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'description' => '<p><strong>As the result of extensive validation, the antibody HDAC1 has been upgraded to Premium category. Please, find it as <a href="../p/hdac1-polyclonal-antibody-premium-50-ug">HDAC1 polyclonal antibody - Premium (C15410325)</a>.</strong></p>
<p><span>Alternative names: HD1, RPD3, RPD3L1, GON-10</span></p>
<p><span>Polyclonal antibody raised in rabbit against the C-terminal region of human HDAC1 (Histone deacetylase 1), using a KLH-conjugated synthetic peptide.</span></p>',
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-Chip.jpg" alt="HDAC1 Antibody ChIP Grade" caption="false" width="288" height="219" /></p>
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode antibody directed against HDAC1</strong><br /> ChIP was performed with the Diagenode antibody against HDAC1 (Cat. No. C15410053) on sheared chromatin from 4,000,000 HeLa cells. An antibody titration 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 specific for the EIF4A2 and GAPDH promoters, used as positive controls, and for the MYOD1 gene and 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><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-A.jpg" alt="HDAC1 Antibody ChIP-seq Grade" caption="false" width="447" height="54" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-B.jpg" alt="HDAC1 Antibody for ChIP-seq " caption="false" width="447" height="72" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-C.jpg" alt="HDAC1 Antibody for ChIP-seq assay" caption="false" width="447" height="68" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-D.jpg" alt="HDAC1 Antibody validated in ChIP-seq " caption="false" width="447" height="84" /></p>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against HDAC1</strong><br /> ChIP was performed on sheared chromatin from 4,000,000 HeLa cells using 2 μg of the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 2 shows the peak distribution along the complete sequence and a 1 Mb 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). </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ELISA.jpg" alt="HDAC1 Antibody validated in ELISA" caption="false" width="288" height="229" /></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 Diagenode antibody directed against HDAC1 (Cat. No. pAb-053-050), crude serum and flow through. The plates were coated with the peptide used for immunization of the rabbit. By plotting the absorbance against the antibody dilution (Figure 2), the titer of the antibody was estimated to be 1:75,000. </small></p>
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-WB.jpg" alt="HDAC1 Antibody validated in Western Blot" caption="false" width="159" height="186" /></p>
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<p><small><strong> Figure 4. Western blot analysis using the Diagenode antibody directed against HDAC1</strong><br /> Whole cell extracts (25 μg, lane 1) and nuclear extracts (25 μg, lane 2) from HeLa cells were analysed by Western blot using the Diagenode antibody against HDAC1 (Cat. No. pAb-053-050) diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right (expected size: 55 kDa); 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/C15410053-IF.jpg" alt="HDAC1 Antibody validated in Immunofluorescence" caption="false" width="367" height="89" /></p>
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<div class="small-7 columns">
<p><small><strong> Figure 5. Immunofluorescence using the Diagenode antibody directed against HDAC1</strong><br /> HeLa cells were stained with the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 HDAC1 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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<td>2 μg/ChIP</td>
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<td>1:4,000</td>
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<td>1:1,000</td>
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<td>Fig 5</td>
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'description' => '<p><strong>As the result of extensive validation, the antibody HDAC1 has been upgraded to Premium category. Please, find it as <a href="../p/hdac1-polyclonal-antibody-premium-50-ug">HDAC1 polyclonal antibody - Premium (C15410325)</a>.</strong></p>
<p><span>Alternative names: HD1, RPD3, RPD3L1, GON-10</span></p>
<p><span>Polyclonal antibody raised in rabbit against the C-terminal region of human HDAC1 (Histone deacetylase 1), using a KLH-conjugated synthetic peptide.</span></p>',
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-Chip.jpg" alt="HDAC1 Antibody ChIP Grade" caption="false" width="288" height="219" /></p>
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode antibody directed against HDAC1</strong><br /> ChIP was performed with the Diagenode antibody against HDAC1 (Cat. No. C15410053) on sheared chromatin from 4,000,000 HeLa cells. An antibody titration 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 specific for the EIF4A2 and GAPDH promoters, used as positive controls, and for the MYOD1 gene and 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><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against HDAC1</strong><br /> ChIP was performed on sheared chromatin from 4,000,000 HeLa cells using 2 μg of the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 2 shows the peak distribution along the complete sequence and a 1 Mb 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). </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 Diagenode antibody directed against HDAC1 (Cat. No. pAb-053-050), crude serum and flow through. The plates were coated with the peptide used for immunization of the rabbit. By plotting the absorbance against the antibody dilution (Figure 2), the titer of the antibody was estimated to be 1:75,000. </small></p>
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<p><small><strong> Figure 4. Western blot analysis using the Diagenode antibody directed against HDAC1</strong><br /> Whole cell extracts (25 μg, lane 1) and nuclear extracts (25 μg, lane 2) from HeLa cells were analysed by Western blot using the Diagenode antibody against HDAC1 (Cat. No. pAb-053-050) diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right (expected size: 55 kDa); the marker (in kDa) is shown on the left. </small></p>
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<p><small><strong> Figure 5. Immunofluorescence using the Diagenode antibody directed against HDAC1</strong><br /> HeLa cells were stained with the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 HDAC1 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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<td>2 μg/ChIP</td>
<td>Fig 1, 2</td>
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<td>1:4,000</td>
<td>Fig 3</td>
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<td>1:1,000</td>
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<p>The Bioruptor® Pico (2013-2019) represented a breakthrough for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml. <span>The new generation keeps the features you like the most and bring even more innovation. Check it now:</span></p>
<center><span></span></center><center><a href="https://www.diagenode.com/p/bioruptorpico2"> <img alt="New Bioruptor Pico" src="https://www.diagenode.com/img/product/shearing_technologies/new-pico-product-banner.jpg" /></a></center>
<p></p>
<p><span>Watch our short video about the Bioruptor Pico and how it can help you accomplish perfect shearing for any application including chromatin shearing, DNA shearing for NGS, unmatched DNA extraction from FFPE samples, RNA shearing, protein extraction, and much more.</span></p>
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'info1' => '<p><a href="https://www.diagenode.com/files/products/shearing_technology/bioruptor/Bioruptor_pico_cooler_manual.pdf">Download</a></p>
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<p></p>
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'info3' => '<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p>
<table style="width: 925px;">
<tbody>
<tr valign="middle">
<td style="width: 213px;"></td>
<td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td>
<td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td>
<td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;">< 0.1%</p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;">0.2%</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">1%</p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;">0.5%</p>
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<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Nuclei isolation</strong></p>
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<td style="text-align: center; width: 208px;">
<p style="text-align: center;">Yes</p>
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<td style="text-align: center; width: 180px;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">No</p>
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<td style="text-align: center; width: 155px;">
<p style="text-align: center;">Yes</p>
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<td style="width: 213px;">
<p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p>
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<p style="text-align: center;">100 million cells</p>
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<td style="text-align: center; width: 180px;">
<p style="text-align: center;">100 million cells</p>
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<td style="text-align: center; width: 154px;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;">up to 25 g of tissue</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
<p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p>
</td>
</tr>
</tbody>
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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>Diagenode offers huge selection of highly sensitive antibodies validated in IF.</p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15200229-IF.jpg" alt="" height="245" width="256" /></p>
<p><sup><strong>Immunofluorescence using the Diagenode monoclonal antibody directed against CRISPR/Cas9</strong></sup></p>
<p><sup>HeLa cells transfected with a Cas9 expression vector (left) or untransfected cells (right) were fixed in methanol at -20°C, permeabilized with acetone at -20°C and blocked with PBS containing 2% BSA. The cells were stained with the Cas9 C-terminal antibody (Cat. No. C15200229) diluted 1:400, followed by incubation with an anti-mouse secondary antibody coupled to AF488. The bottom images show counter-staining of the nuclei with Hoechst 33342.</sup></p>
<h5><sup>Check our selection of antibodies validated in IF.</sup></h5>',
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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>
</div>
</div>
<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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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
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'meta_description' => 'Diagenode Offers Polyclonal and Monoclonal Antibodies Against Histone Modifying Enzymes like: Histone Deacetylases, Histone Demethylases, Histone Transferases.',
'meta_title' => 'Histone modifying enzymes - Antibodies | Diagenode',
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'name' => 'ChIP-grade antibodies',
'description' => '<div class="row">
<div class="small-10 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 class="small-2 columns"><img src="https://www.diagenode.com/emailing/images/epi-success-guaranteed-icon.png" alt="Epigenetic success guaranteed" /></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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'slug' => 'chip-grade-antibodies',
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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 HDAC1 C15410053',
'description' => '<p>Datasheet description</p>',
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'type' => 'Datasheet',
'url' => 'files/products/antibodies/Datasheet_HDAC1_C15410053.pdf',
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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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(int) 2 => array(
'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>',
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'type' => 'Brochure',
'url' => 'files/brochures/Epigenetic_Antibodies_Brochure.pdf',
'slug' => 'epigenetic-antibodies-brochure',
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'modified' => '2016-06-15 11:24:06',
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'id' => '1783',
'name' => 'product/antibodies/chipseq-grade-ab-icon.png',
'alt' => 'ChIP-seq Grade',
'modified' => '2020-11-27 07:04:40',
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(int) 0 => array(
'id' => '4768',
'name' => 'Comprehensive molecular phenotyping of -deficient gastric cancer revealspervasive epigenomic reprogramming and therapeutic opportunities.',
'authors' => 'Xu C. et al.',
'description' => '<p>OBJECTIVE: Gastric cancer (GC) is a leading cause of cancer mortality, with being the second most frequently mutated driver gene in GC. We sought to decipher -specific GC regulatory networks and examine therapeutic vulnerabilities arising from loss. DESIGN: Genomic profiling of GC patients including a Singapore cohort (>200 patients) was performed to derive mutational signatures of inactivation across molecular subtypes. Single-cell transcriptomic profiles of -mutated GCs were analysed to examine tumour microenvironmental changes arising from loss. Genome-wide ARID1A binding and chromatin profiles (H3K27ac, H3K4me3, H3K4me1, ATAC-seq) were generated to identify gastric-specific epigenetic landscapes regulated by ARID1A. Distinct cancer hallmarks of -mutated GCs were converged at the genomic, single-cell and epigenomic level, and targeted by pharmacological inhibition. RESULTS: We observed prevalent inactivation across GC molecular subtypes, with distinct mutational signatures and linked to a NFKB-driven proinflammatory tumour microenvironment. -depletion caused loss of H3K27ac activation signals at -occupied distal enhancers, but unexpectedly gain of H3K27ac at ARID1A-occupied promoters in genes such as and . Promoter activation in -mutated GCs was associated with enhanced gene expression, increased BRD4 binding, and reduced HDAC1 and CTCF occupancy. Combined targeting of promoter activation and tumour inflammation via bromodomain and NFKB inhibitors confirmed therapeutic synergy specific to -genomic status. CONCLUSION: Our results suggest a therapeutic strategy for -mutated GCs targeting both tumour-intrinsic (BRD4-assocatiated promoter activation) and extrinsic (NFKB immunomodulation) cancer phenotypes.</p>',
'date' => '2023-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36918265',
'doi' => '10.1136/gutjnl-2022-328332',
'modified' => '2023-04-17 09:33:37',
'created' => '2023-04-14 13:41:22',
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(int) 1 => array(
'id' => '2942',
'name' => 'Functional incompatibility between the generic NF-κB motif and a subtype-specific Sp1III element drives the formation of HIV-1 subtype C viral promoter',
'authors' => 'Verma A et al.',
'description' => '<p>Of the various genetic subtypes of HIV-1, HIV-2 and SIV, only in subtype C of HIV-1, a genetically variant NF-κB binding site is found at the core of the viral promoter in association with a subtype-specific Sp1III motif. How the subtype-associated variations in the core transcription factor binding sites (TFBS) influence gene expression from the viral promoter has not been examined previously. Using panels of infectious viral molecular clones, we demonstrate that subtype-specific NF-κB and Sp1III motifs have evolved for optimal gene expression, and neither of the motifs can be substituted by a corresponding TFBS variant.The variant NF-κB motif binds NF-κB with an affinity two-fold higher than that of the generic NF-κB site. Importantly, in the context of an infectious virus, the subtype-specific Sp1III motif demonstrates a profound loss of function in association with the generic NF-κB motif. An additional substitution of the Sp1III motif fully restores viral replication suggesting that the subtype C specific Sp1III has evolved to function with the variant, but not generic, NF-κB motif. A change of only two base pairs in the central NF-κB motif completely suppresses viral transcription from the provirus and converts the promoter into heterochromatin refractory to TNF-α induction. The present work represents the first demonstration of functional incompatibility between an otherwise functional NF-κB motif and a unique Sp1 site in the context of HIV-1 promoter. Our work provides important leads as per the evolution of HIV-1 subtype C viral promoter with relevance for gene expression regulation and viral latency.</p>',
'date' => '2016-05-18',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27194770',
'doi' => '10.1128/JVI.00308-16',
'modified' => '2016-06-30 15:57:48',
'created' => '2016-06-06 10:12:54',
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(int) 2 => array(
'id' => '2866',
'name' => 'Genome-wide hydroxymethylcytosine pattern changes in response to oxidative stress',
'authors' => 'Delatte B, Jeschke J, Defrance M, Bachman M, Creppe C, Calonne E, Bizet M, Deplus R, Marroquí L, Libin M, Ravichandran M, Mascart F, Eizirik DL, Murrell A, Jurkowski TP, Fuks F',
'description' => '<div class="pl20 mq875-pl0 js-collapsible-section" id="abstract-content" itemprop="description">
