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H3K4me1 polyclonal antibody (sample size)

CUT&Tag grade Abs

ChIP-seq grade Abs

ChIP grade Abs

Negative IgG control

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Catalog Number

Format

Price

C15410037-10

10 µg

$115.00
Bulk order

Other format

C15410037

50 µg

Polyclonal antibody raised in rabbit against histone H3 containing the monomethylated lysine 4 (H3K4me1), using a KLH-conjugated synthetic peptide.

Lot	A1657D
Concentration	2.9 µg/µl
Species reactivity	Human, mouse, pig
Type	Polyclonal
Purity	Affinity purified polyclonal antibody.
Host	Rabbit
Storage Conditions	Store at -20°C; for long storage, store at -80°C. Avoid multiple freeze-thaw cycles.
Storage Buffer	PBS containing 0.05% azide and 0.05% ProClin 300.
Precautions	This product is for research use only. Not for use in diagnostic or therapeutic procedures.

Applications	Suggested dilution	References
ChIP/ChIP-seq ^*	1-2 μg/IP	Fig 1, 2
ELISA	1:500	Fig 3
Dot Blotting	1:10,000	Fig 4
Western Blotting	1:500	Fig 5
Immunofluorescence	1:500	Fig 6

^* Please note that the optimal antibody amount per IP should be determined by the end-user. We recommend testing 1-5 μg per IP.

Validation Data

A.

B.

Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1
ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the “iDeal ChIP-seq” kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 µg per ChIP experiment was analysed. IgG (2 µg/IP) was used as negative IP control. Figure 1A. Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). Figure 1B. Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification.

A.

B.

C.

D.

Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1
ChIP was performed as described above with 1 µg of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP’d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively.

Figure 3. Determination of the titer
To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100.

Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1
A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest.

Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1
Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left.

Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1
HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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.
Target Description
Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases.

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Cranial neural crest (NC) cells, which can migrate, adopt multiple fates, and form most of the craniofacial skeleton, are an excellent model for studying cell fate decisions. Using time-resolved single-cell multi-omics, spatial transcriptomics, and systematic Perturb-seq, we fully deciphered zebrafish cranial NC pro...

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Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T cell...

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The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are inactive, over ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to interact with regu...

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Mechanisms governing regional human adipose tissue (AT) development remain undefined. Here, we show that the long non-coding RNA HOTAIR (HOX transcript antisense RNA) is exclusively expressed in gluteofemoral AT, where it is essential for adipocyte development. We find that HOTAIR interacts with polycomb repressive ...

Local euchromatin enrichment in lamina-associated domains anticipatestheir repositioning in the adipogenic lineage.
Madsen-Østerbye J. et al.
BACKGROUND: Interactions of chromatin with the nuclear lamina via lamina-associated domains (LADs) confer structural stability to the genome. The dynamics of positioning of LADs during differentiation, and how LADs impinge on developmental gene expression, remains, however, elusive. RESULTS: We examined changes in t...

Loss of KMT2C reprograms the epigenomic landscape in hPSCsresulting in NODAL overexpression and a failure of hemogenic endotheliumspecification.
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BACKGROUND: Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic ...

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Increased H3K9 methylation and impaired expression of Protocadherins are associated with the cognitive dysfunctions of the Kleefstra syndrome.
Iacono G, Dubos A, Méziane H, Benevento M, Habibi E, Mandoli A, Riet F, Selloum M, Feil R, Zhou H, Kleefstra T, Kasri NN, van Bokhoven H, Herault Y, Stunnenberg HG
Kleefstra syndrome, a disease with intellectual disability, autism spectrum disorders and other developmental defects is caused in humans by haploinsufficiency of EHMT1. Although EHMT1 and its paralog EHMT2 were shown to be histone methyltransferases responsible for deposition of the di-methylated H3K9 (H3K9me2), th...

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Lacomme M, Medevielle F, Bourbon HM, Thierion E, Kleinjan DJ, Roussat M, Pituello F, Bel-Vialar S
Proper embryonic development relies on a tight control of spatial and temporal gene expression profiles in a highly regulated manner. One good example is the ON/OFF switching of the transcription factor PAX6 that governs important steps of neurogenesis. In the neural tube PAX6 expression is initiated in neural proge...

