ASCs under active proliferation conditions greatly improves their propensity to differentiate toward osteogenic, adipogenic, and neurogenic lineages. Neurogenic-induced ASCs express early neurogenic genes as well as markers of mature neurons, including voltage-gated ion channels. Nestin, highly expressed in neural progenitors, is upregulated by mitogenic stimulation of ASCs, and as in neural progenitors, then repressed during neurogenic differentiation. Nestin gene (NES) expression under these conditions appears to be regulated by epigenetic mechanisms. The neural-specific, but not muscle-specific, enhancer regions of NES are DNA demethylated by mitogenic stimulation, and remethylated upon neurogenic differentiation. We observe dynamic changes in histone H3K4, H3K9, and H3K27 methylation on the NES locus before and during neurogenic differentiation that are consistent with epigenetic processes involved in the regulation of NES expression. We suggest that ASCs are epigenetically prepatterned to differentiate toward a neural lineage and that this prepatterning is enhanced by demethylation of critical NES enhancer elements upon mitogenic stimulation preceding neurogenic differentiation. Our findings provide molecular evidence that the differentiation repertoire of ASCs may extend beyond mesodermal lineages.',
'date' => '2012-12-21',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/23140086',
'doi' => '',
'modified' => '2015-07-24 15:38:59',
'created' => '2015-07-24 15:38:59',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 51 => array(
'id' => '752',
'name' => 'The histone demethylase Kdm3a is essential to progression through differentiation.',
'authors' => 'Herzog M, Josseaux E, Dedeurwaerder S, Calonne E, Volkmar M, Fuks F',
'description' => 'Histone demethylation has important roles in regulating gene expression and forms part of the epigenetic memory system that regulates cell fate and identity by still poorly understood mechanisms. Here, we examined the role of histone demethylase Kdm3a during cell differentiation, showing that Kdm3a is essential for differentiation into parietal endoderm-like (PE) cells in the F9 mouse embryonal carcinoma model. We identified a number of target genes regulated by Kdm3a during endoderm differentiation; among the most dysregulated were the three developmental master regulators Dab2, Pdlim4 and FoxQ1. We show that dysregulation of the expression of these genes correlates with Kdm3a H3K9me2 demethylase activity. We further demonstrate that either Dab2 depletion or Kdm3a depletion prevents F9 cells from fully differentiating into PE cells, but that ectopic expression of Dab2 cannot compensate for Kdm3a knockdown; Dab2 is thus necessary, but insufficient on its own, to promote complete terminal differentiation. We conclude that Kdm3a plays a crucial role in progression through PE differentiation by regulating expression of a set of endoderm differentiation master genes. The emergence of Kdm3a as a key modulator of cell fate decision strengthens the view that histone demethylases are essential to cell differentiation.',
'date' => '2012-05-11',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22581778',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 52 => array(
'id' => '630',
'name' => 'Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.',
'authors' => 'Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B',
'description' => 'While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA hypomethylation in the cancer cell, primarily at partially methylated domains (PMDs) in normal breast cells. Unexpectedly, genes within these regions are largely silenced in cancer cells. The loss of DNA methylation in these regions is accompanied by formation of repressive chromatin, with a significant fraction displaying allelic DNA methylation where one allele is DNA methylated while the other allele is occupied by histone modifications H3K9me3 or H3K27me3. Our results show a mutually exclusive relationship between DNA methylation and H3K9me3 or H3K27me3. These results suggest that global DNA hypomethylation in breast cancer is tightly linked to the formation of repressive chromatin domains and gene silencing, thus identifying a potential epigenetic pathway for gene regulation in cancer cells.',
'date' => '2012-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22156296',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 53 => array(
'id' => '919',
'name' => 'Prepatterning of developmental gene expression by modified histones before zygotic genome activation.',
'authors' => 'Lindeman LC, Andersen IS, Reiner AH, Li N, Aanes H, Østrup O, Winata C, Mathavan S, Müller F, Aleström P, Collas P',
'description' => 'A hallmark of anamniote vertebrate development is a window of embryonic transcription-independent cell divisions before onset of zygotic genome activation (ZGA). Chromatin determinants of ZGA are unexplored; however, marking of developmental genes by modified histones in sperm suggests a predictive role of histone marks for ZGA. In zebrafish, pre-ZGA development for ten cell cycles provides an opportunity to examine whether genomic enrichment in modified histones is present before initiation of transcription. By profiling histone H3 trimethylation on all zebrafish promoters before and after ZGA, we demonstrate here an epigenetic prepatterning of developmental gene expression. This involves pre-ZGA marking of transcriptionally inactive genes involved in homeostatic and developmental regulation by permissive H3K4me3 with or without repressive H3K9me3 or H3K27me3. Our data suggest that histone modifications are instructive for the developmental gene expression program.',