<p><b>The TET enzymes convert methylcytosine to the newly discovered base hydroxymethylcytosine. While recent reports suggest that TETs may play a role in response to oxidative stress, this role remains uncertain, and results lack</b> <i><b>in vivo</b></i> <b>models. Here we show a global decrease of hydroxymethylcytosine in cells treated with buthionine sulfoximine, and in mice depleted for the major antioxidant enzymes</b> <i><b>GPx</b></i><b>1 and 2. Furthermore, genome-wide profiling revealed differentially hydroxymethylated regions in coding genes, and intriguingly in microRNA genes, both involved in response to oxidative stress. These results thus suggest a profound effect of</b> <i><b>in vivo</b></i> <b>oxidative stress on the global hydroxymethylome.</b></p>
</div>',
'date' => '2015-08-04',
'pmid' => 'http://www.nature.com/articles/srep12714',
'doi' => '10.1038/srep12714',
'modified' => '2016-03-22 10:37:38',
'created' => '2016-03-22 10:37:38',
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[maximum depth reached]
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(int) 3 => array(
'id' => '2274',
'name' => 'SNAIL1 combines competitive displacement of ASCL2 and epigenetic mechanisms to rapidly silence the EPHB3 tumor suppressor in colorectal cancer.',
'authors' => 'Rönsch K, Jägle S, Rose K, Seidl M, Baumgartner F, Freihen V, Yousaf A, Metzger E, Lassmann S, Schüle R, Zeiser R, Michoel T, Hecht A',
'description' => 'EPHB3 is a critical cellular guidance factor in the intestinal epithelium and an important tumor suppressor in colorectal cancer (CRC) whose expression is frequently lost at the adenoma-carcinoma transition when tumor cells become invasive. The molecular mechanisms underlying EPHB3 silencing are incompletely understood. Here we show that EPHB3 expression is anti-correlated with inducers of epithelial-mesenchymal transition (EMT) in primary tumors and CRC cells. In vitro, SNAIL1 and SNAIL2, but not ZEB1, repress EPHB3 reporter constructs and compete with the stem cell factor ASCL2 for binding to an E-box motif. At the endogenous EPHB3 locus, SNAIL1 triggers the displacement of ASCL2, p300 and the Wnt pathway effector TCF7L2 and engages corepressor complexes containing HDACs and the histone demethylase LSD1 to collapse active chromatin structure, resulting in rapid downregulation of EPHB3. Beyond its impact on EPHB3, SNAIL1 deregulates markers of intestinal identity and stemness and in vitro forces CRC cells to undergo EMT with altered morphology, increased motility and invasiveness. In xenotransplants, SNAIL1 expression abrogated tumor cell palisading and led to focal loss of tumor encapsulation and the appearance of areas with tumor cells displaying a migratory phenotype. These changes were accompanied by loss of EPHB3 and CDH1 expression. Intriguingly, SNAIL1-induced phenotypic changes of CRC cells are significantly impaired by sustained EPHB3 expression both in vitro and in vivo. Altogether, our results identify EPHB3 as a novel target of SNAIL1 and suggest that disabling EPHB3 signaling is an important aspect to eliminate a roadblock at the onset of EMT processes.',
'date' => '2014-09-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25277775',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'id' => '2130',
'name' => 'Citrullination of DNMT3A by PADI4 regulates its stability and controls DNA methylation.',
'authors' => 'Deplus R, Denis H, Putmans P, Calonne E, Fourrez M, Yamamoto K, Suzuki A, Fuks F',
'description' => 'DNA methylation is a central epigenetic modification in mammals, with essential roles in development and disease. De novo DNA methyltransferases establish DNA methylation patterns in specific regions within the genome by mechanisms that remain poorly understood. Here we show that protein citrullination by peptidylarginine deiminase 4 (PADI4) affects the function of the DNA methyltransferase DNMT3A. We found that DNMT3A and PADI4 interact, from overexpressed as well as untransfected cells, and associate with each other's enzymatic activity. Both in vitro and in vivo, PADI4 was shown to citrullinate DNMT3A. We identified a sequence upstream of the PWWP domain of DNMT3A as its primary region citrullinated by PADI4. Increasing the PADI4 level caused the DNMT3A protein level to increase as well, provided that the PADI4 was catalytically active, and RNAi targeting PADI4 caused reduced DNMT3A levels. Accordingly, pulse-chase experiments revealed stabilization of the DNMT3A protein by catalytically active PADI4. Citrullination and increased expression of native DNMT3A by PADI4 were confirmed in PADI4-knockout MEFs. Finally, we showed that PADI4 overexpression increases DNA methyltransferase activity in a catalytic-dependent manner and use bisulfite pyrosequencing to demonstrate that PADI4 knockdown causes significant reduction of CpG methylation at the p21 promoter, a known target of DNMT3A and PADI4. Protein citrullination by PADI4 thus emerges as a novel mechanism for controlling a de novo DNA methyltransferase. Our results shed new light on how post-translational modifications might contribute to shaping the genomic CpG methylation landscape.',
'date' => '2014-06-23',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24957603',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '1553',
'name' => 'Dimethyl fumarate regulates histone deacetylase expression in astrocytes.',
'authors' => 'Kalinin S, Polak PE, Lin SX, Braun D, Guizzetti M, Zhang X, Rubinstein I, Feinstein DL',
'description' => 'We previously showed that dimethyl fumarate (DMF) reduces inflammatory activation in astrocytes, involving activation of transcription factor Nrf2. However, the pathways causing Nrf2 activation were not examined. We now show that DMF modifies expression of histone deacetylases (HDACs) in primary rat astrocytes. After 4h incubation, levels of HDAC1, 2, and 4 mRNAs were increased by DMF; however, after 24h, levels returned to or were below control values. At that time, HDAC protein levels and overall activity were also reduced by DMF. Stimulation of astrocytes with pro-inflammatory cytokines significantly increased HDAC mRNA levels after 24h, although protein levels were not increased at that time point. In the presence of cytokines, DMF reduced HDAC mRNAs, proteins, and activity. Proteomic analysis of DMF-treated astrocytes identified 8 proteins in which lysine acetylation was increased by DMF, including histones H2a.1 and H3.3. A role for HDACs in mediating DMF actions is suggested by findings that the selective HDAC inhibitor SAHA increased nuclear Nrf2:DNA binding activity, reduced inflammatory activation of astrocytes which was reversed by a selective inhibitor of the Nrf2 target gene heme-oxygenase 1. These data show that DMF regulates astrocyte HDAC expression, which could contribute to Nrf2 activation, suppression of inflammatory responses and cause long-lasting changes in gene expression.',
'date' => '2013-10-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23916696',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
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(int) 6 => array(
'id' => '800',
'name' => 'Phosphorylation of p65(RelA) on Ser547 by ATM Represses NF-κB-Dependent Transcription of Specific Genes after Genotoxic Stress',
'authors' => 'Sabatel H, Di Valentin E, Gloire G, Dequiedt F, Piette J, Habraken Y',
'description' => '',
'date' => '2012-06-08',
'pmid' => 'http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038246#abstract0',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
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(int) 7 => 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) 8 => array(
'id' => '714',
'name' => 'HDAC1 Regulates Fear Extinction in Mice.',
'authors' => 'Bahari-Javan S, Maddalena A, Kerimoglu C, Wittnam J, Held T, Bähr M, Burkhardt S, Delalle I, Kügler S, Fischer A, Sananbenesi F',
'description' => 'Histone acetylation has been implicated with the pathogenesis of neuropsychiatric disorders and targeting histone deacetylases (HDACs) using HDAC inhibitors was shown to be neuroprotective and to initiate neuroregenerative processes. However, little is known about the role of individual HDAC proteins during the pathogenesis of brain diseases. HDAC1 was found to be upregulated in patients suffering from neuropsychiatric diseases. Here, we show that virus-mediated overexpression of neuronal HDAC1 in the adult mouse hippocampus specifically affects the extinction of contextual fear memories, while other cognitive abilities were unaffected. In subsequent experiments we show that under physiological conditions, hippocampal HDAC1 is required for extinction learning via a mechanism that involves H3K9 deacetylation and subsequent trimethylation of target genes. In conclusion, our data show that hippocampal HDAC1 has a specific role in memory function.',
'date' => '2012-04-11',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22496552',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'id' => '816',
'name' => 'Enhancer of Zeste 2 (EZH2) is up-regulated in malignant gliomas and in glioma stem-like cells.',
'authors' => 'Orzan F, Pellegatta S, Poliani PL, Pisati F, Caldera V, Menghi F, Kapetis D, Marras C, Schiffer D, Finocchiaro G',
'description' => 'AIMS: Proteins of the Polycomb repressive complex 2 (PRC2) are epigenetic gene silencers and are involved in tumour development. Their oncogenic function might be associated with their role in stem cell maintenance. The histone methyltransferase Enhancer of Zeste 2 (EZH2) is a key member of PRC2 function: we have investigated its expression and function in gliomas. METHODS: EZH2 expression was studied in grade II-IV gliomas and in glioma stem-like cells (GSC) by quantitative PCR and immunohistochemistry. Effects of EZH2 down-regulation were analysed by treating GSC with the histone deacetylase (HDAC) inhibitor suberoylanide hydroxamic acid (SAHA) and by shRNA. RESULTS: DNA microarray analysis showed that EZH2 is highly expressed in murine and human GSC. Real-time PCR on gliomas of different grade (n = 66) indicated that EZH2 is more expressed in glioblastoma multiforme (GBM) than in low-grade gliomas (P = 0.0013). This was confirmed by immunohistochemistry on an independent set of 106 gliomas. Treatment with SAHA caused significant up-regulation of PRC2 predicted target genes, GSC disruption and decreased expression of EZH2 and of the stem cell marker CD133. Inhibition of EZH2 expression by shRNA was associated with a significant decrease of glioma proliferation. CONCLUSION: The data suggest that EZH2 plays a role in glioma progression and encourage the therapeutic targeting of these malignancies by HDAC inhibitors.',
'date' => '2011-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/20946108',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
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),
(int) 10 => array(
'id' => '77',
'name' => 'The core binding factor CBF negatively regulates skeletal muscle terminal differentiation.',
'authors' => 'Philipot O, Joliot V, Ait-Mohamed O, Pellentz C, Robin P, Fritsch L, Ait-Si-Ali S',
'description' => 'BACKGROUND: Core Binding Factor or CBF is a transcription factor composed of two subunits, Runx1/AML-1 and CBF beta or CBFbeta. CBF was originally described as a regulator of hematopoiesis. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that CBF is involved in the control of skeletal muscle terminal differentiation. Indeed, downregulation of either Runx1 or CBFbeta protein level accelerates cell cycle exit and muscle terminal differentiation. Conversely, overexpression of CBFbeta in myoblasts slows terminal differentiation. CBF interacts directly with the master myogenic transcription factor MyoD, preferentially in proliferating myoblasts, via Runx1 subunit. In addition, we show a preferential recruitment of Runx1 protein to MyoD target genes in proliferating myoblasts. The MyoD/CBF complex contains several chromatin modifying enzymes that inhibits MyoD activity, such as HDACs, Suv39h1 and HP1beta. When overexpressed, CBFbeta induced an inhibition of activating histone modification marks concomitant with an increase in repressive modifications at MyoD target promoters. CONCLUSIONS/SIGNIFICANCE: Taken together, our data show a new role for Runx1/CBFbeta in the control of the proliferation/differentiation in skeletal myoblasts.',
'date' => '2010-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/20195544',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 11 => array(
'id' => '78',
'name' => 'Functional connection between deimination and deacetylation of histones.',
'authors' => 'Denis H, Deplus R, Putmans P, Yamada M, Métivier R, Fuks F',
'description' => 'Histone methylation plays key roles in regulating chromatin structure and function. The recent identification of enzymes that antagonize or remove histone methylation offers new opportunities to appreciate histone methylation plasticity in the regulation of epigenetic pathways. Peptidylarginine deiminase 4 (PADI4; also known as PAD4) was the first enzyme shown to antagonize histone methylation. PADI4 functions as a histone deiminase converting a methylarginine residue to citrulline at specific sites on the tails of histones H3 and H4. This activity is linked to repression of the estrogen-regulated pS2 promoter. Very little is known as to how PADI4 silences gene expression. We show here that PADI4 associates with the histone deacetylase 1 (HDAC1). Kinetic chromatin immunoprecipitation assays revealed that PADI4 and HDAC1, and the corresponding activities, associate cyclically and coordinately with the pS2 promoter during repression phases. Knockdown of HDAC1 led to decreased H3 citrullination, concomitantly with increased histone arginine methylation. In cells with a reduced HDAC1 and a slightly decreased PADI4 level, these effects were more pronounced. Our data thus suggest that PADI4 and HDAC1 collaborate to generate a repressive chromatin environment on the pS2 promoter. These findings further substantiate the "transcriptional clock" concept, highlighting the dynamic connection between deimination and deacetylation of histones.',
'date' => '2009-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19581286',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
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'Area' => array(),
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(int) 0 => array(
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'name' => 'HDAC1 Antibody SDS GB en',
'language' => 'en',
'url' => 'files/SDS/HDAC1/SDS-C15410325-HDAC1_Antibody-GB-en-GHS_2_0.pdf',
'countries' => 'GB',
'modified' => '2021-08-30 15:33:52',
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[maximum depth reached]
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(int) 1 => array(
'id' => '1512',
'name' => 'HDAC1 Antibody SDS US en',
'language' => 'en',
'url' => 'files/SDS/HDAC1/SDS-C15410325-HDAC1_Antibody-US-en-GHS_2_0.pdf',
'countries' => 'US',
'modified' => '2021-08-30 15:33:52',
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),
(int) 2 => array(
'id' => '1507',
'name' => 'HDAC1 Antibody SDS DE de',
'language' => 'de',
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<p>The Bioruptor® Pico (2013-2019) represented a breakthrough for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml. <span>The new generation keeps the features you like the most and bring even more innovation. Check it now:</span></p>
<center><span></span></center><center><a href="https://www.diagenode.com/p/bioruptorpico2"> <img alt="New Bioruptor Pico" src="https://www.diagenode.com/img/product/shearing_technologies/new-pico-product-banner.jpg" /></a></center>
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<p><span>Watch our short video about the Bioruptor Pico and how it can help you accomplish perfect shearing for any application including chromatin shearing, DNA shearing for NGS, unmatched DNA extraction from FFPE samples, RNA shearing, protein extraction, and much more.</span></p>
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<td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td>
<td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td>
<td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td>
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<p style="text-align: center;">Yes</p>
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<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
<p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p>
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<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
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<p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
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<p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p>
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'description' => 'Histone methylation plays key roles in regulating chromatin structure and function. The recent identification of enzymes that antagonize or remove histone methylation offers new opportunities to appreciate histone methylation plasticity in the regulation of epigenetic pathways. Peptidylarginine deiminase 4 (PADI4; also known as PAD4) was the first enzyme shown to antagonize histone methylation. PADI4 functions as a histone deiminase converting a methylarginine residue to citrulline at specific sites on the tails of histones H3 and H4. This activity is linked to repression of the estrogen-regulated pS2 promoter. Very little is known as to how PADI4 silences gene expression. We show here that PADI4 associates with the histone deacetylase 1 (HDAC1). Kinetic chromatin immunoprecipitation assays revealed that PADI4 and HDAC1, and the corresponding activities, associate cyclically and coordinately with the pS2 promoter during repression phases. Knockdown of HDAC1 led to decreased H3 citrullination, concomitantly with increased histone arginine methylation. In cells with a reduced HDAC1 and a slightly decreased PADI4 level, these effects were more pronounced. Our data thus suggest that PADI4 and HDAC1 collaborate to generate a repressive chromatin environment on the pS2 promoter. These findings further substantiate the "transcriptional clock" concept, highlighting the dynamic connection between deimination and deacetylation of histones.',