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Judson RN, Quarta M, Oudhoff MJ, Soliman H, Yi L, Chang CK, Loi G, Vander Werff R, Cait A, Hamer M, Blonigan J, Paine P, Doan LTN, Groppa E, He W, Su L, Zhang RH, Xu P, Eisner C, Low M, Barta I, Lewis CB, Zaph C, Karimi MM, Rando TA, Rossi FM
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Metabolic Induction of Trained Immunity through the Mevalonate Pathway.
Bekkering S, Arts RJW, Novakovic B, Kourtzelis I, van der Heijden CDCC, Li Y, Popa CD, Ter Horst R, van Tuijl J, Netea-Maier RT, van de Veerdonk FL, Chavakis T, Joosten LAB, van der Meer JWM, Stunnenberg H, Riksen NP, Netea MG
Innate immune cells can develop long-term memory after stimulation by microbial products during infections or vaccinations. Here, we report that metabolic signals can induce trained immunity. Pharmacological and genetic experiments reveal that activation of the cholesterol synthesis pathway, but not the synthesis of...

Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements
Thierion E. et al.
Developmental genes can harbour multiple transcriptional enhancers that act simultaneously or in succession to achieve robust and precise spatiotemporal expression. However, the mechanisms underlying cooperation between cis-acting elements are poorly documented, notably in vertebrates. The mouse gene Krox20 encodes ...

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Iberg-Badeaux A. et al.
Short-term and long-term transcriptional memory is the phenomenon whereby the kinetics or magnitude of gene induction is enhanced following a prior induction period. Short-term memory persists within one cell generation or in post-mitotic cells, while long-term memory can survive multiple rounds of cell division. We...

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Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as lipopolysaccharide (LPS). We apply an integrated epigenomic approach to characterize the molecular events involved in LPS-induced to...

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Psoriasis is an immune-mediated skin disorder that is inherited as a complex genetic trait. Although genome-wide association scans (GWAS) have identified 36 disease susceptibility regions, more than 50% of the genetic variance can be attributed to a single Major Histocompatibility Complex (MHC) locus, known as PSORS...

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Coronary heart disease (CHD) is the leading cause of mortality in both developed and developing countries worldwide. Genome-wide association studies (GWAS) have now identified 46 independent susceptibility loci for CHD, however, the biological and disease-relevant mechanisms for these associations remain elusive. Th...

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Outchkourov NS, Muiño JM, Kaufmann K, van Ijcken WF, Groot Koerkamp MJ, van Leenen D, de Graaf P, Holstege FC, Grosveld FG, Timmers HT
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The H3K9me3 histone modification is often found at promoter regions, where it functions to repress transcription. However, we have previously shown that 3' exons of zinc finger genes (ZNFs) are marked by high levels of H3K9me3. We have now further investigated this unusual location for H3K9me3 in ZNF genes. Neither ...

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The dynamic modification of DNA and histones plays a key role in transcriptional regulation through - altering the packaging of DNA and modifying the nucleosome surface. These chromatin states, also referred to as the epigenome, are distinctive for different tissues, developmental stages, and disease states and can ...