'date' => '2011-12-13',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22137762',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
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[maximum depth reached]
)
),
(int) 54 => array(
'id' => '637',
'name' => 'H3.5 is a novel hominid-specific histone H3 variant that is specifically expressed in the seminiferous tubules of human testes.',
'authors' => 'Schenk R, Jenke A, Zilbauer M, Wirth S, Postberg J',
'description' => 'The incorporation of histone variants into chromatin plays an important role for the establishment of particular chromatin states. Six human histone H3 variants are known to date, not counting CenH3 variants: H3.1, H3.2, H3.3 and the testis-specific H3.1t as well as the recently described variants H3.X and H3.Y. We report the discovery of H3.5, a novel non-CenH3 histone H3 variant. H3.5 is encoded on human chromosome 12p11.21 and probably evolved in a common ancestor of all recent great apes (Hominidae) as a consequence of H3F3B gene duplication by retrotransposition. H3.5 mRNA is specifically expressed in seminiferous tubules of human testis. Interestingly, H3.5 has two exact copies of ARKST motifs adjacent to lysine-9 or lysine-27, and lysine-79 is replaced by asparagine. In the Hek293 cell line, ectopically expressed H3.5 is assembled into chromatin and targeted by PTM. H3.5 preferentially colocalizes with euchromatin, and it is associated with actively transcribed genes and can replace an essential function of RNAi-depleted H3.3 in cell growth.',
'date' => '2011-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21274551',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
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[maximum depth reached]
)
),
(int) 55 => array(
'id' => '274',
'name' => 'Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability.',
'authors' => 'Cortázar D, Kunz C, Selfridge J, Lettieri T, Saito Y, MacDougall E, Wirz A, Schuermann D, Jacobs AL, Siegrist F, Steinacher R, Jiricny J, Bird A, Schär P',
'description' => 'Thymine DNA glycosylase (TDG) is a member of the uracil DNA glycosylase (UDG) superfamily of DNA repair enzymes. Owing to its ability to excise thymine when mispaired with guanine, it was proposed to act against the mutability of 5-methylcytosine (5-mC) deamination in mammalian DNA. However, TDG was also found to interact with transcription factors, histone acetyltransferases and de novo DNA methyltransferases, and it has been associated with DNA demethylation in gene promoters following activation of transcription, altogether implicating an engagement in gene regulation rather than DNA repair. Here we use a mouse genetic approach to determine the biological function of this multifaceted DNA repair enzyme. We find that, unlike other DNA glycosylases, TDG is essential for embryonic development, and that this phenotype is associated with epigenetic aberrations affecting the expression of developmental genes. Fibroblasts derived from Tdg null embryos (mouse embryonic fibroblasts, MEFs) show impaired gene regulation, coincident with imbalanced histone modification and CpG methylation at promoters of affected genes. TDG associates with the promoters of such genes both in fibroblasts and in embryonic stem cells (ESCs), but epigenetic aberrations only appear upon cell lineage commitment. We show that TDG contributes to the maintenance of active and bivalent chromatin throughout cell differentiation, facilitating a proper assembly of chromatin-modifying complexes and initiating base excision repair to counter aberrant de novo methylation. We thus conclude that TDG-dependent DNA repair has evolved to provide epigenetic stability in lineage committed cells.',
'date' => '2011-02-17',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21278727',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
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[maximum depth reached]
)
),
(int) 56 => array(
'id' => '592',
'name' => 'Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.',
'authors' => 'Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ',
'description' => 'The H3K9me3 histone modification is often found at promoter regions, where it functions to repress transcription. However, we have previously shown that 3' exons of zinc finger genes (ZNFs) are marked by high levels of H3K9me3. We have now further investigated this unusual location for H3K9me3 in ZNF genes. Neither bioinformatic nor experimental approaches support the hypothesis that the 3' exons of ZNFs are promoters. We further characterized the histone modifications at the 3' ZNF exons and found that these regions also contain H3K36me3, a mark of transcriptional elongation. A genome-wide analysis of ChIP-seq data revealed that ZNFs constitute the majority of genes that have high levels of both H3K9me3 and H3K36me3. These results suggested the possibility that the ZNF genes may be imprinted, with one allele transcribed and one allele repressed. To test the hypothesis that the contradictory modifications are due to imprinting, we used a SNP analysis of RNA-seq data to demonstrate that both alleles of certain ZNF genes having H3K9me3 and H3K36me3 are transcribed. We next analyzed isolated ZNF 3' exons using stably integrated episomes. We found that although the H3K36me3 mark was lost when the 3' ZNF exon was removed from its natural genomic location, the isolated ZNF 3' exons retained the H3K9me3 mark. Thus, the H3K9me3 mark at ZNF 3' exons does not impede transcription and it is regulated independently of the H3K36me3 mark. Finally, we demonstrate a strong relationship between the number of tandemly repeated domains in the 3' exons and the H3K9me3 mark. We suggest that the H3K9me3 at ZNF 3' exons may function to protect the genome from inappropriate recombination rather than to regulate transcription.',