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'description' => '<p><strong>As the result of extensive validation, the antibody HDAC1 has been upgraded to Premium category. Please, find it as <a href="../p/hdac1-polyclonal-antibody-premium-50-ug">HDAC1 polyclonal antibody - Premium (C15410325)</a>.</strong></p>
<p><span>Alternative names: HD1, RPD3, RPD3L1, GON-10</span></p>
<p><span>Polyclonal antibody raised in rabbit against the C-terminal region of human HDAC1 (Histone deacetylase 1), 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 HDAC1</strong><br /> ChIP was performed with the Diagenode antibody against HDAC1 (Cat. No. C15410053) on sheared chromatin from 4,000,000 HeLa cells. An antibody titration 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 specific for the EIF4A2 and GAPDH promoters, used as positive controls, and for the MYOD1 gene and 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><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against HDAC1</strong><br /> ChIP was performed on sheared chromatin from 4,000,000 HeLa cells using 2 μg of the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 2 shows the peak distribution along the complete sequence and a 1 Mb 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). </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 Diagenode antibody directed against HDAC1 (Cat. No. pAb-053-050), crude serum and flow through. The plates were coated with the peptide used for immunization of the rabbit. By plotting the absorbance against the antibody dilution (Figure 2), the titer of the antibody was estimated to be 1:75,000. </small></p>
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<p><small><strong> Figure 4. Western blot analysis using the Diagenode antibody directed against HDAC1</strong><br /> Whole cell extracts (25 μg, lane 1) and nuclear extracts (25 μg, lane 2) from HeLa cells were analysed by Western blot using the Diagenode antibody against HDAC1 (Cat. No. pAb-053-050) diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right (expected size: 55 kDa); the marker (in kDa) is shown on the left. </small></p>
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<p><small><strong> Figure 5. Immunofluorescence using the Diagenode antibody directed against HDAC1</strong><br /> HeLa cells were stained with the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 HDAC1 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 HDAC1</strong><br /> ChIP was performed with the Diagenode antibody against HDAC1 (Cat. No. C15410053) on sheared chromatin from 4,000,000 HeLa cells. An antibody titration 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 specific for the EIF4A2 and GAPDH promoters, used as positive controls, and for the MYOD1 gene and 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><small><strong> Figure 4. Western blot analysis using the Diagenode antibody directed against HDAC1</strong><br /> Whole cell extracts (25 μg, lane 1) and nuclear extracts (25 μg, lane 2) from HeLa cells were analysed by Western blot using the Diagenode antibody against HDAC1 (Cat. No. pAb-053-050) diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right (expected size: 55 kDa); the marker (in kDa) is shown on the left. </small></p>
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<p><small><strong> Figure 5. Immunofluorescence using the Diagenode antibody directed against HDAC1</strong><br /> HeLa cells were stained with the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 HDAC1 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' => 'HDAC1 (UniProt/Swiss-Prot entry Q13547) catalyses the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Acetylation and deacetylation of these highly conserved lysine residues is important for the control of gene expression and HDAC activity is often associated with gene repression. Histone deacetylation is established by the formation of large multiprotein complexes. HDAC1 also interacts with the retinoblastoma tumor suppressor protein and is able to deacetylate p53. Therefore, it also plays an essential role in cell proliferation and differentiation and in apoptosis.',
'clonality' => '',
'isotype' => '',
'lot' => 'A21-001P',
'concentration' => '1.73 µg/µl',
'reactivity' => 'Human, mouse',
'type' => 'Polyclonal',
'purity' => 'Affinity purified',
'classification' => 'Classic',
'application_table' => '<table>
<thead>
<tr>
<th>Applications</th>
<th>Suggested dilution</th>
<th>References</th>
</tr>
</thead>
<tbody>
<tr>
<td>ChIP <sup>*</sup></td>
<td>2 μg/ChIP</td>
<td>Fig 1, 2</td>
</tr>
<tr>
<td>ELISA</td>
<td>1:4,000</td>
<td>Fig 3</td>
</tr>
<tr>
<td>Western Blotting</td>
<td>1:1,000</td>
<td>Fig 4</td>
</tr>
<tr>
<td>Immunofluorescence</td>
<td>1:500</td>
<td>Fig 5</td>
</tr>
</tbody>
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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 1-5 μg per IP.</small></p>',
'storage_conditions' => '',
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'precautions' => 'This product is for research use only. Not for use in diagnostic or therapeutic procedures.',
'uniprot_acc' => '',
'slug' => '',
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'meta_description' => '',
'modified' => '2016-08-03 11:54:18',
'created' => '0000-00-00 00:00:00',
'select_label' => '192 - HDAC1 polyclonal antibody (A21-001P - 1.73 µg/µl - Human, mouse - Affinity purified - Rabbit)'
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'id' => '1787',
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'name' => 'Bioruptor<sup>®</sup> Pico sonication device',
'description' => '<p><a href="https://go.diagenode.com/bioruptor-upgrade"><img src="https://www.diagenode.com/img/banners/banner-br-trade.png" /></a></p>
<p>The Bioruptor® Pico (2013-2019) represented a breakthrough for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml. <span>The new generation keeps the features you like the most and bring even more innovation. Check it now:</span></p>
<center><span></span></center><center><a href="https://www.diagenode.com/p/bioruptorpico2"> <img alt="New Bioruptor Pico" src="https://www.diagenode.com/img/product/shearing_technologies/new-pico-product-banner.jpg" /></a></center>
<p></p>
<p><span>Watch our short video about the Bioruptor Pico and how it can help you accomplish perfect shearing for any application including chromatin shearing, DNA shearing for NGS, unmatched DNA extraction from FFPE samples, RNA shearing, protein extraction, and much more.</span></p>
<p>
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'info1' => '<p><a href="https://www.diagenode.com/files/products/shearing_technology/bioruptor/Bioruptor_pico_cooler_manual.pdf">Download</a></p>
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'label2' => 'Recommended settings for DNA shearing with Bioruptor® Pico',
'info2' => '<p>Follow our guidelines and find the good parameters for your expected DNA size: <a href="https://pybrevet.typeform.com/to/o8cQfM">DNA shearing with the Bioruptor® Pico</a></p>
<p></p>
<p>
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'label3' => 'Available chromatin shearing kits',
'info3' => '<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p>
<table style="width: 925px;">
<tbody>
<tr valign="middle">
<td style="width: 213px;"></td>
<td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td>
<td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td>
<td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td>
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<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;">< 0.1%</p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;">0.2%</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">1%</p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;">0.5%</p>
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<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Nuclei isolation</strong></p>
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<td style="text-align: center; width: 208px;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">No</p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;">Yes</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;">up to 25 g of tissue</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
<p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p>
</td>
</tr>
</tbody>
</table>
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'meta_title' => 'Bioruptor® Pico sonication device for RNA,Chromatin and DNA shearing for Next-Generation-Sequencing | Diagenode',
'meta_keywords' => 'Bioruptor, sonication, Next-Generation-Sequencing,DNA shearing,Protein extraction',
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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>Diagenode offers huge selection of highly sensitive antibodies validated in IF.</p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15200229-IF.jpg" alt="" height="245" width="256" /></p>
<p><sup><strong>Immunofluorescence using the Diagenode monoclonal antibody directed against CRISPR/Cas9</strong></sup></p>
<p><sup>HeLa cells transfected with a Cas9 expression vector (left) or untransfected cells (right) were fixed in methanol at -20°C, permeabilized with acetone at -20°C and blocked with PBS containing 2% BSA. The cells were stained with the Cas9 C-terminal antibody (Cat. No. C15200229) diluted 1:400, followed by incubation with an anti-mouse secondary antibody coupled to AF488. The bottom images show counter-staining of the nuclei with Hoechst 33342.</sup></p>
<h5><sup>Check our selection of antibodies validated in IF.</sup></h5>',
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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>
</div>
<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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'meta_title' => 'Chromatin Immunoprecipitation ChIP-Seq Grade 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>
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'meta_title' => 'Diagenode's selection of Antibodies is exclusively dedicated for Epigenetic Research | Diagenode',
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'description' => '<p><span style="font-weight: 400;">Diagenode offers the large number of antibodies raised against histone modifying enzymes. The list below includes the antibodies against enzymes like: histone deacetylases, histone demethylases, histone transferases.</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 Polyclonal and Monoclonal Antibodies Against Histone Modifying Enzymes like: Histone Deacetylases, Histone Demethylases, Histone Transferases.',
'meta_title' => 'Histone modifying enzymes - Antibodies | Diagenode',
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'name' => 'ChIP-grade antibodies',
'description' => '<div class="row">
<div class="small-10 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>
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<div class="small-2 columns"><img src="https://www.diagenode.com/emailing/images/epi-success-guaranteed-icon.png" alt="Epigenetic success guaranteed" /></div>
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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>
<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',
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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' => '<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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'id' => '4768',
'name' => 'Comprehensive molecular phenotyping of -deficient gastric cancer revealspervasive epigenomic reprogramming and therapeutic opportunities.',
'authors' => 'Xu C. et al.',
'description' => '<p>OBJECTIVE: Gastric cancer (GC) is a leading cause of cancer mortality, with being the second most frequently mutated driver gene in GC. We sought to decipher -specific GC regulatory networks and examine therapeutic vulnerabilities arising from loss. DESIGN: Genomic profiling of GC patients including a Singapore cohort (>200 patients) was performed to derive mutational signatures of inactivation across molecular subtypes. Single-cell transcriptomic profiles of -mutated GCs were analysed to examine tumour microenvironmental changes arising from loss. Genome-wide ARID1A binding and chromatin profiles (H3K27ac, H3K4me3, H3K4me1, ATAC-seq) were generated to identify gastric-specific epigenetic landscapes regulated by ARID1A. Distinct cancer hallmarks of -mutated GCs were converged at the genomic, single-cell and epigenomic level, and targeted by pharmacological inhibition. RESULTS: We observed prevalent inactivation across GC molecular subtypes, with distinct mutational signatures and linked to a NFKB-driven proinflammatory tumour microenvironment. -depletion caused loss of H3K27ac activation signals at -occupied distal enhancers, but unexpectedly gain of H3K27ac at ARID1A-occupied promoters in genes such as and . Promoter activation in -mutated GCs was associated with enhanced gene expression, increased BRD4 binding, and reduced HDAC1 and CTCF occupancy. Combined targeting of promoter activation and tumour inflammation via bromodomain and NFKB inhibitors confirmed therapeutic synergy specific to -genomic status. CONCLUSION: Our results suggest a therapeutic strategy for -mutated GCs targeting both tumour-intrinsic (BRD4-assocatiated promoter activation) and extrinsic (NFKB immunomodulation) cancer phenotypes.</p>',
'date' => '2023-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36918265',
'doi' => '10.1136/gutjnl-2022-328332',
'modified' => '2023-04-17 09:33:37',
'created' => '2023-04-14 13:41:22',
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(int) 1 => array(
'id' => '2942',
'name' => 'Functional incompatibility between the generic NF-κB motif and a subtype-specific Sp1III element drives the formation of HIV-1 subtype C viral promoter',
'authors' => 'Verma A et al.',
'description' => '<p>Of the various genetic subtypes of HIV-1, HIV-2 and SIV, only in subtype C of HIV-1, a genetically variant NF-κB binding site is found at the core of the viral promoter in association with a subtype-specific Sp1III motif. How the subtype-associated variations in the core transcription factor binding sites (TFBS) influence gene expression from the viral promoter has not been examined previously. Using panels of infectious viral molecular clones, we demonstrate that subtype-specific NF-κB and Sp1III motifs have evolved for optimal gene expression, and neither of the motifs can be substituted by a corresponding TFBS variant.The variant NF-κB motif binds NF-κB with an affinity two-fold higher than that of the generic NF-κB site. Importantly, in the context of an infectious virus, the subtype-specific Sp1III motif demonstrates a profound loss of function in association with the generic NF-κB motif. An additional substitution of the Sp1III motif fully restores viral replication suggesting that the subtype C specific Sp1III has evolved to function with the variant, but not generic, NF-κB motif. A change of only two base pairs in the central NF-κB motif completely suppresses viral transcription from the provirus and converts the promoter into heterochromatin refractory to TNF-α induction. The present work represents the first demonstration of functional incompatibility between an otherwise functional NF-κB motif and a unique Sp1 site in the context of HIV-1 promoter. Our work provides important leads as per the evolution of HIV-1 subtype C viral promoter with relevance for gene expression regulation and viral latency.</p>',
'date' => '2016-05-18',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27194770',
'doi' => '10.1128/JVI.00308-16',
'modified' => '2016-06-30 15:57:48',
'created' => '2016-06-06 10:12:54',
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(int) 2 => array(
'id' => '2866',
'name' => 'Genome-wide hydroxymethylcytosine pattern changes in response to oxidative stress',
'authors' => 'Delatte B, Jeschke J, Defrance M, Bachman M, Creppe C, Calonne E, Bizet M, Deplus R, Marroquí L, Libin M, Ravichandran M, Mascart F, Eizirik DL, Murrell A, Jurkowski TP, Fuks F',
'description' => '<div class="pl20 mq875-pl0 js-collapsible-section" id="abstract-content" itemprop="description">
<p><b>The TET enzymes convert methylcytosine to the newly discovered base hydroxymethylcytosine. While recent reports suggest that TETs may play a role in response to oxidative stress, this role remains uncertain, and results lack</b> <i><b>in vivo</b></i> <b>models. Here we show a global decrease of hydroxymethylcytosine in cells treated with buthionine sulfoximine, and in mice depleted for the major antioxidant enzymes</b> <i><b>GPx</b></i><b>1 and 2. Furthermore, genome-wide profiling revealed differentially hydroxymethylated regions in coding genes, and intriguingly in microRNA genes, both involved in response to oxidative stress. These results thus suggest a profound effect of</b> <i><b>in vivo</b></i> <b>oxidative stress on the global hydroxymethylome.</b></p>
</div>',
'date' => '2015-08-04',
'pmid' => 'http://www.nature.com/articles/srep12714',
'doi' => '10.1038/srep12714',
'modified' => '2016-03-22 10:37:38',
'created' => '2016-03-22 10:37:38',
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(int) 3 => array(
'id' => '2274',
'name' => 'SNAIL1 combines competitive displacement of ASCL2 and epigenetic mechanisms to rapidly silence the EPHB3 tumor suppressor in colorectal cancer.',
'authors' => 'Rönsch K, Jägle S, Rose K, Seidl M, Baumgartner F, Freihen V, Yousaf A, Metzger E, Lassmann S, Schüle R, Zeiser R, Michoel T, Hecht A',