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<td>ChIP/ChIP-seq <sup>*</sup></td>
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<td>1:500</td>
<td>Fig 5</td>
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<td>1:500</td>
<td>Fig 6</td>
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$language = 'jp'
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$product = array(
	'Product' => array(
		'id' => '2900',
		'antibody_id' => '110',
		'name' => 'H3K4me1 polyclonal antibody (sample size)',
		'description' => '<p>Polyclonal antibody raised in rabbit against histone H3 containing the monomethylated lysine 4 (H3K4me1), using a KLH-conjugated synthetic peptide.</p>',
		'label1' => 'Validation Data',
		'info1' => '<div class="row">
<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
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</div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
</div>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_DotBlot.png" alt="H3K4me1 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-7 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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>
</div>
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		'label2' => 'Target Description',
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		'price_CNY' => '',
		'price_AUD' => '288',
		'country' => 'ALL',
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		'slug' => 'h3k4me1-polyclonal-antibody-classic-10-ug',
		'meta_title' => '',
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		'modified' => '2024-01-16 14:13:51',
		'created' => '2017-06-07 16:05:55',
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	'Antibody' => array(
		'host' => '*****',
		'id' => '110',
		'name' => 'H3K4me1 polyclonal antibody ',
		'description' => 'Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases.',
		'clonality' => '',
		'isotype' => '',
		'lot' => 'A1657D',
		'concentration' => '2.9 &micro;g/&micro;l',
		'reactivity' => 'Human, mouse, pig',
		'type' => 'Polyclonal',
		'purity' => 'Affinity purified polyclonal antibody.',
		'classification' => 'Classic',
		'application_table' => '<table>
<thead>
<tr>
<th>Applications</th>
<th>Suggested dilution</th>
<th>References</th>
</tr>
</thead>
<tbody>
<tr>
<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>1-2 &mu;g/IP</td>
<td>Fig 1, 2</td>
</tr>
<tr>
<td>ELISA</td>
<td>1:500</td>
<td>Fig 3</td>
</tr>
<tr>
<td>Dot Blotting</td>
<td>1:10,000</td>
<td>Fig 4</td>
</tr>
<tr>
<td>Western Blotting</td>
<td>1:500</td>
<td>Fig 5</td>
</tr>
<tr>
<td>Immunofluorescence</td>
<td>1:500</td>
<td>Fig 6</td>
</tr>
</tbody>
</table>
<p></p>
<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 &mu;g per IP.</small></p>',
		'storage_conditions' => 'Store at -20°C; for long storage, store at -80°C. Avoid multiple freeze-thaw cycles.',
		'storage_buffer' => 'PBS containing 0.05% azide and 0.05% ProClin 300.',
		'precautions' => 'This product is for research use only. Not for use in diagnostic or therapeutic procedures.',
		'uniprot_acc' => '',
		'slug' => '',
		'meta_keywords' => '',
		'meta_description' => '',
		'modified' => '2022-10-04 15:01:10',
		'created' => '0000-00-00 00:00:00',
		'select_label' => '110 - H3K4me1 polyclonal antibody  (A1657D - 2.9 &micro;g/&micro;l - Human, mouse, pig - Affinity purified polyclonal antibody. - Rabbit)'
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			'name' => 'C15410037',
			'product_id' => '2202',
			'modified' => '2017-06-07 16:16:20',
			'created' => '2017-06-07 16:16:20'
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			'id' => '2202',
			'antibody_id' => '110',
			'name' => 'H3K4me1 Antibody',
			'description' => '<p><span>Polyclonal antibody raised in rabbit against histone <strong>H3 containing the monomethylated lysine 4</strong> (<strong>H3K4me1</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
			'label1' => 'Validation Data',
			'info1' => '<div class="row">
<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
</div>
</div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_DotBlot.png" alt="H3K4me1 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-7 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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>
</div>
</div>',
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			'info2' => '<p>Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called &ldquo;histone code&rdquo;. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases.</p>',
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			'modified' => '2024-11-19 16:55:49',
			'created' => '2015-06-29 14:08:20'
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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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<div class="small-12 medium-12 large-12 columns">Enzyme-linked immunosorbent assay.</div>
</div>',
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			'slug' => 'chip-seq-antibodies',
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			'meta_description' => 'Diagenode offers a wide range of antibodies and technical support for ChIP Sequencing applications',
			'meta_title' => 'ChIP Sequencing Antibodies (ChIP-Seq) | Diagenode',
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			'slug' => 'chip-qpcr-antibodies',