'date' => '2011-02-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21347206',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
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[maximum depth reached]
)
),
(int) 57 => array(
'id' => '599',
'name' => 'ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes.',
'authors' => 'Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ',
'description' => 'Only a small percentage of human transcription factors (e.g. those associated with a specific differentiation program) are expressed in a given cell type. Thus, cell fate is mainly determined by cell type-specific silencing of transcription factors that drive different cellular lineages. Several histone modifications have been associated with gene silencing, including H3K27me3 and H3K9me3. We have previously shown that genes for the two largest classes of mammalian transcription factors are marked by distinct histone modifications; homeobox genes are marked by H3K27me3 and zinc finger genes are marked by H3K9me3. Several histone methyltransferases (e.g. G9a and SETDB1) may be involved in mediating the H3K9me3 silencing mark. We have used ChIP-chip and ChIP-seq to demonstrate that SETDB1, but not G9a, is associated with regions of the genome enriched for H3K9me3. One current model is that SETDB1 is recruited to specific genomic locations via interaction with the corepressor TRIM28 (KAP1), which is in turn recruited to the genome via interaction with zinc finger transcription factors that contain a Kruppel-associated box (KRAB) domain. However, specific KRAB-ZNFs that recruit TRIM28 (KAP1) and SETDB1 to the genome have not been identified. We now show that ZNF274 (a KRAB-ZNF that contains 5 C2H2 zinc finger domains), can interact with KAP1 both in vivo and in vitro and, using ChIP-seq, we show that ZNF274 binding sites co-localize with SETDB1, KAP1, and H3K9me3 at the 3' ends of zinc finger genes. Knockdown of ZNF274 with siRNAs reduced the levels of KAP1 and SETDB1 recruitment to the binding sites. These studies provide the first identification of a KRAB domain-containing ZNF that is involved in recruitment of the KAP1 and SETDB1 to specific regions of the human genome.',
'date' => '2010-12-08',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21170338',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 58 => array(
'id' => '74',
'name' => 'In vivo chromatin organization of mouse rod photoreceptors correlates with histone modifications.',
'authors' => 'Kizilyaprak C, Spehner D, Devys D, Schultz P',
'description' => 'BACKGROUND: The folding of genetic information into chromatin plays important regulatory roles in many nuclear processes and particularly in gene transcription. Post translational histone modifications are associated with specific chromatin condensation states and with distinct transcriptional activities. The peculiar chromatin organization of rod photoreceptor nuclei, with a large central domain of condensed chromatin surrounded by a thin border of extended chromatin was used as a model to correlate in vivo chromatin structure, histone modifications and transcriptional activity. METHODOLOGY: We investigated the functional relationships between chromatin compaction, distribution of histone modifications and location of RNA polymerase II in intact murine rod photoreceptors using cryo-preparation methods, electron tomography and immunogold labeling. Our results show that the characteristic central heterochromatin of rod nuclei is organized into concentric domains characterized by a progressive loosening of the chromatin architecture from inside towards outside and by specific combinations of silencing histone marks. The peripheral heterochromatin is formed by closely packed 30 nm fibers as revealed by a characteristic optical diffraction signal. Unexpectedly, the still highly condensed most external heterochromatin domain contains acetylated histones, which are usually associated with active transcription and decondensed chromatin. Histone acetylation is thus not sufficient in vivo for complete chromatin decondensation. The euchromatin domain contains several degrees of chromatin compaction and the histone tails are hyperacetylated, enriched in H3K4 monomethylation and hypo trimethylated on H3K9, H3K27 and H4K20. The transcriptionally active RNA polymerases II molecules are confined in the euchromatin domain and are preferentially located at the vicinity of the interface with heterochromatin. CONCLUSIONS: Our results show that transcription is located in the most decondensed and highly acetylated chromatin regions, but since acetylation is found associated with compact chromatin it is not sufficient to decondense chromatin in vivo. We also show that a combination of histone marks defines distinct concentric heterochromatin domains.',