'description' => 'EPHB3 is a critical cellular guidance factor in the intestinal epithelium and an important tumor suppressor in colorectal cancer (CRC) whose expression is frequently lost at the adenoma-carcinoma transition when tumor cells become invasive. The molecular mechanisms underlying EPHB3 silencing are incompletely understood. Here we show that EPHB3 expression is anti-correlated with inducers of epithelial-mesenchymal transition (EMT) in primary tumors and CRC cells. In vitro, SNAIL1 and SNAIL2, but not ZEB1, repress EPHB3 reporter constructs and compete with the stem cell factor ASCL2 for binding to an E-box motif. At the endogenous EPHB3 locus, SNAIL1 triggers the displacement of ASCL2, p300 and the Wnt pathway effector TCF7L2 and engages corepressor complexes containing HDACs and the histone demethylase LSD1 to collapse active chromatin structure, resulting in rapid downregulation of EPHB3. Beyond its impact on EPHB3, SNAIL1 deregulates markers of intestinal identity and stemness and in vitro forces CRC cells to undergo EMT with altered morphology, increased motility and invasiveness. In xenotransplants, SNAIL1 expression abrogated tumor cell palisading and led to focal loss of tumor encapsulation and the appearance of areas with tumor cells displaying a migratory phenotype. These changes were accompanied by loss of EPHB3 and CDH1 expression. Intriguingly, SNAIL1-induced phenotypic changes of CRC cells are significantly impaired by sustained EPHB3 expression both in vitro and in vivo. Altogether, our results identify EPHB3 as a novel target of SNAIL1 and suggest that disabling EPHB3 signaling is an important aspect to eliminate a roadblock at the onset of EMT processes.',
'date' => '2014-09-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25277775',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
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[maximum depth reached]
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(int) 4 => array(
'id' => '2130',
'name' => 'Citrullination of DNMT3A by PADI4 regulates its stability and controls DNA methylation.',
'authors' => 'Deplus R, Denis H, Putmans P, Calonne E, Fourrez M, Yamamoto K, Suzuki A, Fuks F',
'description' => 'DNA methylation is a central epigenetic modification in mammals, with essential roles in development and disease. De novo DNA methyltransferases establish DNA methylation patterns in specific regions within the genome by mechanisms that remain poorly understood. Here we show that protein citrullination by peptidylarginine deiminase 4 (PADI4) affects the function of the DNA methyltransferase DNMT3A. We found that DNMT3A and PADI4 interact, from overexpressed as well as untransfected cells, and associate with each other's enzymatic activity. Both in vitro and in vivo, PADI4 was shown to citrullinate DNMT3A. We identified a sequence upstream of the PWWP domain of DNMT3A as its primary region citrullinated by PADI4. Increasing the PADI4 level caused the DNMT3A protein level to increase as well, provided that the PADI4 was catalytically active, and RNAi targeting PADI4 caused reduced DNMT3A levels. Accordingly, pulse-chase experiments revealed stabilization of the DNMT3A protein by catalytically active PADI4. Citrullination and increased expression of native DNMT3A by PADI4 were confirmed in PADI4-knockout MEFs. Finally, we showed that PADI4 overexpression increases DNA methyltransferase activity in a catalytic-dependent manner and use bisulfite pyrosequencing to demonstrate that PADI4 knockdown causes significant reduction of CpG methylation at the p21 promoter, a known target of DNMT3A and PADI4. Protein citrullination by PADI4 thus emerges as a novel mechanism for controlling a de novo DNA methyltransferase. Our results shed new light on how post-translational modifications might contribute to shaping the genomic CpG methylation landscape.',
'date' => '2014-06-23',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24957603',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
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(int) 5 => array(
'id' => '1553',
'name' => 'Dimethyl fumarate regulates histone deacetylase expression in astrocytes.',
'authors' => 'Kalinin S, Polak PE, Lin SX, Braun D, Guizzetti M, Zhang X, Rubinstein I, Feinstein DL',
'description' => 'We previously showed that dimethyl fumarate (DMF) reduces inflammatory activation in astrocytes, involving activation of transcription factor Nrf2. However, the pathways causing Nrf2 activation were not examined. We now show that DMF modifies expression of histone deacetylases (HDACs) in primary rat astrocytes. After 4h incubation, levels of HDAC1, 2, and 4 mRNAs were increased by DMF; however, after 24h, levels returned to or were below control values. At that time, HDAC protein levels and overall activity were also reduced by DMF. Stimulation of astrocytes with pro-inflammatory cytokines significantly increased HDAC mRNA levels after 24h, although protein levels were not increased at that time point. In the presence of cytokines, DMF reduced HDAC mRNAs, proteins, and activity. Proteomic analysis of DMF-treated astrocytes identified 8 proteins in which lysine acetylation was increased by DMF, including histones H2a.1 and H3.3. A role for HDACs in mediating DMF actions is suggested by findings that the selective HDAC inhibitor SAHA increased nuclear Nrf2:DNA binding activity, reduced inflammatory activation of astrocytes which was reversed by a selective inhibitor of the Nrf2 target gene heme-oxygenase 1. These data show that DMF regulates astrocyte HDAC expression, which could contribute to Nrf2 activation, suppression of inflammatory responses and cause long-lasting changes in gene expression.',
'date' => '2013-10-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23916696',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
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(int) 6 => array(
'id' => '800',
'name' => 'Phosphorylation of p65(RelA) on Ser547 by ATM Represses NF-κB-Dependent Transcription of Specific Genes after Genotoxic Stress',
'authors' => 'Sabatel H, Di Valentin E, Gloire G, Dequiedt F, Piette J, Habraken Y',
'description' => '',
'date' => '2012-06-08',
'pmid' => 'http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038246#abstract0',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
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(int) 7 => 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',
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(int) 8 => array(
'id' => '714',
'name' => 'HDAC1 Regulates Fear Extinction in Mice.',
'authors' => 'Bahari-Javan S, Maddalena A, Kerimoglu C, Wittnam J, Held T, Bähr M, Burkhardt S, Delalle I, Kügler S, Fischer A, Sananbenesi F',
'description' => 'Histone acetylation has been implicated with the pathogenesis of neuropsychiatric disorders and targeting histone deacetylases (HDACs) using HDAC inhibitors was shown to be neuroprotective and to initiate neuroregenerative processes. However, little is known about the role of individual HDAC proteins during the pathogenesis of brain diseases. HDAC1 was found to be upregulated in patients suffering from neuropsychiatric diseases. Here, we show that virus-mediated overexpression of neuronal HDAC1 in the adult mouse hippocampus specifically affects the extinction of contextual fear memories, while other cognitive abilities were unaffected. In subsequent experiments we show that under physiological conditions, hippocampal HDAC1 is required for extinction learning via a mechanism that involves H3K9 deacetylation and subsequent trimethylation of target genes. In conclusion, our data show that hippocampal HDAC1 has a specific role in memory function.',
'date' => '2012-04-11',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22496552',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
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(int) 9 => array(
'id' => '816',
'name' => 'Enhancer of Zeste 2 (EZH2) is up-regulated in malignant gliomas and in glioma stem-like cells.',
'authors' => 'Orzan F, Pellegatta S, Poliani PL, Pisati F, Caldera V, Menghi F, Kapetis D, Marras C, Schiffer D, Finocchiaro G',
'description' => 'AIMS: Proteins of the Polycomb repressive complex 2 (PRC2) are epigenetic gene silencers and are involved in tumour development. Their oncogenic function might be associated with their role in stem cell maintenance. The histone methyltransferase Enhancer of Zeste 2 (EZH2) is a key member of PRC2 function: we have investigated its expression and function in gliomas. METHODS: EZH2 expression was studied in grade II-IV gliomas and in glioma stem-like cells (GSC) by quantitative PCR and immunohistochemistry. Effects of EZH2 down-regulation were analysed by treating GSC with the histone deacetylase (HDAC) inhibitor suberoylanide hydroxamic acid (SAHA) and by shRNA. RESULTS: DNA microarray analysis showed that EZH2 is highly expressed in murine and human GSC. Real-time PCR on gliomas of different grade (n = 66) indicated that EZH2 is more expressed in glioblastoma multiforme (GBM) than in low-grade gliomas (P = 0.0013). This was confirmed by immunohistochemistry on an independent set of 106 gliomas. Treatment with SAHA caused significant up-regulation of PRC2 predicted target genes, GSC disruption and decreased expression of EZH2 and of the stem cell marker CD133. Inhibition of EZH2 expression by shRNA was associated with a significant decrease of glioma proliferation. CONCLUSION: The data suggest that EZH2 plays a role in glioma progression and encourage the therapeutic targeting of these malignancies by HDAC inhibitors.',
'date' => '2011-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/20946108',
'doi' => '',
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'name' => 'The core binding factor CBF negatively regulates skeletal muscle terminal differentiation.',
'authors' => 'Philipot O, Joliot V, Ait-Mohamed O, Pellentz C, Robin P, Fritsch L, Ait-Si-Ali S',
'description' => 'BACKGROUND: Core Binding Factor or CBF is a transcription factor composed of two subunits, Runx1/AML-1 and CBF beta or CBFbeta. CBF was originally described as a regulator of hematopoiesis. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that CBF is involved in the control of skeletal muscle terminal differentiation. Indeed, downregulation of either Runx1 or CBFbeta protein level accelerates cell cycle exit and muscle terminal differentiation. Conversely, overexpression of CBFbeta in myoblasts slows terminal differentiation. CBF interacts directly with the master myogenic transcription factor MyoD, preferentially in proliferating myoblasts, via Runx1 subunit. In addition, we show a preferential recruitment of Runx1 protein to MyoD target genes in proliferating myoblasts. The MyoD/CBF complex contains several chromatin modifying enzymes that inhibits MyoD activity, such as HDACs, Suv39h1 and HP1beta. When overexpressed, CBFbeta induced an inhibition of activating histone modification marks concomitant with an increase in repressive modifications at MyoD target promoters. CONCLUSIONS/SIGNIFICANCE: Taken together, our data show a new role for Runx1/CBFbeta in the control of the proliferation/differentiation in skeletal myoblasts.',
'date' => '2010-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/20195544',
'doi' => '',
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'description' => 'Histone methylation plays key roles in regulating chromatin structure and function. The recent identification of enzymes that antagonize or remove histone methylation offers new opportunities to appreciate histone methylation plasticity in the regulation of epigenetic pathways. Peptidylarginine deiminase 4 (PADI4; also known as PAD4) was the first enzyme shown to antagonize histone methylation. PADI4 functions as a histone deiminase converting a methylarginine residue to citrulline at specific sites on the tails of histones H3 and H4. This activity is linked to repression of the estrogen-regulated pS2 promoter. Very little is known as to how PADI4 silences gene expression. We show here that PADI4 associates with the histone deacetylase 1 (HDAC1). Kinetic chromatin immunoprecipitation assays revealed that PADI4 and HDAC1, and the corresponding activities, associate cyclically and coordinately with the pS2 promoter during repression phases. Knockdown of HDAC1 led to decreased H3 citrullination, concomitantly with increased histone arginine methylation. In cells with a reduced HDAC1 and a slightly decreased PADI4 level, these effects were more pronounced. Our data thus suggest that PADI4 and HDAC1 collaborate to generate a repressive chromatin environment on the pS2 promoter. These findings further substantiate the "transcriptional clock" concept, highlighting the dynamic connection between deimination and deacetylation of histones.',
'date' => '2009-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19581286',
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<a href="/jp/p/bioruptor-pico-sonication-device"><img src="/img/product/shearing_technologies/bioruptor_pico.jpg" alt="Bioruptor pico next gen sequencing " class="th"/></a> </div>
<div class="small-12 columns">
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<span class="success label" style="">B01060010</span>
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<h6 style="height:60px">Picoruptor Sonicator</h6>
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'name' => 'Bioruptor<sup>®</sup> Pico sonication device',
'description' => '<p><a href="https://go.diagenode.com/bioruptor-upgrade"><img src="https://www.diagenode.com/img/banners/banner-br-trade.png" /></a></p>
<p>The Bioruptor® Pico (2013-2019) represented a breakthrough for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml. <span>The new generation keeps the features you like the most and bring even more innovation. Check it now:</span></p>
<center><span></span></center><center><a href="https://www.diagenode.com/p/bioruptorpico2"> <img alt="New Bioruptor Pico" src="https://www.diagenode.com/img/product/shearing_technologies/new-pico-product-banner.jpg" /></a></center>
<p></p>
<p><span>Watch our short video about the Bioruptor Pico and how it can help you accomplish perfect shearing for any application including chromatin shearing, DNA shearing for NGS, unmatched DNA extraction from FFPE samples, RNA shearing, protein extraction, and much more.</span></p>
<p>
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'label1' => 'User manual ',
'info1' => '<p><a href="https://www.diagenode.com/files/products/shearing_technology/bioruptor/Bioruptor_pico_cooler_manual.pdf">Download</a></p>
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'label2' => 'Recommended settings for DNA shearing with Bioruptor® Pico',
'info2' => '<p>Follow our guidelines and find the good parameters for your expected DNA size: <a href="https://pybrevet.typeform.com/to/o8cQfM">DNA shearing with the Bioruptor® Pico</a></p>
<p></p>
<p>
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'label3' => 'Available chromatin shearing kits',
'info3' => '<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p>
<table style="width: 925px;">
<tbody>
<tr valign="middle">
<td style="width: 213px;"></td>
<td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td>
<td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td>
<td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>SDS concentration</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;">< 0.1%</p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;">0.2%</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">1%</p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;">0.5%</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">No</p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;">Yes</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;">up to 25 g of tissue</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
<p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p>
</td>
</tr>
</tbody>
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'description' => '<p><strong>As the result of extensive validation, the antibody HDAC1 has been upgraded to Premium category. Please, find it as <a href="../p/hdac1-polyclonal-antibody-premium-50-ug">HDAC1 polyclonal antibody - Premium (C15410325)</a>.</strong></p>
<p><span>Alternative names: HD1, RPD3, RPD3L1, GON-10</span></p>
<p><span>Polyclonal antibody raised in rabbit against the C-terminal region of human HDAC1 (Histone deacetylase 1), 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 HDAC1</strong><br /> ChIP was performed with the Diagenode antibody against HDAC1 (Cat. No. C15410053) on sheared chromatin from 4,000,000 HeLa cells. An antibody titration 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 specific for the EIF4A2 and GAPDH promoters, used as positive controls, and for the MYOD1 gene and 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><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against HDAC1</strong><br /> ChIP was performed on sheared chromatin from 4,000,000 HeLa cells using 2 μg of the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 2 shows the peak distribution along the complete sequence and a 1 Mb 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). </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 Diagenode antibody directed against HDAC1 (Cat. No. pAb-053-050), crude serum and flow through. The plates were coated with the peptide used for immunization of the rabbit. By plotting the absorbance against the antibody dilution (Figure 2), the titer of the antibody was estimated to be 1:75,000. </small></p>