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			'meta_description' => 'Diagenode offers a wide range of antibodies and technical support for ChIP-qPCR applications',
			'meta_title' => 'ChIP Quantitative PCR  Antibodies (ChIP-qPCR) | Diagenode',
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			'description' => '<h1><strong>Validated epigenetics antibodies</strong>&nbsp;&ndash; care for a sample?<br />&nbsp;</h1>
<p>Diagenode has partnered with leading epigenetics experts and numerous epigenetics consortiums to bring to you a validated and comprehensive collection of epigenetic antibodies. As an expert in epigenetics, we are committed to offering highly-specific antibodies validated for ChIP/ChIP-seq and many other applications. All batch-specific validation data is available on our website.<br /><a href="../categories/antibodies">Read about our expertise in antibody production</a>.</p>
<ul>
<li><strong>Focused</strong> -&nbsp;Diagenode's selection of antibodies is exclusively dedicated for epigenetic research. <a title="See the full collection." href="../categories/all-antibodies">See the full collection.</a></li>
<li><strong>Strict quality standards</strong>&nbsp;with rigorous QC and validation</li>
<li><strong>Classified</strong>&nbsp;based on level of validation for flexibility of application</li>
</ul>
<p>Existing sample sizes are listed below. We will soon expand our collection. &nbsp;Are you looking for a sample size of another antibody? Just <a href="mailto:agnieszka.zelisko@diagenode.com?Subject=Sample%20Size%20Request" target="_top">Contact us</a>.</p>',
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			'name' => 'All antibodies',
			'description' => '<p><span style="font-weight: 400;">All Diagenode&rsquo;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&rsquo;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_description' => 'Diagenode Offers Strict quality standards with Rigorous QC and validated Antibodies. Classified based on level of validation for flexibility of Application. Comprehensive selection of histone and non-histone Antibodies',
			'meta_title' => 'Diagenode's selection of Antibodies is exclusively dedicated for Epigenetic Research | Diagenode',
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			'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 &micro;g of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 &micro;g 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&rsquo;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_keywords' => 'ChIP-seq grade antibodies,polyclonal antibody,WB, ELISA, ChIP-seq (ab), ChIP-qPCR (ab)',
			'meta_description' => 'Diagenode Offers Wide Range of Validated ChIP-Seq Grade Antibodies for Unparalleled ChIP-Seq Results',
			'meta_title' => 'Chromatin Immunoprecipitation ChIP-Seq Grade Antibodies | Diagenode',
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			'name' => 'ChIP-grade antibodies',
			'description' => '<div class="row">
<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
<p></p>
</div>
</div>
<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>).&nbsp;</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" />&nbsp;</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_keywords' => 'ChIP-grade antibodies, polyclonal antibody, monoclonal antibody, Diagenode',
			'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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		(int) 4 => array(
			'id' => '111',
			'position' => '40',
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			'name' => 'Histone antibodies',
			'description' => '<p>Histones are the main protein components of chromatin involved in the compaction of DNA into nucleosomes, the basic units of chromatin. A <strong>nucleosome</strong> consists of one pair of each of the core histones (<strong>H2A</strong>, <strong>H2B</strong>, <strong>H3</strong> and <strong>H4</strong>) forming an octameric structure wrapped by 146 base pairs of DNA. The different nucleosomes are linked by the linker histone<strong> H1, </strong>allowing for further condensation of chromatin.</p>
<p>The core histones have a globular structure with large unstructured N-terminal tails protruding from the nucleosome.&nbsp; They can undergo to multiple post-translational modifications (PTM), mainly at the N-terminal tails. These <strong>post-translational modifications </strong>include&nbsp; methylation, acetylation, phosphorylation, ubiquitinylation, citrullination, sumoylation, deamination and crotonylation.&nbsp; The most well characterized PTMs are <strong>methylation,</strong> <strong>acetylation and phosphorylation</strong>. Histone methylation occurs mainly on lysine (K) residues, which can be mono-, di- or tri-methylated, and on arginines (R), which can be mono-methylated and symmetrically or asymmetrically di-methylated. Histone acetylation occurs on lysines and histone phosphorylation mainly on serines (S), threonines (T) and tyrosines (Y).</p>
<p>The PTMs of the different residues are involved in numerous processes such as DNA repair, DNA replication and chromosome condensation. They influence the chromatin organization and can be positively or negatively associated with gene expression. Trimethylation of H3K4, H3K36 and H3K79, and lysine acetylation generally result in an open chromatin configuration (figure below) and are therefore associated with <strong>euchromatin</strong> and gene activation. Trimethylation of H3K9, K3K27 and H4K20, on the other hand, is enriched in <strong>heterochromatin </strong>and associated with gene silencing. The combination of different histone modifications is called the "<strong>histone code</strong>&rdquo;, analogous to the genetic code.</p>