'date' => '2010-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/20543957',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
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[maximum depth reached]
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(int) 59 => array(
'id' => '95',
'name' => 'MicroChIP--a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies.',
'authors' => 'Dahl JA, Collas P',
'description' => 'Chromatin immunoprecipitation (ChIP) is a powerful technique for studying protein-DNA interactions. Drawbacks of current ChIP assays however are a requirement for large cell numbers, which limits applicability of ChIP to rare cell samples, and/or lengthy procedures with limited applications. There are to date no protocols for fast and parallel ChIPs of post-translationally modified histones from small cell numbers or biopsies, and importantly, no protocol allowing for investigations of transcription factor binding in small cell numbers. We report here the development of a micro (micro) ChIP assay suitable for up to nine parallel quantitative ChIPs of modified histones or RNA polymerase II from a single batch of 1000 cells. MicroChIP can also be downscaled to monitor the association of one protein with multiple genomic sites in as few as 100 cells. MicroChIP is applicable to small fresh tissue biopsies, and a cross-link-while-thawing procedure makes the assay suitable for frozen biopsies. Using MicroChIP, we characterize transcriptionally permissive and repressive histone H3 modifications on developmentally regulated promoters in human embryonal carcinoma cells and in osteosarcoma biopsies. muChIP creates possibilities for multiple parallel and rapid transcription factor binding and epigenetic analyses of rare cell and tissue samples.',
'date' => '2008-02-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/18202078',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
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(int) 60 => array(
'id' => '76',
'name' => 'A rapid micro chromatin immunoprecipitation assay (microChIP).',
'authors' => 'Dahl JA, Collas P',
'description' => 'Interactions of proteins with DNA mediate many critical nuclear functions. Chromatin immunoprecipitation (ChIP) is a robust technique for studying protein-DNA interactions. Current ChIP assays, however, either require large cell numbers, which prevent their application to rare cell samples or small-tissue biopsies, or involve lengthy procedures. We describe here a 1-day micro ChIP (microChIP) protocol suitable for up to eight parallel histone and/or transcription factor immunoprecipitations from a single batch of 1,000 cells. MicroChIP technique is also suitable for monitoring the association of one protein with multiple genomic sites in 100 cells. Alterations in cross-linking and chromatin preparation steps also make microChIP applicable to approximately 1-mm(3) fresh- or frozen-tissue biopsies. From cell fixation to PCR-ready DNA, the procedure takes approximately 8 h for 16 ChIPs.',
'date' => '2008-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/18536650',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
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),
(int) 61 => array(
'id' => '75',
'name' => 'Fast genomic muChIP-chip from 1,000 cells',
'authors' => 'Dahl JA, Reiner AH, Collas P.',
'description' => 'Genome-wide location analysis of histone modifications and transcription factor binding relies on chromatin immunoprecipitation (ChIP) assays. These assays are, however, time-consuming and require large numbers of cells, hindering their application to the analysis of many interesting cell types. We report here a fast microChIP (μChIP) assay for 1,000 cells in combination with microarrays to produce genome-scale surveys of histone modifications. μChIP-chip reliably reproduces data obtained by large-scale assays: H3K9ac and H3K9m3 enrichment profiles are conserved and nucleosome-free regions are revealed.',
'date' => '0000-00-00',
'pmid' => '',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
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[maximum depth reached]
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(int) 62 => array(
'id' => '73',
'name' => 'Promoter DNA Methylation Patterns of Differentiated Cells Are Largely Programmed at the Progenitor Stage',
'authors' => 'Sørensen AL, Jacobsen BM, Reiner AH, Andersen IS, Collas P',
'description' => 'Mesenchymal stem cells (MSCs) isolated from various tissues share common phenotypic and functional properties. However, intrinsic molecular evidence supporting these observations has been lacking. Here, we unravel overlapping genome-wide promoter DNA methylation patterns between MSCs from adipose tissue, bone marrow, and skeletal muscle, whereas hematopoietic progenitors are more epigenetically distant from MSCs as a whole. Commonly hypermethylated genes are enriched in signaling, metabolic, and developmental functions, whereas genes hypermethylated only in MSCs are associated with early development functions. We find that most lineage-specification promoters are DNA hypomethylated and harbor a combination of trimethylated H3K4 and H3K27, whereas early developmental genes are DNA hypermethylated with or without H3K27 methylation. Promoter DNA methylation patterns of differentiated cells are largely established at the progenitor stage; yet, differentiation segregates a minor fraction of the commonly hypermethylated promoters, generating greater epigenetic divergence between differentiated cell types than between their undifferentiated counterparts. We also show an effect of promoter CpG content on methylation dynamics upon differentiation and distinct methylation profiles on transcriptionally active and inactive promoters. We infer that methylation state of lineage-specific promoters in MSCs is not a primary determinant of differentiation capacity. Our results support the view of a common origin of mesenchymal progenitors.',