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<p><small><strong> Figure 4. Western blot analysis using the Diagenode antibody directed against HDAC1</strong><br /> Whole cell extracts (25 μg, lane 1) and nuclear extracts (25 μg, lane 2) from HeLa cells were analysed by Western blot using the Diagenode antibody against HDAC1 (Cat. No. pAb-053-050) diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right (expected size: 55 kDa); the marker (in kDa) is shown on the left. </small></p>
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<p><small><strong> Figure 5. Immunofluorescence using the Diagenode antibody directed against HDAC1</strong><br /> HeLa cells were stained with the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 HDAC1 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/C15410053-ChipSeq-A.jpg" alt="HDAC1 Antibody ChIP-seq Grade" caption="false" width="447" height="54" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-B.jpg" alt="HDAC1 Antibody for ChIP-seq " caption="false" width="447" height="72" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-C.jpg" alt="HDAC1 Antibody for ChIP-seq assay" caption="false" width="447" height="68" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-D.jpg" alt="HDAC1 Antibody validated in ChIP-seq " caption="false" width="447" height="84" /></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 HDAC1</strong><br /> ChIP was performed on sheared chromatin from 4,000,000 HeLa cells using 2 μg of the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 2 shows the peak distribution along the complete sequence and a 1 Mb 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). </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ELISA.jpg" alt="HDAC1 Antibody validated in ELISA" caption="false" width="288" height="229" /></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 Diagenode antibody directed against HDAC1 (Cat. No. pAb-053-050), crude serum and flow through. The plates were coated with the peptide used for immunization of the rabbit. By plotting the absorbance against the antibody dilution (Figure 2), the titer of the antibody was estimated to be 1:75,000. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-WB.jpg" alt="HDAC1 Antibody validated in Western Blot" caption="false" width="159" height="186" /></p>
</div>
<div class="small-8 columns">
<p><small><strong> Figure 4. Western blot analysis using the Diagenode antibody directed against HDAC1</strong><br /> Whole cell extracts (25 μg, lane 1) and nuclear extracts (25 μg, lane 2) from HeLa cells were analysed by Western blot using the Diagenode antibody against HDAC1 (Cat. No. pAb-053-050) diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right (expected size: 55 kDa); 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/C15410053-IF.jpg" alt="HDAC1 Antibody validated in Immunofluorescence" caption="false" width="367" height="89" /></p>
</div>
<div class="small-7 columns">
<p><small><strong> Figure 5. Immunofluorescence using the Diagenode antibody directed against HDAC1</strong><br /> HeLa cells were stained with the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 HDAC1 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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'info2' => '<p>HDAC1 (UniProt/Swiss-Prot entry Q13547) catalyses the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Acetylation and deacetylation of these highly conserved lysine residues is important for the control of gene expression and HDAC activity is often associated with gene repression. Histone deacetylation is established by the formation of large multiprotein complexes. HDAC1 also interacts with the retinoblastoma tumor suppressor protein and is able to deacetylate p53. Therefore, it also plays an essential role in cell proliferation and differentiation and in apoptosis.</p>',
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'old_catalog_number' => 'pAb-053-050',
'sf_code' => 'C15410053-D001-000581',
'type' => 'FRE',
'search_order' => '03-Antibody',
'price_EUR' => '410',
'price_USD' => '400',
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'meta_title' => 'HDAC1 polyclonal antibody - Classic',
'meta_keywords' => '',
'meta_description' => 'HDAC1 polyclonal antibody - Classic',
'modified' => '2022-01-05 14:51:09',
'created' => '2015-06-29 14:08:20',
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'description' => 'HDAC1 (UniProt/Swiss-Prot entry Q13547) catalyses the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Acetylation and deacetylation of these highly conserved lysine residues is important for the control of gene expression and HDAC activity is often associated with gene repression. Histone deacetylation is established by the formation of large multiprotein complexes. HDAC1 also interacts with the retinoblastoma tumor suppressor protein and is able to deacetylate p53. Therefore, it also plays an essential role in cell proliferation and differentiation and in apoptosis.',
'clonality' => '',
'isotype' => '',
'lot' => 'A21-001P',
'concentration' => '1.73 µg/µl',
'reactivity' => 'Human, mouse',
'type' => 'Polyclonal',
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'application_table' => '<table>
<thead>
<tr>
<th>Applications</th>
<th>Suggested dilution</th>
<th>References</th>
</tr>
</thead>
<tbody>
<tr>
<td>ChIP <sup>*</sup></td>
<td>2 μg/ChIP</td>
<td>Fig 1, 2</td>
</tr>
<tr>
<td>ELISA</td>
<td>1:4,000</td>
<td>Fig 3</td>
</tr>
<tr>
<td>Western Blotting</td>
<td>1:1,000</td>
<td>Fig 4</td>
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<tr>
<td>Immunofluorescence</td>
<td>1:500</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 1-5 μg per IP.</small></p>',
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'description' => '<p><a href="https://go.diagenode.com/bioruptor-upgrade"><img src="https://www.diagenode.com/img/banners/banner-br-trade.png" /></a></p>
<p>The Bioruptor® Pico (2013-2019) represented a breakthrough for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml. <span>The new generation keeps the features you like the most and bring even more innovation. Check it now:</span></p>
<center><span></span></center><center><a href="https://www.diagenode.com/p/bioruptorpico2"> <img alt="New Bioruptor Pico" src="https://www.diagenode.com/img/product/shearing_technologies/new-pico-product-banner.jpg" /></a></center>
<p></p>
<p><span>Watch our short video about the Bioruptor Pico and how it can help you accomplish perfect shearing for any application including chromatin shearing, DNA shearing for NGS, unmatched DNA extraction from FFPE samples, RNA shearing, protein extraction, and much more.</span></p>
<p>
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'label2' => 'Recommended settings for DNA shearing with Bioruptor® Pico',
'info2' => '<p>Follow our guidelines and find the good parameters for your expected DNA size: <a href="https://pybrevet.typeform.com/to/o8cQfM">DNA shearing with the Bioruptor® Pico</a></p>
<p></p>
<p>
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'label3' => 'Available chromatin shearing kits',
'info3' => '<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p>
<table style="width: 925px;">
<tbody>
<tr valign="middle">
<td style="width: 213px;"></td>
<td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td>
<td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td>
<td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td>
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<td style="width: 213px;">
<p style="text-align: left;"><strong>SDS concentration</strong></p>
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<p style="text-align: center;">< 0.1%</p>
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<td style="text-align: center; width: 180px;">
<p style="text-align: center;">0.2%</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">1%</p>
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<td style="text-align: center; width: 155px;">
<p style="text-align: center;">0.5%</p>
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<td style="width: 213px;">
<p style="text-align: left;"><strong>Nuclei isolation</strong></p>
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<td style="text-align: center; width: 208px;">
<p style="text-align: center;">Yes</p>
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<td style="text-align: center; width: 180px;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">No</p>
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<td style="text-align: center; width: 155px;">
<p style="text-align: center;">Yes</p>
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<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;">up to 25 g of tissue</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
<p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p>
</td>
</tr>
</tbody>
</table>
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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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<p>Diagenode offers huge selection of highly sensitive antibodies validated in IF.</p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15200229-IF.jpg" alt="" height="245" width="256" /></p>
<p><sup><strong>Immunofluorescence using the Diagenode monoclonal antibody directed against CRISPR/Cas9</strong></sup></p>
<p><sup>HeLa cells transfected with a Cas9 expression vector (left) or untransfected cells (right) were fixed in methanol at -20°C, permeabilized with acetone at -20°C and blocked with PBS containing 2% BSA. The cells were stained with the Cas9 C-terminal antibody (Cat. No. C15200229) diluted 1:400, followed by incubation with an anti-mouse secondary antibody coupled to AF488. The bottom images show counter-staining of the nuclei with Hoechst 33342.</sup></p>
<h5><sup>Check our selection of antibodies validated in IF.</sup></h5>',
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'meta_description' => 'Diagenode offers a wide range of antibodies and technical support for ChIP Sequencing applications',
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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><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>
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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>
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<li>Sample sizes available</li>
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'meta_title' => 'Diagenode's selection of Antibodies is exclusively dedicated for Epigenetic Research | Diagenode',
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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>
<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-10 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 class="small-2 columns"><img src="https://www.diagenode.com/emailing/images/epi-success-guaranteed-icon.png" alt="Epigenetic success guaranteed" /></div>
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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>
<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>
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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 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' => '<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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'id' => '4768',
'name' => 'Comprehensive molecular phenotyping of -deficient gastric cancer revealspervasive epigenomic reprogramming and therapeutic opportunities.',
'authors' => 'Xu C. et al.',
'description' => '<p>OBJECTIVE: Gastric cancer (GC) is a leading cause of cancer mortality, with being the second most frequently mutated driver gene in GC. We sought to decipher -specific GC regulatory networks and examine therapeutic vulnerabilities arising from loss. DESIGN: Genomic profiling of GC patients including a Singapore cohort (>200 patients) was performed to derive mutational signatures of inactivation across molecular subtypes. Single-cell transcriptomic profiles of -mutated GCs were analysed to examine tumour microenvironmental changes arising from loss. Genome-wide ARID1A binding and chromatin profiles (H3K27ac, H3K4me3, H3K4me1, ATAC-seq) were generated to identify gastric-specific epigenetic landscapes regulated by ARID1A. Distinct cancer hallmarks of -mutated GCs were converged at the genomic, single-cell and epigenomic level, and targeted by pharmacological inhibition. RESULTS: We observed prevalent inactivation across GC molecular subtypes, with distinct mutational signatures and linked to a NFKB-driven proinflammatory tumour microenvironment. -depletion caused loss of H3K27ac activation signals at -occupied distal enhancers, but unexpectedly gain of H3K27ac at ARID1A-occupied promoters in genes such as and . Promoter activation in -mutated GCs was associated with enhanced gene expression, increased BRD4 binding, and reduced HDAC1 and CTCF occupancy. Combined targeting of promoter activation and tumour inflammation via bromodomain and NFKB inhibitors confirmed therapeutic synergy specific to -genomic status. CONCLUSION: Our results suggest a therapeutic strategy for -mutated GCs targeting both tumour-intrinsic (BRD4-assocatiated promoter activation) and extrinsic (NFKB immunomodulation) cancer phenotypes.</p>',
'date' => '2023-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36918265',
'doi' => '10.1136/gutjnl-2022-328332',
'modified' => '2023-04-17 09:33:37',
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'id' => '2942',
'name' => 'Functional incompatibility between the generic NF-κB motif and a subtype-specific Sp1III element drives the formation of HIV-1 subtype C viral promoter',
'authors' => 'Verma A et al.',
'description' => '<p>Of the various genetic subtypes of HIV-1, HIV-2 and SIV, only in subtype C of HIV-1, a genetically variant NF-κB binding site is found at the core of the viral promoter in association with a subtype-specific Sp1III motif. How the subtype-associated variations in the core transcription factor binding sites (TFBS) influence gene expression from the viral promoter has not been examined previously. Using panels of infectious viral molecular clones, we demonstrate that subtype-specific NF-κB and Sp1III motifs have evolved for optimal gene expression, and neither of the motifs can be substituted by a corresponding TFBS variant.The variant NF-κB motif binds NF-κB with an affinity two-fold higher than that of the generic NF-κB site. Importantly, in the context of an infectious virus, the subtype-specific Sp1III motif demonstrates a profound loss of function in association with the generic NF-κB motif. An additional substitution of the Sp1III motif fully restores viral replication suggesting that the subtype C specific Sp1III has evolved to function with the variant, but not generic, NF-κB motif. A change of only two base pairs in the central NF-κB motif completely suppresses viral transcription from the provirus and converts the promoter into heterochromatin refractory to TNF-α induction. The present work represents the first demonstration of functional incompatibility between an otherwise functional NF-κB motif and a unique Sp1 site in the context of HIV-1 promoter. Our work provides important leads as per the evolution of HIV-1 subtype C viral promoter with relevance for gene expression regulation and viral latency.</p>',
'date' => '2016-05-18',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27194770',
'doi' => '10.1128/JVI.00308-16',
'modified' => '2016-06-30 15:57:48',
'created' => '2016-06-06 10:12:54',
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'id' => '2866',
'name' => 'Genome-wide hydroxymethylcytosine pattern changes in response to oxidative stress',
'authors' => 'Delatte B, Jeschke J, Defrance M, Bachman M, Creppe C, Calonne E, Bizet M, Deplus R, Marroquí L, Libin M, Ravichandran M, Mascart F, Eizirik DL, Murrell A, Jurkowski TP, Fuks F',
'description' => '<div class="pl20 mq875-pl0 js-collapsible-section" id="abstract-content" itemprop="description">
<p><b>The TET enzymes convert methylcytosine to the newly discovered base hydroxymethylcytosine. While recent reports suggest that TETs may play a role in response to oxidative stress, this role remains uncertain, and results lack</b> <i><b>in vivo</b></i> <b>models. Here we show a global decrease of hydroxymethylcytosine in cells treated with buthionine sulfoximine, and in mice depleted for the major antioxidant enzymes</b> <i><b>GPx</b></i><b>1 and 2. Furthermore, genome-wide profiling revealed differentially hydroxymethylated regions in coding genes, and intriguingly in microRNA genes, both involved in response to oxidative stress. These results thus suggest a profound effect of</b> <i><b>in vivo</b></i> <b>oxidative stress on the global hydroxymethylome.</b></p>
</div>',
'date' => '2015-08-04',
'pmid' => 'http://www.nature.com/articles/srep12714',
'doi' => '10.1038/srep12714',
'modified' => '2016-03-22 10:37:38',
'created' => '2016-03-22 10:37:38',
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'id' => '2274',
'name' => 'SNAIL1 combines competitive displacement of ASCL2 and epigenetic mechanisms to rapidly silence the EPHB3 tumor suppressor in colorectal cancer.',
'authors' => 'Rönsch K, Jägle S, Rose K, Seidl M, Baumgartner F, Freihen V, Yousaf A, Metzger E, Lassmann S, Schüle R, Zeiser R, Michoel T, Hecht A',