<p><img src="https://www.diagenode.com/img/categories/antibodies/histone-marks-illustration.png" /></p>
<p>Diagenode is proud to offer a large range of antibodies against histones and histone modifications. Our&nbsp; antibodies are highly specific and have been validated in many applications, including <strong>ChIP</strong> and <strong>ChIP-seq</strong>.</p>
<p>Diagenode&rsquo;s collection includes antibodies recognizing:</p>
<ul>
<li><strong>Histone H1 variants</strong></li>
<li><strong>Histone H2A, H2A variants and histone H2A</strong> <strong>modifications</strong> (serine phosphorylation, lysine acetylation, lysine ubiquitinylation)</li>
<li><strong>Histone H2B and H2B</strong> <strong>modifications </strong>(serine phosphorylation, lysine acetylation)</li>
<li><strong>Histone H3 and H3 modifications </strong>(lysine methylation (mono-, di- and tri-methylated), lysine acetylation, serine phosphorylation, threonine phosphorylation, arginine methylation (mono-methylated, symmetrically and asymmetrically di-methylated))</li>
<li><strong>Histone H4 and H4 modifications (</strong>lysine methylation (mono-, di- and tri-methylated), lysine acetylation, arginine methylation (mono-methylated and symmetrically di-methylated), serine phosphorylation )</li>
</ul>
<p><span style="font-weight: 400;"><strong>HDAC's HAT's, HMT's and other</strong> <strong>enzymes</strong> which modify histones can be found in the category <a href="../categories/chromatin-modifying-proteins-histone-transferase">Histone modifying enzymes</a><br /></span></p>
<p><span style="font-weight: 400;"> Diagenode&rsquo;s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Expert technical support</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sample sizes available</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 100% satisfaction guarantee</span></li>
</ul>',
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			'slug' => 'histone-antibodies',
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			'meta_keywords' => 'Histone, antibody, histone h1, histone h2, histone h3, histone h4',
			'meta_description' => 'Polyclonal and Monoclonal Antibodies against Histones and their modifications validated for many applications, including Chromatin Immunoprecipitation (ChIP) and ChIP-Sequencing (ChIP-seq)',
			'meta_title' => 'Histone and Modified Histone Antibodies | Diagenode',
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			'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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			'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',
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			'id' => '342',
			'name' => 'Datasheet H3K4me1 C15410037',
			'description' => '<p><span>Polyclonal antibody raised in rabbit against histone H3 containing the monomethylated lysine 4 (H3K4me1), using a KLH-conjugated synthetic peptide.</span></p>',
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			'type' => 'Datasheet',
			'url' => 'files/products/antibodies/Datasheet_H3K4me1_C15410037.pdf',
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			'alt' => 'ChIP-seq Grade',
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			'id' => '4977',
			'name' => 'Single-cell multi-omics, spatial transcriptomics and systematic perturbation decode circuitry of neural crest fate decisions',
			'authors' => 'Hu Z. et al.',
			'description' => '<p><span>Cranial neural crest (NC) cells, which can migrate, adopt multiple fates, and form most of the craniofacial skeleton, are an excellent model for studying cell fate decisions. Using time-resolved single-cell multi-omics, spatial transcriptomics, and systematic Perturb-seq, we fully deciphered zebrafish cranial NC programs, including 23 cell states and three spatial trajectories, reconstructed and tested the complete gene regulatory network (GRN). Our GRN model, combined with a novel velocity-embedded simulation method, accurately predicted functions of all major regulons, with over a 3-fold increase in correlation between in vivo and in silico perturbations. Using our new approach based on regulatory synchronization, we discovered a post-epithelial-mesenchymal-transition endothelial-like program crucial for migration, identified motif coordinators for dual-fate priming, and quantified lineage-specific cooperative transcription factor functions. This study provides a comprehensive and validated NC regulatory landscape with unprecedented resolution, offering general regulatory models for cell fate decisions in vertebrates.</span></p>',
			'date' => '2024-09-17',
			'pmid' => 'https://www.biorxiv.org/content/10.1101/2024.09.17.613303v1',
			'doi' => ' https://doi.org/10.1101/2024.09.17.613303',
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			'id' => '4943',
			'name' => 'KRAS promotes GLI2-dependent transcription during pancreatic carcinogenesis',
			'authors' => 'Sigafoos A.N. et al.',