'date' => '0000-00-00',
'pmid' => '',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
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(int) 63 => array(
'id' => '72',
'name' => 'Chromatin Environment of Histone Variant H3.3 Revealed by Quantitative Imaging and Genome-scale Chromatin and DNA Immunoprecipitation',
'authors' => 'Delbarre E, Jacobsen BM, Reiner AH, Sørensen AL, Kuntziger T, Collas P',
'description' => 'In contrast to canonical histones, histone variant H3.3 is incorporated into chromatin in a replication-independent manner. Posttranslational modifications of H3.3 have been identified; however, the epigenetic environment of incorporated H3.3 is unclear. We have investigated the genomic distribution of epitope-tagged H3.3 in relation to histone modifications, DNA methylation, and transcription in mesenchymal stem cells. Quantitative imaging at the nucleus level shows that H3.3, relative to replicative H3.2 or canonical H2B, is enriched in chromatin domains marked by histone modifications of active or potentially active genes. Chromatin immunoprecipitation of epitope-tagged H3.3 and array hybridization identified 1649 H3.3-enriched promoters, a fraction of which is coenriched in H3K4me3 alone or together with H3K27me3, whereas H3K9me3 is excluded, corroborating nucleus-level imaging data. H3.3-enriched promoters are predominantly CpG-rich and preferentially DNA methylated, relative to the proportion of methylated RefSeq promoters in the genome. Most but not all H3.3-enriched promoters are transcriptionally active, and coenrichment of H3.3 with repressive H3K27me3 correlates with an enhanced proportion of expressed genes carrying this mark. H3.3-target genes are enriched in mesodermal differentiation and signaling functions. Our data suggest that in mesenchymal stem cells, H3.3 targets lineage-priming genes with a potential for activation facilitated by H3K4me3 in facultative association with H3K27me3.',
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<p><small> <strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022 ) on the SX-8G IP-Star automated system. A titration of the antibody consisting of 1, 2, 5, and 10 μg per ChIP experiment was analysed. IgG (2 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active c-fos and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="432" height="61" /> <img src="https://www.diagenode.com/img/product/antibodies/C15410056-FigD.jpg" alt="H3K9me3 Antibody validated in ChIP-seq " caption="false" width="700" height="112" /></p>
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<p><small> <strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 0.5 μg of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) on sheared chromatin from 1 million HeLa cells using the “iDeal ChIP-seq” kit (Cat. No. C01010051). The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoter regions of the active GAPDH and EIF4A2 genes, for the coding region of the ZNF510 gene and for the Sat2 satellite repeat (figure 2A). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the BWA algorithm. Figure 2B shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2C and D show the enrichment at ZNF510 and ZNF12 on chromosome 9 and 7, respectively. These results clearly show an enrichment of H3K9me3 at ZNF repeat genes. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" caption="false" width="278" height="212" /></p>
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<p><small> <strong>Figure 3. Determination of the antibody titer</strong><br /> To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (Cat. No. C15410056), crude serum and flow through in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:60,000. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" caption="false" width="400" height="304" /></p>
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<p><small> <strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western Blot" caption="false" width="200" height="213" /></p>
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<p><small> <strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot analysis was performed on histone extracts from HeLa cells (15 μg, lane 1) and on recombinant H3 (1 μg, lane2) using the Diagenode antibody against H3K9me3 (Cat. No. C15410056). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left. </small></p>
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<p><small> <strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " caption="false" width="432" height="214" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="432" height="61" /> <img src="https://www.diagenode.com/img/product/antibodies/C15410056-FigD.jpg" alt="H3K9me3 Antibody validated in ChIP-seq " caption="false" width="700" height="112" /></p>