'description' => 'EPHB3 is a critical cellular guidance factor in the intestinal epithelium and an important tumor suppressor in colorectal cancer (CRC) whose expression is frequently lost at the adenoma-carcinoma transition when tumor cells become invasive. The molecular mechanisms underlying EPHB3 silencing are incompletely understood. Here we show that EPHB3 expression is anti-correlated with inducers of epithelial-mesenchymal transition (EMT) in primary tumors and CRC cells. In vitro, SNAIL1 and SNAIL2, but not ZEB1, repress EPHB3 reporter constructs and compete with the stem cell factor ASCL2 for binding to an E-box motif. At the endogenous EPHB3 locus, SNAIL1 triggers the displacement of ASCL2, p300 and the Wnt pathway effector TCF7L2 and engages corepressor complexes containing HDACs and the histone demethylase LSD1 to collapse active chromatin structure, resulting in rapid downregulation of EPHB3. Beyond its impact on EPHB3, SNAIL1 deregulates markers of intestinal identity and stemness and in vitro forces CRC cells to undergo EMT with altered morphology, increased motility and invasiveness. In xenotransplants, SNAIL1 expression abrogated tumor cell palisading and led to focal loss of tumor encapsulation and the appearance of areas with tumor cells displaying a migratory phenotype. These changes were accompanied by loss of EPHB3 and CDH1 expression. Intriguingly, SNAIL1-induced phenotypic changes of CRC cells are significantly impaired by sustained EPHB3 expression both in vitro and in vivo. Altogether, our results identify EPHB3 as a novel target of SNAIL1 and suggest that disabling EPHB3 signaling is an important aspect to eliminate a roadblock at the onset of EMT processes.',
'date' => '2014-09-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25277775',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
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(int) 4 => array(
'id' => '2130',
'name' => 'Citrullination of DNMT3A by PADI4 regulates its stability and controls DNA methylation.',
'authors' => 'Deplus R, Denis H, Putmans P, Calonne E, Fourrez M, Yamamoto K, Suzuki A, Fuks F',
'description' => 'DNA methylation is a central epigenetic modification in mammals, with essential roles in development and disease. De novo DNA methyltransferases establish DNA methylation patterns in specific regions within the genome by mechanisms that remain poorly understood. Here we show that protein citrullination by peptidylarginine deiminase 4 (PADI4) affects the function of the DNA methyltransferase DNMT3A. We found that DNMT3A and PADI4 interact, from overexpressed as well as untransfected cells, and associate with each other's enzymatic activity. Both in vitro and in vivo, PADI4 was shown to citrullinate DNMT3A. We identified a sequence upstream of the PWWP domain of DNMT3A as its primary region citrullinated by PADI4. Increasing the PADI4 level caused the DNMT3A protein level to increase as well, provided that the PADI4 was catalytically active, and RNAi targeting PADI4 caused reduced DNMT3A levels. Accordingly, pulse-chase experiments revealed stabilization of the DNMT3A protein by catalytically active PADI4. Citrullination and increased expression of native DNMT3A by PADI4 were confirmed in PADI4-knockout MEFs. Finally, we showed that PADI4 overexpression increases DNA methyltransferase activity in a catalytic-dependent manner and use bisulfite pyrosequencing to demonstrate that PADI4 knockdown causes significant reduction of CpG methylation at the p21 promoter, a known target of DNMT3A and PADI4. Protein citrullination by PADI4 thus emerges as a novel mechanism for controlling a de novo DNA methyltransferase. Our results shed new light on how post-translational modifications might contribute to shaping the genomic CpG methylation landscape.',
'date' => '2014-06-23',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24957603',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
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(int) 5 => array(
'id' => '1553',
'name' => 'Dimethyl fumarate regulates histone deacetylase expression in astrocytes.',
'authors' => 'Kalinin S, Polak PE, Lin SX, Braun D, Guizzetti M, Zhang X, Rubinstein I, Feinstein DL',
'description' => 'We previously showed that dimethyl fumarate (DMF) reduces inflammatory activation in astrocytes, involving activation of transcription factor Nrf2. However, the pathways causing Nrf2 activation were not examined. We now show that DMF modifies expression of histone deacetylases (HDACs) in primary rat astrocytes. After 4h incubation, levels of HDAC1, 2, and 4 mRNAs were increased by DMF; however, after 24h, levels returned to or were below control values. At that time, HDAC protein levels and overall activity were also reduced by DMF. Stimulation of astrocytes with pro-inflammatory cytokines significantly increased HDAC mRNA levels after 24h, although protein levels were not increased at that time point. In the presence of cytokines, DMF reduced HDAC mRNAs, proteins, and activity. Proteomic analysis of DMF-treated astrocytes identified 8 proteins in which lysine acetylation was increased by DMF, including histones H2a.1 and H3.3. A role for HDACs in mediating DMF actions is suggested by findings that the selective HDAC inhibitor SAHA increased nuclear Nrf2:DNA binding activity, reduced inflammatory activation of astrocytes which was reversed by a selective inhibitor of the Nrf2 target gene heme-oxygenase 1. These data show that DMF regulates astrocyte HDAC expression, which could contribute to Nrf2 activation, suppression of inflammatory responses and cause long-lasting changes in gene expression.',
'date' => '2013-10-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23916696',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
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'id' => '800',
'name' => 'Phosphorylation of p65(RelA) on Ser547 by ATM Represses NF-κB-Dependent Transcription of Specific Genes after Genotoxic Stress',
'authors' => 'Sabatel H, Di Valentin E, Gloire G, Dequiedt F, Piette J, Habraken Y',
'description' => '',
'date' => '2012-06-08',
'pmid' => 'http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038246#abstract0',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
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(int) 7 => 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',
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(int) 8 => array(
'id' => '714',
'name' => 'HDAC1 Regulates Fear Extinction in Mice.',
'authors' => 'Bahari-Javan S, Maddalena A, Kerimoglu C, Wittnam J, Held T, Bähr M, Burkhardt S, Delalle I, Kügler S, Fischer A, Sananbenesi F',
'description' => 'Histone acetylation has been implicated with the pathogenesis of neuropsychiatric disorders and targeting histone deacetylases (HDACs) using HDAC inhibitors was shown to be neuroprotective and to initiate neuroregenerative processes. However, little is known about the role of individual HDAC proteins during the pathogenesis of brain diseases. HDAC1 was found to be upregulated in patients suffering from neuropsychiatric diseases. Here, we show that virus-mediated overexpression of neuronal HDAC1 in the adult mouse hippocampus specifically affects the extinction of contextual fear memories, while other cognitive abilities were unaffected. In subsequent experiments we show that under physiological conditions, hippocampal HDAC1 is required for extinction learning via a mechanism that involves H3K9 deacetylation and subsequent trimethylation of target genes. In conclusion, our data show that hippocampal HDAC1 has a specific role in memory function.',
'date' => '2012-04-11',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22496552',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
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(int) 9 => array(
'id' => '816',
'name' => 'Enhancer of Zeste 2 (EZH2) is up-regulated in malignant gliomas and in glioma stem-like cells.',
'authors' => 'Orzan F, Pellegatta S, Poliani PL, Pisati F, Caldera V, Menghi F, Kapetis D, Marras C, Schiffer D, Finocchiaro G',
'description' => 'AIMS: Proteins of the Polycomb repressive complex 2 (PRC2) are epigenetic gene silencers and are involved in tumour development. Their oncogenic function might be associated with their role in stem cell maintenance. The histone methyltransferase Enhancer of Zeste 2 (EZH2) is a key member of PRC2 function: we have investigated its expression and function in gliomas. METHODS: EZH2 expression was studied in grade II-IV gliomas and in glioma stem-like cells (GSC) by quantitative PCR and immunohistochemistry. Effects of EZH2 down-regulation were analysed by treating GSC with the histone deacetylase (HDAC) inhibitor suberoylanide hydroxamic acid (SAHA) and by shRNA. RESULTS: DNA microarray analysis showed that EZH2 is highly expressed in murine and human GSC. Real-time PCR on gliomas of different grade (n = 66) indicated that EZH2 is more expressed in glioblastoma multiforme (GBM) than in low-grade gliomas (P = 0.0013). This was confirmed by immunohistochemistry on an independent set of 106 gliomas. Treatment with SAHA caused significant up-regulation of PRC2 predicted target genes, GSC disruption and decreased expression of EZH2 and of the stem cell marker CD133. Inhibition of EZH2 expression by shRNA was associated with a significant decrease of glioma proliferation. CONCLUSION: The data suggest that EZH2 plays a role in glioma progression and encourage the therapeutic targeting of these malignancies by HDAC inhibitors.',
'date' => '2011-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/20946108',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
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(int) 10 => array(
'id' => '77',
'name' => 'The core binding factor CBF negatively regulates skeletal muscle terminal differentiation.',
'authors' => 'Philipot O, Joliot V, Ait-Mohamed O, Pellentz C, Robin P, Fritsch L, Ait-Si-Ali S',
'description' => 'BACKGROUND: Core Binding Factor or CBF is a transcription factor composed of two subunits, Runx1/AML-1 and CBF beta or CBFbeta. CBF was originally described as a regulator of hematopoiesis. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that CBF is involved in the control of skeletal muscle terminal differentiation. Indeed, downregulation of either Runx1 or CBFbeta protein level accelerates cell cycle exit and muscle terminal differentiation. Conversely, overexpression of CBFbeta in myoblasts slows terminal differentiation. CBF interacts directly with the master myogenic transcription factor MyoD, preferentially in proliferating myoblasts, via Runx1 subunit. In addition, we show a preferential recruitment of Runx1 protein to MyoD target genes in proliferating myoblasts. The MyoD/CBF complex contains several chromatin modifying enzymes that inhibits MyoD activity, such as HDACs, Suv39h1 and HP1beta. When overexpressed, CBFbeta induced an inhibition of activating histone modification marks concomitant with an increase in repressive modifications at MyoD target promoters. CONCLUSIONS/SIGNIFICANCE: Taken together, our data show a new role for Runx1/CBFbeta in the control of the proliferation/differentiation in skeletal myoblasts.',
'date' => '2010-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/20195544',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
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(int) 11 => array(
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'name' => 'Functional connection between deimination and deacetylation of histones.',
'authors' => 'Denis H, Deplus R, Putmans P, Yamada M, Métivier R, Fuks F',
'description' => 'Histone methylation plays key roles in regulating chromatin structure and function. The recent identification of enzymes that antagonize or remove histone methylation offers new opportunities to appreciate histone methylation plasticity in the regulation of epigenetic pathways. Peptidylarginine deiminase 4 (PADI4; also known as PAD4) was the first enzyme shown to antagonize histone methylation. PADI4 functions as a histone deiminase converting a methylarginine residue to citrulline at specific sites on the tails of histones H3 and H4. This activity is linked to repression of the estrogen-regulated pS2 promoter. Very little is known as to how PADI4 silences gene expression. We show here that PADI4 associates with the histone deacetylase 1 (HDAC1). Kinetic chromatin immunoprecipitation assays revealed that PADI4 and HDAC1, and the corresponding activities, associate cyclically and coordinately with the pS2 promoter during repression phases. Knockdown of HDAC1 led to decreased H3 citrullination, concomitantly with increased histone arginine methylation. In cells with a reduced HDAC1 and a slightly decreased PADI4 level, these effects were more pronounced. Our data thus suggest that PADI4 and HDAC1 collaborate to generate a repressive chromatin environment on the pS2 promoter. These findings further substantiate the "transcriptional clock" concept, highlighting the dynamic connection between deimination and deacetylation of histones.',
'date' => '2009-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19581286',
'doi' => '',
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'
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'id' => '1787',
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'name' => 'Bioruptor<sup>®</sup> Pico sonication device',
'description' => '<p><a href="https://go.diagenode.com/bioruptor-upgrade"><img src="https://www.diagenode.com/img/banners/banner-br-trade.png" /></a></p>
<p>The Bioruptor® Pico (2013-2019) represented a breakthrough for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml. <span>The new generation keeps the features you like the most and bring even more innovation. Check it now:</span></p>
<center><span></span></center><center><a href="https://www.diagenode.com/p/bioruptorpico2"> <img alt="New Bioruptor Pico" src="https://www.diagenode.com/img/product/shearing_technologies/new-pico-product-banner.jpg" /></a></center>
<p></p>
<p><span>Watch our short video about the Bioruptor Pico and how it can help you accomplish perfect shearing for any application including chromatin shearing, DNA shearing for NGS, unmatched DNA extraction from FFPE samples, RNA shearing, protein extraction, and much more.</span></p>
<p>
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'label1' => 'User manual ',
'info1' => '<p><a href="https://www.diagenode.com/files/products/shearing_technology/bioruptor/Bioruptor_pico_cooler_manual.pdf">Download</a></p>
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'label2' => 'Recommended settings for DNA shearing with Bioruptor® Pico',
'info2' => '<p>Follow our guidelines and find the good parameters for your expected DNA size: <a href="https://pybrevet.typeform.com/to/o8cQfM">DNA shearing with the Bioruptor® Pico</a></p>
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'label3' => 'Available chromatin shearing kits',
'info3' => '<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p>
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<tbody>
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<td style="width: 213px;"></td>
<td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td>
<td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td>
<td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td>
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<td style="width: 213px;">
<p style="text-align: left;"><strong>SDS concentration</strong></p>
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<p style="text-align: center;">< 0.1%</p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;">0.2%</p>
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<td style="text-align: center; width: 154px;">
<p style="text-align: center;">1%</p>
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<td style="text-align: center; width: 155px;">
<p style="text-align: center;">0.5%</p>
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<td style="width: 213px;">
<p style="text-align: left;"><strong>Nuclei isolation</strong></p>
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<p style="text-align: center;">Yes</p>
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<td style="text-align: center; width: 180px;">
<p style="text-align: center;">Yes</p>
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<td style="text-align: center; width: 154px;">
<p style="text-align: center;">No</p>
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<td style="text-align: center; width: 155px;">
<p style="text-align: center;">Yes</p>
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<td style="width: 213px;">
<p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p>
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<p style="text-align: center;">100 million cells</p>
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<td style="text-align: center; width: 180px;">
<p style="text-align: center;">100 million cells</p>
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<td style="text-align: center; width: 154px;">
<p style="text-align: center;">100 million cells</p>
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<td style="text-align: center; width: 155px;">
<p style="text-align: center;">up to 25 g of tissue</p>
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<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
<p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p>
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'name' => 'HDAC1 polyclonal antibody ',
'description' => '<p><strong>As the result of extensive validation, the antibody HDAC1 has been upgraded to Premium category. Please, find it as <a href="../p/hdac1-polyclonal-antibody-premium-50-ug">HDAC1 polyclonal antibody - Premium (C15410325)</a>.</strong></p>
<p><span>Alternative names: HD1, RPD3, RPD3L1, GON-10</span></p>
<p><span>Polyclonal antibody raised in rabbit against the C-terminal region of human HDAC1 (Histone deacetylase 1), 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/C15410053-Chip.jpg" alt="HDAC1 Antibody ChIP Grade" caption="false" width="288" height="219" /></p>
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<div class="small-8 columns">