			'description' => '<p><span>Aberrant activation of GLI transcription factors has been implicated in the pathogenesis of different tumor types including pancreatic ductal adenocarcinoma (PDAC). However, the mechanistic link with established drivers of this disease remains in part elusive. Here, using a new genetically-engineered mouse model overexpressing constitutively active mouse form of GLI2 and a combination of genome wide assays, we provide evidence of a novel mechanism underlying the interplay between KRAS, a major driver of PDAC development, and GLI2 to control oncogenic gene expression. These mice, also expressing KrasG12D, show significantly reduced median survival rate and accelerated tumorigenesis compared to the KrasG12D only expressing mice. Analysis of the mechanism using RNA-seq demonstrate higher levels of GLI2 targets, particularly tumor growth promoting genes including Ccnd1, N-Myc and Bcl2, in KrasG12D mutant cells. Further, ChIP-seq studies showed that in these cells KrasG12D increases the levels of H3K4me3 at the promoter of GLI2 targets without affecting significantly the levels of other major active chromatin marks. Importantly, Gli2 knockdown reduces H3K4me3 enrichment and gene expression induced by mutant Kras. In summary, we demonstrate that Gli2 plays a significant role in pancreatic carcinogenesis by acting as a downstream effector of KrasG12D to control gene expression.</span></p>',
			'date' => '2024-06-24',
			'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38896052/',
			'doi' => '10.1158/2767-9764.CRC-23-0464',
			'modified' => '2024-06-24 17:07:26',
			'created' => '2024-06-24 17:07:26',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '4925',
			'name' => 'Chromatin profiling reveals TFAP4 as a critical transcriptional regulator of bovine satellite cell differentiation',
			'authors' => 'Pengcheng Lyu et al.',
			'description' => '<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Background</h3>
<p>Satellite cells are myogenic precursor cells in adult skeletal muscle and play a crucial role in skeletal muscle regeneration, maintenance, and growth. Like embryonic myoblasts, satellite cells have the ability to proliferate, differentiate, and fuse to form multinucleated myofibers. In this study, we aimed to identify additional transcription factors that control gene expression during bovine satellite cell proliferation and differentiation.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Results</h3>
<p>Using chromatin immunoprecipitation followed by sequencing, we identified 56,973 and 54,470 genomic regions marked with both the histone modifications H3K4me1 and H3K27ac, which were considered active enhancers, and 50,956 and 59,174 genomic regions marked with H3K27me3, which were considered repressed enhancers, in proliferating and differentiating bovine satellite cells, respectively. In addition, we identified 1,216 and 1,171 super-enhancers in proliferating and differentiating bovine satellite cells, respectively. Analyzing these enhancers showed that in proliferating bovine satellite cells, active enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation whereas repressed enhancers were associated with genes essential for myoblast differentiation, and that in differentiating satellite cells, active enhancers were associated with genes essential for myoblast differentiation or muscle contraction whereas repressed enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation. Active enhancers in proliferating bovine satellite cells were enriched with binding sites for many transcription factors such as MYF5 and the AP-1 family transcription factors; active enhancers in differentiating bovine satellite cells were enriched with binding sites for many transcription factors such as MYOG and TFAP4; and repressed enhancers in both proliferating and differentiating bovine satellite cells were enriched with binding sites for NF-kB, ZEB-1, and several other transcription factors. The role of TFAP4 in satellite cell or myoblast differentiation was previously unknown, and through gene knockdown and overexpression, we experimentally validated a critical role for TFAP4 in the differentiation and fusion of bovine satellite cells into myofibers.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Conclusions</h3>
<p>Satellite cell proliferation and differentiation are controlled by many transcription factors such as AP-1, TFAP4, NF-kB, and ZEB-1 whose roles in these processes were previously unknown in addition to those transcription factors such as MYF5 and MYOG whose roles in these processes are widely known.</p>',
			'date' => '2024-03-12',
			'pmid' => 'https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10189-2',
			'doi' => 'https://doi.org/10.1186/s12864-024-10189-2',
			'modified' => '2024-03-15 15:06:06',
			'created' => '2024-03-15 15:06:06',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'id' => '4822',
			'name' => 'RUNX1 colludes with NOTCH1 to reprogram chromatin in T-cell acutelymphoblastic leukemia',
			'authors' => 'Islam  R. et al.',
			'description' => '<p><span>Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T&nbsp;cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including&nbsp;</span><em>MYC, DTX1, HES4, IL7R,</em><span><span>&nbsp;</span>and<span>&nbsp;</span></span><em>NOTCH3</em><span>. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.</span></p>',
			'date' => '2023-05-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.isci.2023.106795',
			'doi' => '10.1016/j.isci.2023.106795',
			'modified' => '2023-06-19 10:14:27',