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<p><small> <strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 0.5 μg of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) on sheared chromatin from 1 million HeLa cells using the “iDeal ChIP-seq” kit (Cat. No. C01010051). The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoter regions of the active GAPDH and EIF4A2 genes, for the coding region of the ZNF510 gene and for the Sat2 satellite repeat (figure 2A). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the BWA algorithm. Figure 2B shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2C and D show the enrichment at ZNF510 and ZNF12 on chromosome 9 and 7, respectively. These results clearly show an enrichment of H3K9me3 at ZNF repeat genes. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" caption="false" width="278" height="212" /></p>
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<p><small> <strong>Figure 3. Determination of the antibody titer</strong><br /> To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (Cat. No. C15410056), crude serum and flow through in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:60,000. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" caption="false" width="400" height="304" /></p>
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<p><small> <strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western Blot" caption="false" width="200" height="213" /></p>
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<p><small> <strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot analysis was performed on histone extracts from HeLa cells (15 μg, lane 1) and on recombinant H3 (1 μg, lane2) using the Diagenode antibody against H3K9me3 (Cat. No. C15410056). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left. </small></p>
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<p><small> <strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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'name' => 'H3K27ac Antibody',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the acetylated lysine 27</strong> (<strong>H3K27ac</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
'label1' => 'Validation Data',
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<div class="small-6 columns">A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1a.png" width="356" /><br /> B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig1b.png" width="356" /></div>
<div class="small-6 columns">
<p><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>Figure 1A ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196) and optimized PCR primer pairs for qPCR. ChIP was performed with the “Auto Histone ChIP-seq” kit on the IP-Star automated system, using sheared chromatin from 1,000,000 cells. A titration consisting of 1, 2, 5 and 10 µg of antibody per ChIP experiment was analyzed. IgG (2 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active EIF4A2 and ACTB genes, used as positive controls, and for the inactive TSH2B and MYT1 genes, used as negative controls.</p>
<p>Figure 1B ChIP assays were performed using human K562 cells, the Diagenode antibody against H3K27ac (Cat. No. C15410196)and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 100,000 cells. A titration consisting of 0.2, 0.5, 1 and 2 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control. Quantitative PCR was performed with primers for the promoters of the active GAPDH and EIF4A2 genes, used as positive controls, and for the coding regions of the inactive MB and MYT1 genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis)</p>
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<div class="small-12 columns"><center>
<p>A.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2a.png" /></p>
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<p>B.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2b.png" /></p>
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<p>C.<img src="https://www.diagenode.com/img/product/antibodies/C15410196-ChIP-Fig2c.png" /></p>
</center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>ChIP was performed on sheared chromatin from 100,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) as described above. The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A shows the peak distribution along the complete human X-chromosome. Figure 2 B and C show the peak distribution in two regions surrounding the EIF4A2 and GAPDH positive control genes, respectively. The position of the PCR amplicon, used for validating the ChIP assay is indicated with an arrow.</p>
</div>
</div>
<div class="row">
<div class="small-12 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-fig3.jpg" /></center></div>
</div>
<div class="row">
<div class="small-12 columns">
<p><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27ac</strong></p>
<p>CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27ac (cat. No. C15410196) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions surrounding the EIF2S3 gene on the X-chromosome and the CCT5 gene on chromosome 5 (figure 3A and B, respectively).</p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-ELISA-Fig3.png" /></div>
<div class="small-6 columns">
<p><strong>Figure 4. Determination of the antibody titer</strong></p>
<p>To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:8,300.</p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-DB-Fig4.png" /></center></div>
<div class="small-8 columns">