<p><small><strong> Figure 1. ChIP results obtained with the Diagenode antibody directed against HDAC1</strong><br /> ChIP was performed with the Diagenode antibody against HDAC1 (Cat. No. C15410053) on sheared chromatin from 4,000,000 HeLa cells. An antibody titration 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 specific for the EIF4A2 and GAPDH promoters, used as positive controls, and for the MYOD1 gene and 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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<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-A.jpg" alt="HDAC1 Antibody ChIP-seq Grade" caption="false" width="447" height="54" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-B.jpg" alt="HDAC1 Antibody for ChIP-seq " caption="false" width="447" height="72" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-C.jpg" alt="HDAC1 Antibody for ChIP-seq assay" caption="false" width="447" height="68" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-D.jpg" alt="HDAC1 Antibody validated in ChIP-seq " caption="false" width="447" height="84" /></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 HDAC1</strong><br /> ChIP was performed on sheared chromatin from 4,000,000 HeLa cells using 2 μg of the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 2 shows the peak distribution along the complete sequence and a 1 Mb 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). </small></p>
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ELISA.jpg" alt="HDAC1 Antibody validated in ELISA" caption="false" width="288" height="229" /></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 Diagenode antibody directed against HDAC1 (Cat. No. pAb-053-050), crude serum and flow through. The plates were coated with the peptide used for immunization of the rabbit. By plotting the absorbance against the antibody dilution (Figure 2), the titer of the antibody was estimated to be 1:75,000. </small></p>
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-WB.jpg" alt="HDAC1 Antibody validated in Western Blot" caption="false" width="159" height="186" /></p>
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<div class="small-8 columns">
<p><small><strong> Figure 4. Western blot analysis using the Diagenode antibody directed against HDAC1</strong><br /> Whole cell extracts (25 μg, lane 1) and nuclear extracts (25 μg, lane 2) from HeLa cells were analysed by Western blot using the Diagenode antibody against HDAC1 (Cat. No. pAb-053-050) diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right (expected size: 55 kDa); 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/C15410053-IF.jpg" alt="HDAC1 Antibody validated in Immunofluorescence" caption="false" width="367" height="89" /></p>
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<div class="small-7 columns">
<p><small><strong> Figure 5. Immunofluorescence using the Diagenode antibody directed against HDAC1</strong><br /> HeLa cells were stained with the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 HDAC1 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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<th>Suggested dilution</th>
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<td>ChIP <sup>*</sup></td>
<td>2 μg/ChIP</td>
<td>Fig 1, 2</td>
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<td>ELISA</td>
<td>1:4,000</td>
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<td>1:1,000</td>
<td>Fig 4</td>
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<td>1:500</td>
<td>Fig 5</td>
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'id' => '2215',
'antibody_id' => '192',
'name' => 'HDAC1 polyclonal antibody ',
'description' => '<p><strong>As the result of extensive validation, the antibody HDAC1 has been upgraded to Premium category. Please, find it as <a href="../p/hdac1-polyclonal-antibody-premium-50-ug">HDAC1 polyclonal antibody - Premium (C15410325)</a>.</strong></p>
<p><span>Alternative names: HD1, RPD3, RPD3L1, GON-10</span></p>
<p><span>Polyclonal antibody raised in rabbit against the C-terminal region of human HDAC1 (Histone deacetylase 1), 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/C15410053-Chip.jpg" alt="HDAC1 Antibody ChIP Grade" caption="false" width="288" height="219" /></p>
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<div class="small-8 columns">
<p><small><strong> Figure 1. ChIP results obtained with the Diagenode antibody directed against HDAC1</strong><br /> ChIP was performed with the Diagenode antibody against HDAC1 (Cat. No. C15410053) on sheared chromatin from 4,000,000 HeLa cells. An antibody titration 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 specific for the EIF4A2 and GAPDH promoters, used as positive controls, and for the MYOD1 gene and 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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<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-A.jpg" alt="HDAC1 Antibody ChIP-seq Grade" caption="false" width="447" height="54" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-B.jpg" alt="HDAC1 Antibody for ChIP-seq " caption="false" width="447" height="72" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-C.jpg" alt="HDAC1 Antibody for ChIP-seq assay" caption="false" width="447" height="68" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ChipSeq-D.jpg" alt="HDAC1 Antibody validated in ChIP-seq " caption="false" width="447" height="84" /></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 HDAC1</strong><br /> ChIP was performed on sheared chromatin from 4,000,000 HeLa cells using 2 μg of the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 2 shows the peak distribution along the complete sequence and a 1 Mb 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). </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-ELISA.jpg" alt="HDAC1 Antibody validated in ELISA" caption="false" width="288" height="229" /></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 Diagenode antibody directed against HDAC1 (Cat. No. pAb-053-050), crude serum and flow through. The plates were coated with the peptide used for immunization of the rabbit. By plotting the absorbance against the antibody dilution (Figure 2), the titer of the antibody was estimated to be 1:75,000. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-WB.jpg" alt="HDAC1 Antibody validated in Western Blot" caption="false" width="159" height="186" /></p>
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<div class="small-8 columns">
<p><small><strong> Figure 4. Western blot analysis using the Diagenode antibody directed against HDAC1</strong><br /> Whole cell extracts (25 μg, lane 1) and nuclear extracts (25 μg, lane 2) from HeLa cells were analysed by Western blot using the Diagenode antibody against HDAC1 (Cat. No. pAb-053-050) diluted 1:1,000 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right (expected size: 55 kDa); the marker (in kDa) is shown on the left. </small></p>
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<div class="row">
<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410053-IF.jpg" alt="HDAC1 Antibody validated in Immunofluorescence" caption="false" width="367" height="89" /></p>
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<div class="small-7 columns">
<p><small><strong> Figure 5. Immunofluorescence using the Diagenode antibody directed against HDAC1</strong><br /> HeLa cells were stained with the Diagenode antibody against HDAC1 (Cat. No. C15410053) 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 HDAC1 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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'slug' => 'hdac1-polyclonal-antibody-classic-50-ug-79-ul',
'meta_title' => 'HDAC1 polyclonal antibody - Classic',
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'clonality' => '',
'isotype' => '',
'lot' => 'A21-001P',
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<thead>
<tr>
<th>Applications</th>
<th>Suggested dilution</th>
<th>References</th>
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<tbody>
<tr>
<td>ChIP <sup>*</sup></td>
<td>2 μg/ChIP</td>
<td>Fig 1, 2</td>
</tr>
<tr>
<td>ELISA</td>
<td>1:4,000</td>
<td>Fig 3</td>
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<tr>
<td>Western Blotting</td>
<td>1:1,000</td>
<td>Fig 4</td>
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<td>Immunofluorescence</td>
<td>1:500</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 1-5 μg per IP.</small></p>',
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'description' => '<p><a href="https://go.diagenode.com/bioruptor-upgrade"><img src="https://www.diagenode.com/img/banners/banner-br-trade.png" /></a></p>
<p>The Bioruptor® Pico (2013-2019) represented a breakthrough for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml. <span>The new generation keeps the features you like the most and bring even more innovation. Check it now:</span></p>
<center><span></span></center><center><a href="https://www.diagenode.com/p/bioruptorpico2"> <img alt="New Bioruptor Pico" src="https://www.diagenode.com/img/product/shearing_technologies/new-pico-product-banner.jpg" /></a></center>
<p></p>
<p><span>Watch our short video about the Bioruptor Pico and how it can help you accomplish perfect shearing for any application including chromatin shearing, DNA shearing for NGS, unmatched DNA extraction from FFPE samples, RNA shearing, protein extraction, and much more.</span></p>
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'label1' => 'User manual ',
'info1' => '<p><a href="https://www.diagenode.com/files/products/shearing_technology/bioruptor/Bioruptor_pico_cooler_manual.pdf">Download</a></p>
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'label2' => 'Recommended settings for DNA shearing with Bioruptor® Pico',
'info2' => '<p>Follow our guidelines and find the good parameters for your expected DNA size: <a href="https://pybrevet.typeform.com/to/o8cQfM">DNA shearing with the Bioruptor® Pico</a></p>
<p></p>
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'label3' => 'Available chromatin shearing kits',
'info3' => '<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p>
<table style="width: 925px;">
<tbody>
<tr valign="middle">
<td style="width: 213px;"></td>
<td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td>
<td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td>
<td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>SDS concentration</strong></p>
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<td style="text-align: center; width: 208px;">
<p style="text-align: center;">< 0.1%</p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;">0.2%</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">1%</p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;">0.5%</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Nuclei isolation</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;">Yes</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">No</p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;">Yes</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Allows for shearing of... cells/tissue</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;">100 million cells</p>
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<td style="text-align: center; width: 180px;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;">100 million cells</p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;">up to 25 g of tissue</p>
</td>
</tr>
<tr style="background-color: #fff;" valign="middle">
<td style="width: 213px;">
<p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
<p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p>
</td>
</tr>
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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><img src="https://www.diagenode.com/img/product/antibodies/C15200229-IF.jpg" alt="" height="245" width="256" /></p>
<p><sup><strong>Immunofluorescence using the Diagenode monoclonal antibody directed against CRISPR/Cas9</strong></sup></p>
<p><sup>HeLa cells transfected with a Cas9 expression vector (left) or untransfected cells (right) were fixed in methanol at -20°C, permeabilized with acetone at -20°C and blocked with PBS containing 2% BSA. The cells were stained with the Cas9 C-terminal antibody (Cat. No. C15200229) diluted 1:400, followed by incubation with an anti-mouse secondary antibody coupled to AF488. The bottom images show counter-staining of the nuclei with Hoechst 33342.</sup></p>
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<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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<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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<div class="small-2 columns"><img src="https://www.diagenode.com/emailing/images/epi-success-guaranteed-icon.png" alt="Epigenetic success guaranteed" /></div>
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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' => 'Functional incompatibility between the generic NF-κB motif and a subtype-specific Sp1III element drives the formation of HIV-1 subtype C viral promoter',
'authors' => 'Verma A et al.',
'description' => '<p>Of the various genetic subtypes of HIV-1, HIV-2 and SIV, only in subtype C of HIV-1, a genetically variant NF-κB binding site is found at the core of the viral promoter in association with a subtype-specific Sp1III motif. How the subtype-associated variations in the core transcription factor binding sites (TFBS) influence gene expression from the viral promoter has not been examined previously. Using panels of infectious viral molecular clones, we demonstrate that subtype-specific NF-κB and Sp1III motifs have evolved for optimal gene expression, and neither of the motifs can be substituted by a corresponding TFBS variant.The variant NF-κB motif binds NF-κB with an affinity two-fold higher than that of the generic NF-κB site. Importantly, in the context of an infectious virus, the subtype-specific Sp1III motif demonstrates a profound loss of function in association with the generic NF-κB motif. An additional substitution of the Sp1III motif fully restores viral replication suggesting that the subtype C specific Sp1III has evolved to function with the variant, but not generic, NF-κB motif. A change of only two base pairs in the central NF-κB motif completely suppresses viral transcription from the provirus and converts the promoter into heterochromatin refractory to TNF-α induction. The present work represents the first demonstration of functional incompatibility between an otherwise functional NF-κB motif and a unique Sp1 site in the context of HIV-1 promoter. Our work provides important leads as per the evolution of HIV-1 subtype C viral promoter with relevance for gene expression regulation and viral latency.</p>',
'date' => '2016-05-18',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27194770',
'doi' => '10.1128/JVI.00308-16',
'modified' => '2016-06-30 15:57:48',
'created' => '2016-06-06 10:12:54',
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[maximum depth reached]
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(int) 2 => array(
'id' => '2866',
'name' => 'Genome-wide hydroxymethylcytosine pattern changes in response to oxidative stress',
'authors' => 'Delatte B, Jeschke J, Defrance M, Bachman M, Creppe C, Calonne E, Bizet M, Deplus R, Marroquí L, Libin M, Ravichandran M, Mascart F, Eizirik DL, Murrell A, Jurkowski TP, Fuks F',
'description' => '<div class="pl20 mq875-pl0 js-collapsible-section" id="abstract-content" itemprop="description">
<p><b>The TET enzymes convert methylcytosine to the newly discovered base hydroxymethylcytosine. While recent reports suggest that TETs may play a role in response to oxidative stress, this role remains uncertain, and results lack</b> <i><b>in vivo</b></i> <b>models. Here we show a global decrease of hydroxymethylcytosine in cells treated with buthionine sulfoximine, and in mice depleted for the major antioxidant enzymes</b> <i><b>GPx</b></i><b>1 and 2. Furthermore, genome-wide profiling revealed differentially hydroxymethylated regions in coding genes, and intriguingly in microRNA genes, both involved in response to oxidative stress. These results thus suggest a profound effect of</b> <i><b>in vivo</b></i> <b>oxidative stress on the global hydroxymethylome.</b></p>
</div>',
'date' => '2015-08-04',
'pmid' => 'http://www.nature.com/articles/srep12714',
'doi' => '10.1038/srep12714',
'modified' => '2016-03-22 10:37:38',
'created' => '2016-03-22 10:37:38',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'id' => '2274',
'name' => 'SNAIL1 combines competitive displacement of ASCL2 and epigenetic mechanisms to rapidly silence the EPHB3 tumor suppressor in colorectal cancer.',
'authors' => 'Rönsch K, Jägle S, Rose K, Seidl M, Baumgartner F, Freihen V, Yousaf A, Metzger E, Lassmann S, Schüle R, Zeiser R, Michoel T, Hecht A',
'description' => 'EPHB3 is a critical cellular guidance factor in the intestinal epithelium and an important tumor suppressor in colorectal cancer (CRC) whose expression is frequently lost at the adenoma-carcinoma transition when tumor cells become invasive. The molecular mechanisms underlying EPHB3 silencing are incompletely understood. Here we show that EPHB3 expression is anti-correlated with inducers of epithelial-mesenchymal transition (EMT) in primary tumors and CRC cells. In vitro, SNAIL1 and SNAIL2, but not ZEB1, repress EPHB3 reporter constructs and compete with the stem cell factor ASCL2 for binding to an E-box motif. At the endogenous EPHB3 locus, SNAIL1 triggers the displacement of ASCL2, p300 and the Wnt pathway effector TCF7L2 and engages corepressor complexes containing HDACs and the histone demethylase LSD1 to collapse active chromatin structure, resulting in rapid downregulation of EPHB3. Beyond its impact on EPHB3, SNAIL1 deregulates markers of intestinal identity and stemness and in vitro forces CRC cells to undergo EMT with altered morphology, increased motility and invasiveness. In xenotransplants, SNAIL1 expression abrogated tumor cell palisading and led to focal loss of tumor encapsulation and the appearance of areas with tumor cells displaying a migratory phenotype. These changes were accompanied by loss of EPHB3 and CDH1 expression. Intriguingly, SNAIL1-induced phenotypic changes of CRC cells are significantly impaired by sustained EPHB3 expression both in vitro and in vivo. Altogether, our results identify EPHB3 as a novel target of SNAIL1 and suggest that disabling EPHB3 signaling is an important aspect to eliminate a roadblock at the onset of EMT processes.',