			'created' => '2023-06-13 21:11:31',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 4 => array(
			'id' => '4748',
			'name' => 'Incomplete transcriptional dosage compensation of vertebrate sexchromosomes is balanced by post-transcriptional compensation',
			'authors' => 'Lister  N. C. et al.',
			'description' => '<p>Heteromorphic sex chromosomes (XY or ZW) present problems of gene dosage imbalance between the sexes, and with the autosomes. Mammalian X chromosome inactivation was long thought to imply a critical need for dosage compensation in vertebrates. However, the universal importance of sex chromosome dosage compensation was questioned by mRNA abundance measurements that demonstrated sex chromosome transcripts are neither balanced between the sexes or with autosomes in monotreme mammals or birds. Here, we demonstrate unbalanced mRNA levels of X genes in platypus males and females that correlate with differential loading of histone modifications, and confirm that transcripts of Z genes are unbalanced between males and females also in chicken. However, we found that in both species, median male to female protein abundance ratios were 1:1, implying an additional level of post-transcriptional control. We conclude that parity of sex chromosome output is achieved in birds, as well as all mammal groups, by a combination of transcriptional and post-transcriptional control, consistent with an essential role for sex chromosome dosage compensation in vertebrates.</p>',
			'date' => '2023-02-01',
			'pmid' => 'https://doi.org/10.1101%2F2023.02.23.529605',
			'doi' => '10.1101/2023.02.23.529605',
			'modified' => '2023-06-14 08:59:05',
			'created' => '2023-03-02 17:27:08',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '4605',
			'name' => 'Gene Regulatory Interactions at Lamina-Associated Domains',
			'authors' => 'Madsen-Østerbye  J. et al.',
			'description' => '<p>The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are inactive, over ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to interact with regulatory elements remain unclear. Here, we integrate publicly available enhancer-capture Hi-C data with our own chromatin state and transcriptomic datasets to show that inferred enhancers of active genes in LADs are able to form connections with other enhancers within LADs and outside LADs. Fluorescence in situ hybridization analyses show proximity changes between differentially expressed genes in LADs and distant enhancers upon the induction of adipogenic differentiation. We also provide evidence of involvement of lamin A/C, but not lamin B1, in repressing genes at the border of an in-LAD active region within a topological domain. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with gene expression in this dynamic nuclear compartment.</p>',
			'date' => '2023-01-01',
			'pmid' => 'https://doi.org/10.3390%2Fgenes14020334',
			'doi' => '10.3390/genes14020334',
			'modified' => '2023-04-04 08:57:32',
			'created' => '2023-02-21 09:59:46',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '4490',
			'name' => 'Repression and 3D-restructuring resolves regulatory conflicts inevolutionarily rearranged genomes.',
			'authors' => 'Ringel  A. et al.',
			'description' => '<p>Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36179666',
			'doi' => '10.1016/j.cell.2022.09.006',
			'modified' => '2022-11-18 12:39:16',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '4417',
			'name' => 'HOTAIR interacts with PRC2 complex regulating the regional preadipocytetranscriptome and human fat distribution.',
			'authors' => 'Kuo  Feng-Chih et al.',
			'description' => '<p>Mechanisms governing regional human adipose tissue (AT) development remain undefined. Here, we show that the long non-coding RNA HOTAIR (HOX transcript antisense RNA) is exclusively expressed in gluteofemoral AT, where it is essential for adipocyte development. We find that HOTAIR interacts with polycomb repressive complex 2 (PRC2) and we identify core HOTAIR-PRC2 target genes involved in adipocyte lineage determination. Repression of target genes coincides with PRC2 promoter occupancy and H3K27 trimethylation. HOTAIR is also involved in modifying the gluteal adipocyte transcriptome through alternative splicing. Gluteal-specific expression of HOTAIR is maintained by defined regions of open chromatin across the HOTAIR promoter. HOTAIR expression levels can be modified by hormonal (estrogen, glucocorticoids) and genetic variation (rs1443512 is a HOTAIR eQTL associated with reduced gynoid fat mass). These data identify HOTAIR as a dynamic regulator of the gluteal adipocyte transcriptome and epigenome with functional importance for human regional AT development.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35905723',
			'doi' => '10.1016/j.celrep.2022.111136',
			'modified' => '2022-09-27 14:41:23',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '4524',
			'name' => 'Local euchromatin enrichment in lamina-associated domains anticipatestheir repositioning in the adipogenic lineage.',
			'authors' => 'Madsen-Østerbye  J. et al.',