<p><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27ac</strong><br />To test the cross reactivity of the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>), a Dot Blot analysis was performed with peptides containing other histone modifications and the unmodified H3K27. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 5 shows a high specificity of the antibody for the modification of interest.</p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><center><img src="https://www.diagenode.com/img/product/antibodies/C15410196-WB-Fig5.png" /></center></div>
<div class="small-8 columns">
<p><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27ac</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27ac (Cat. No. C1541196). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The marker (in kDa) is shown on the left.</p>
</div>
</div>
<div class="row">
<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410196-IF-Fig6.png" /></div>
<div class="small-8 columns">
<p><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27ac</strong></p>
<p>HeLa cells were stained with the Diagenode antibody against H3K27ac (Cat. No. C15410196<span class="label-primary"></span>) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/ TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K27ac antibody (top) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown at the bottom.</p>
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'name' => 'H3K9me3 Antibody (sample size)',
'description' => '<p><span>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 9 (H3K9me3)</strong>, using a KLH-conjugated synthetic peptide.</span></p>',
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_ChIP.jpg" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="278" height="189" /></p>
</div>
<div class="small-8 columns">
<p><small> <strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022 ) on the SX-8G IP-Star automated system. A titration of the antibody consisting of 1, 2, 5, and 10 μg per ChIP experiment was analysed. IgG (2 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active c-fos and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2A.jpg" alt="H3K9me3 Antibody ChIP-seq assay" caption="false" width="400" height="358" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2B.jpg" alt="H3K9me3 Antibody for ChIP-seq " caption="false" width="432" height="214" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig2C.jpg" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="432" height="61" /> <img src="https://www.diagenode.com/img/product/antibodies/C15410056-FigD.jpg" alt="H3K9me3 Antibody validated in ChIP-seq " caption="false" width="700" height="112" /></p>
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<div class="small-6 columns">
<p><small> <strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K9me3</strong><br /> ChIP was performed with 0.5 μg of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) on sheared chromatin from 1 million HeLa cells using the “iDeal ChIP-seq” kit (Cat. No. C01010051). The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoter regions of the active GAPDH and EIF4A2 genes, for the coding region of the ZNF510 gene and for the Sat2 satellite repeat (figure 2A). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the BWA algorithm. Figure 2B shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2C and D show the enrichment at ZNF510 and ZNF12 on chromosome 9 and 7, respectively. These results clearly show an enrichment of H3K9me3 at ZNF repeat genes. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Elisa.jpg" alt="H3K9me3 Antibody ELISA validation" caption="false" width="278" height="212" /></p>
</div>
<div class="small-8 columns">
<p><small> <strong>Figure 3. Determination of the antibody titer</strong><br /> To determine the titer of the antibody, an ELISA was performed using a serial dilution of the antibody directed against human H3K9me3 (Cat. No. C15410056), crude serum and flow through in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:60,000. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-Fig4.jpg" alt="H3K9me3 Antibody validated in Dot Blot" caption="false" width="400" height="304" /></p>
</div>
<div class="small-8 columns">
<p><small> <strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K9me3</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K9me3 (Cat. No. C15410056) with peptides containing other modifications and unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:20,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
</div>
</div>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056_WB.jpg" alt="H3K9me3 Antibody validated in Western Blot" caption="false" width="200" height="213" /></p>
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<p><small> <strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K9me3</strong><br /> Western blot analysis was performed on histone extracts from HeLa cells (15 μg, lane 1) and on recombinant H3 (1 μg, lane2) using the Diagenode antibody against H3K9me3 (Cat. No. C15410056). The antibody was diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410056-IF.jpg" alt="H3K9me3 Antibody validated in Immunofluorescence " caption="false" width="354" height="117" /></p>
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<div class="small-7 columns">
<p><small> <strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K9me3</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K9me3 (Cat. No. C15410056) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K9me3 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
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