'date' => '2014-09-16',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25277775',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'id' => '2130',
'name' => 'Citrullination of DNMT3A by PADI4 regulates its stability and controls DNA methylation.',
'authors' => 'Deplus R, Denis H, Putmans P, Calonne E, Fourrez M, Yamamoto K, Suzuki A, Fuks F',
'description' => 'DNA methylation is a central epigenetic modification in mammals, with essential roles in development and disease. De novo DNA methyltransferases establish DNA methylation patterns in specific regions within the genome by mechanisms that remain poorly understood. Here we show that protein citrullination by peptidylarginine deiminase 4 (PADI4) affects the function of the DNA methyltransferase DNMT3A. We found that DNMT3A and PADI4 interact, from overexpressed as well as untransfected cells, and associate with each other's enzymatic activity. Both in vitro and in vivo, PADI4 was shown to citrullinate DNMT3A. We identified a sequence upstream of the PWWP domain of DNMT3A as its primary region citrullinated by PADI4. Increasing the PADI4 level caused the DNMT3A protein level to increase as well, provided that the PADI4 was catalytically active, and RNAi targeting PADI4 caused reduced DNMT3A levels. Accordingly, pulse-chase experiments revealed stabilization of the DNMT3A protein by catalytically active PADI4. Citrullination and increased expression of native DNMT3A by PADI4 were confirmed in PADI4-knockout MEFs. Finally, we showed that PADI4 overexpression increases DNA methyltransferase activity in a catalytic-dependent manner and use bisulfite pyrosequencing to demonstrate that PADI4 knockdown causes significant reduction of CpG methylation at the p21 promoter, a known target of DNMT3A and PADI4. Protein citrullination by PADI4 thus emerges as a novel mechanism for controlling a de novo DNA methyltransferase. Our results shed new light on how post-translational modifications might contribute to shaping the genomic CpG methylation landscape.',
'date' => '2014-06-23',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24957603',
'doi' => '',
'modified' => '2015-07-24 15:39:03',
'created' => '2015-07-24 15:39:03',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '1553',
'name' => 'Dimethyl fumarate regulates histone deacetylase expression in astrocytes.',
'authors' => 'Kalinin S, Polak PE, Lin SX, Braun D, Guizzetti M, Zhang X, Rubinstein I, Feinstein DL',
'description' => 'We previously showed that dimethyl fumarate (DMF) reduces inflammatory activation in astrocytes, involving activation of transcription factor Nrf2. However, the pathways causing Nrf2 activation were not examined. We now show that DMF modifies expression of histone deacetylases (HDACs) in primary rat astrocytes. After 4h incubation, levels of HDAC1, 2, and 4 mRNAs were increased by DMF; however, after 24h, levels returned to or were below control values. At that time, HDAC protein levels and overall activity were also reduced by DMF. Stimulation of astrocytes with pro-inflammatory cytokines significantly increased HDAC mRNA levels after 24h, although protein levels were not increased at that time point. In the presence of cytokines, DMF reduced HDAC mRNAs, proteins, and activity. Proteomic analysis of DMF-treated astrocytes identified 8 proteins in which lysine acetylation was increased by DMF, including histones H2a.1 and H3.3. A role for HDACs in mediating DMF actions is suggested by findings that the selective HDAC inhibitor SAHA increased nuclear Nrf2:DNA binding activity, reduced inflammatory activation of astrocytes which was reversed by a selective inhibitor of the Nrf2 target gene heme-oxygenase 1. These data show that DMF regulates astrocyte HDAC expression, which could contribute to Nrf2 activation, suppression of inflammatory responses and cause long-lasting changes in gene expression.',
'date' => '2013-10-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23916696',
'doi' => '',
'modified' => '2015-07-24 15:39:00',
'created' => '2015-07-24 15:39:00',
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[maximum depth reached]
)
),
(int) 6 => array(
'id' => '800',
'name' => 'Phosphorylation of p65(RelA) on Ser547 by ATM Represses NF-κB-Dependent Transcription of Specific Genes after Genotoxic Stress',
'authors' => 'Sabatel H, Di Valentin E, Gloire G, Dequiedt F, Piette J, Habraken Y',
'description' => '',
'date' => '2012-06-08',
'pmid' => 'http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038246#abstract0',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 7 => 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) 8 => array(
'id' => '714',
'name' => 'HDAC1 Regulates Fear Extinction in Mice.',
'authors' => 'Bahari-Javan S, Maddalena A, Kerimoglu C, Wittnam J, Held T, Bähr M, Burkhardt S, Delalle I, Kügler S, Fischer A, Sananbenesi F',
'description' => 'Histone acetylation has been implicated with the pathogenesis of neuropsychiatric disorders and targeting histone deacetylases (HDACs) using HDAC inhibitors was shown to be neuroprotective and to initiate neuroregenerative processes. However, little is known about the role of individual HDAC proteins during the pathogenesis of brain diseases. HDAC1 was found to be upregulated in patients suffering from neuropsychiatric diseases. Here, we show that virus-mediated overexpression of neuronal HDAC1 in the adult mouse hippocampus specifically affects the extinction of contextual fear memories, while other cognitive abilities were unaffected. In subsequent experiments we show that under physiological conditions, hippocampal HDAC1 is required for extinction learning via a mechanism that involves H3K9 deacetylation and subsequent trimethylation of target genes. In conclusion, our data show that hippocampal HDAC1 has a specific role in memory function.',
'date' => '2012-04-11',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22496552',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'id' => '816',
'name' => 'Enhancer of Zeste 2 (EZH2) is up-regulated in malignant gliomas and in glioma stem-like cells.',
'authors' => 'Orzan F, Pellegatta S, Poliani PL, Pisati F, Caldera V, Menghi F, Kapetis D, Marras C, Schiffer D, Finocchiaro G',
'description' => 'AIMS: Proteins of the Polycomb repressive complex 2 (PRC2) are epigenetic gene silencers and are involved in tumour development. Their oncogenic function might be associated with their role in stem cell maintenance. The histone methyltransferase Enhancer of Zeste 2 (EZH2) is a key member of PRC2 function: we have investigated its expression and function in gliomas. METHODS: EZH2 expression was studied in grade II-IV gliomas and in glioma stem-like cells (GSC) by quantitative PCR and immunohistochemistry. Effects of EZH2 down-regulation were analysed by treating GSC with the histone deacetylase (HDAC) inhibitor suberoylanide hydroxamic acid (SAHA) and by shRNA. RESULTS: DNA microarray analysis showed that EZH2 is highly expressed in murine and human GSC. Real-time PCR on gliomas of different grade (n = 66) indicated that EZH2 is more expressed in glioblastoma multiforme (GBM) than in low-grade gliomas (P = 0.0013). This was confirmed by immunohistochemistry on an independent set of 106 gliomas. Treatment with SAHA caused significant up-regulation of PRC2 predicted target genes, GSC disruption and decreased expression of EZH2 and of the stem cell marker CD133. Inhibition of EZH2 expression by shRNA was associated with a significant decrease of glioma proliferation. CONCLUSION: The data suggest that EZH2 plays a role in glioma progression and encourage the therapeutic targeting of these malignancies by HDAC inhibitors.',
'date' => '2011-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/20946108',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
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),
(int) 10 => array(
'id' => '77',
'name' => 'The core binding factor CBF negatively regulates skeletal muscle terminal differentiation.',
'authors' => 'Philipot O, Joliot V, Ait-Mohamed O, Pellentz C, Robin P, Fritsch L, Ait-Si-Ali S',
'description' => 'BACKGROUND: Core Binding Factor or CBF is a transcription factor composed of two subunits, Runx1/AML-1 and CBF beta or CBFbeta. CBF was originally described as a regulator of hematopoiesis. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that CBF is involved in the control of skeletal muscle terminal differentiation. Indeed, downregulation of either Runx1 or CBFbeta protein level accelerates cell cycle exit and muscle terminal differentiation. Conversely, overexpression of CBFbeta in myoblasts slows terminal differentiation. CBF interacts directly with the master myogenic transcription factor MyoD, preferentially in proliferating myoblasts, via Runx1 subunit. In addition, we show a preferential recruitment of Runx1 protein to MyoD target genes in proliferating myoblasts. The MyoD/CBF complex contains several chromatin modifying enzymes that inhibits MyoD activity, such as HDACs, Suv39h1 and HP1beta. When overexpressed, CBFbeta induced an inhibition of activating histone modification marks concomitant with an increase in repressive modifications at MyoD target promoters. CONCLUSIONS/SIGNIFICANCE: Taken together, our data show a new role for Runx1/CBFbeta in the control of the proliferation/differentiation in skeletal myoblasts.',
'date' => '2010-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/20195544',
'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) 11 => array(
'id' => '78',
'name' => 'Functional connection between deimination and deacetylation of histones.',
'authors' => 'Denis H, Deplus R, Putmans P, Yamada M, Métivier R, Fuks F',
'description' => 'Histone methylation plays key roles in regulating chromatin structure and function. The recent identification of enzymes that antagonize or remove histone methylation offers new opportunities to appreciate histone methylation plasticity in the regulation of epigenetic pathways. Peptidylarginine deiminase 4 (PADI4; also known as PAD4) was the first enzyme shown to antagonize histone methylation. PADI4 functions as a histone deiminase converting a methylarginine residue to citrulline at specific sites on the tails of histones H3 and H4. This activity is linked to repression of the estrogen-regulated pS2 promoter. Very little is known as to how PADI4 silences gene expression. We show here that PADI4 associates with the histone deacetylase 1 (HDAC1). Kinetic chromatin immunoprecipitation assays revealed that PADI4 and HDAC1, and the corresponding activities, associate cyclically and coordinately with the pS2 promoter during repression phases. Knockdown of HDAC1 led to decreased H3 citrullination, concomitantly with increased histone arginine methylation. In cells with a reduced HDAC1 and a slightly decreased PADI4 level, these effects were more pronounced. Our data thus suggest that PADI4 and HDAC1 collaborate to generate a repressive chromatin environment on the pS2 promoter. These findings further substantiate the "transcriptional clock" concept, highlighting the dynamic connection between deimination and deacetylation of histones.',
'date' => '2009-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19581286',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
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<div class="row">
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<a href="/jp/p/bioruptor-pico-sonication-device"><img src="/img/product/shearing_technologies/bioruptor_pico.jpg" alt="Bioruptor pico next gen sequencing " class="th"/></a> </div>
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<span class="success label" style="">B01060010</span>
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<h6 style="height:60px">Picoruptor Sonicator</h6>
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</li>
'
$related = array(
'id' => '1787',
'antibody_id' => null,
'name' => 'Bioruptor<sup>®</sup> Pico sonication device',
'description' => '<p><a href="https://go.diagenode.com/bioruptor-upgrade"><img src="https://www.diagenode.com/img/banners/banner-br-trade.png" /></a></p>
<p>The Bioruptor® Pico (2013-2019) represented a breakthrough for shearing micro-volumes of 5 μl to larger volumes of up to 2 ml. <span>The new generation keeps the features you like the most and bring even more innovation. Check it now:</span></p>
<center><span></span></center><center><a href="https://www.diagenode.com/p/bioruptorpico2"> <img alt="New Bioruptor Pico" src="https://www.diagenode.com/img/product/shearing_technologies/new-pico-product-banner.jpg" /></a></center>
<p></p>
<p><span>Watch our short video about the Bioruptor Pico and how it can help you accomplish perfect shearing for any application including chromatin shearing, DNA shearing for NGS, unmatched DNA extraction from FFPE samples, RNA shearing, protein extraction, and much more.</span></p>
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'info1' => '<p><a href="https://www.diagenode.com/files/products/shearing_technology/bioruptor/Bioruptor_pico_cooler_manual.pdf">Download</a></p>
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'info2' => '<p>Follow our guidelines and find the good parameters for your expected DNA size: <a href="https://pybrevet.typeform.com/to/o8cQfM">DNA shearing with the Bioruptor® Pico</a></p>
<p></p>
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'info3' => '<p>It is important to establish optimal conditions to shear crosslinked chromatin to get the correct fragment sizes needed for ChIP. Usually this process requires both optimizing sonication conditions as well as optimizing SDS concentration, which is laborious. With the Chromatin Shearing Optimization Kits, optimization is fast and easy - we provide optimization reagents with varying concentrations of SDS. Moreover, our Chromatin Shearing Optimization Kits can be used for the optimization of chromatin preparation with our kits for ChIP.</p>
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<td style="width: 213px;"></td>
<td style="text-align: center; width: 208px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-100-million-cells">Chromatin Shearing Kit Low SDS (for Histones)</a></strong></td>
<td style="text-align: center; width: 180px;"><strong><a href="../p/chromatin-shearing-optimization-kit-low-sds-for-tfs-25-rxns">Chromatin Shearing Kit Low SDS (for TF)</a></strong></td>
<td style="text-align: center; width: 154px;"><strong><a href="../p/chromatin-shearing-optimization-kit-high-sds-100-million-cells">Chromatin Shearing Kit High SDS</a></strong></td>
<td style="text-align: center; width: 155px;"><strong><a href="../p/chromatin-shearing-plant-chip-seq-kit">Chromatin Shearing Kit (for Plant)</a></strong></td>
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<p style="text-align: center;">< 0.1%</p>
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<td style="text-align: center; width: 180px;">
<p style="text-align: center;">0.2%</p>
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<td style="text-align: center; width: 154px;">
<p style="text-align: center;">1%</p>
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<td style="text-align: center; width: 155px;">
<p style="text-align: center;">0.5%</p>
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<p style="text-align: center;">Yes</p>
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<td style="text-align: center; width: 180px;">
<p style="text-align: center;">Yes</p>
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<td style="text-align: center; width: 154px;">
<p style="text-align: center;">No</p>
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<td style="text-align: center; width: 155px;">
<p style="text-align: center;">Yes</p>
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<p style="text-align: center;">100 million cells</p>
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<p style="text-align: center;">100 million cells</p>
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<td style="text-align: center; width: 154px;">
<p style="text-align: center;">100 million cells</p>
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<p style="text-align: center;">up to 25 g of tissue</p>
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<p style="text-align: left;"><strong>Corresponding to shearing buffers from</strong></p>
</td>
<td style="text-align: center; width: 208px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq kit for Histones</a></p>
<p style="text-align: center;"><a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a></p>
</td>
<td style="text-align: center; width: 180px;">
<p style="text-align: center;"><a href="../p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></p>
<p style="text-align: center;"><a href="../p/ideal-chip-qpcr-kit">iDeal ChIP qPCR kit</a></p>
</td>
<td style="text-align: center; width: 154px;">
<p style="text-align: center;"><a href="../p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a></p>
</td>
<td style="text-align: center; width: 155px;">
<p style="text-align: center;"><a href="../p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant <br />ChIP-seq kit</a></p>
</td>
</tr>
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