			'description' => '<p>BACKGROUND: Interactions of chromatin with the nuclear lamina via lamina-associated domains (LADs) confer structural stability to the genome. The dynamics of positioning of LADs during differentiation, and how LADs impinge on developmental gene expression, remains, however, elusive. RESULTS: We examined changes in the association of lamin B1 with the genome in the first 72 h of differentiation of adipose stem cells into adipocytes. We demonstrate a repositioning of entire stand-alone LADs and of LAD edges as a prominent nuclear structural feature of early adipogenesis. Whereas adipogenic genes are released from LADs, LADs sequester downregulated or repressed genes irrelevant for the adipose lineage. However, LAD repositioning only partly concurs with gene expression changes. Differentially expressed genes in LADs, including LADs conserved throughout differentiation, reside in local euchromatic and lamin-depleted sub-domains. In these sub-domains, pre-differentiation histone modification profiles correlate with the LAD versus inter-LAD outcome of these genes during adipogenic commitment. Lastly, we link differentially expressed genes in LADs to short-range enhancers which overall co-partition with these genes in LADs versus inter-LADs during differentiation. CONCLUSIONS: We conclude that LADs are predictable structural features of adipose nuclear architecture that restrain non-adipogenic genes in a repressive environment.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35410387',
			'doi' => '10.1186/s13059-022-02662-6',
			'modified' => '2022-11-24 09:08:01',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '4326',
			'name' => 'Loss of KMT2C reprograms the epigenomic landscape in hPSCsresulting in NODAL overexpression and a failure of hemogenic endotheliumspecification.',
			'authors' => 'Maurya Shailendra et al.',
			'description' => '<p>Germline or somatic variation in the family of KMT2 lysine methyltransferases have been associated with a variety of congenital disorders and cancers. Notably, -fusions are prevalent in 70\% of infant leukaemias but fail to phenocopy short latency leukaemogenesis in mammalian models, suggesting additional factors are necessary for transformation. Given the lack of additional somatic mutation, the role of epigenetic regulation in cell specification, and our prior results of germline variation in infant leukaemia patients, we hypothesized that germline dysfunction of KMT2C altered haematopoietic specification. In isogenic KO hPSCs, we found genome-wide differences in histone modifications at active and poised enhancers, leading to gene expression profiles akin to mesendoderm rather than mesoderm highlighted by a significant increase in NODAL expression and WNT inhibition, ultimately resulting in a lack of hemogenic endothelium specification. These unbiased multi-omic results provide new evidence for germline mechanisms increasing risk of early leukaemogenesis.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://doi.org/10.1080%2F15592294.2021.1954780',
			'doi' => '10.1080/15592294.2021.1954780',
			'modified' => '2022-06-20 09:27:45',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '4196',
			'name' => 'Functional annotations of three domestic animal genomes provide vitalresources for comparative and agricultural research.',
			'authors' => 'Kern C. et al.',
			'description' => '<p>Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken (Gallus gallus), pig (Sus scrofa), and cattle (Bos taurus). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://doi.org/10.1038%2Fs41467-021-22100-8',
			'doi' => '10.1038/s41467-021-22100-8',
			'modified' => '2022-01-06 14:30:41',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '3711',
			'name' => 'Long intergenic non-coding RNAs regulate human lung fibroblast function: Implications for idiopathic pulmonary fibrosis.',
			'authors' => 'Hadjicharalambous MR, Roux BT, Csomor E, Feghali-Bostwick CA, Murray LA, Clarke DL, Lindsay MA',
			'description' => '<p>Phenotypic changes in lung fibroblasts are believed to contribute to the development of Idiopathic Pulmonary Fibrosis (IPF), a progressive and fatal lung disease. Long intergenic non-coding RNAs (lincRNAs) have been identified as novel regulators of gene expression and protein activity. In non-stimulated cells, we observed reduced proliferation and inflammation but no difference in the fibrotic response of IPF fibroblasts. These functional changes in non-stimulated cells were associated with changes in the expression of the histone marks, H3K4me1, H3K4me3 and H3K27ac indicating a possible involvement of epigenetics. Following activation with TGF-&beta;1 and IL-1&beta;, we demonstrated an increased fibrotic but reduced inflammatory response in IPF fibroblasts. There was no significant difference in proliferation following PDGF exposure. The lincRNAs, LINC00960 and LINC01140 were upregulated in IPF fibroblasts. Knockdown studies showed that LINC00960 and LINC01140 were positive regulators of proliferation in both control and IPF fibroblasts but had no effect upon the fibrotic response. Knockdown of LINC01140 but not LINC00960 increased the inflammatory response, which was greater in IPF compared to control fibroblasts. Overall, these studies demonstrate for the first time that lincRNAs are important regulators of proliferation and inflammation in human lung fibroblasts and that these might mediate the reduced inflammatory response observed in IPF-derived fibroblasts.</p>',
			'date' => '2019-04-15',
			'pmid' => 'http://www.pubmed.gov/30988425',
			'doi' => '10.1038/s41598-019-42292-w',
			'modified' => '2019-07-05 14:31:28',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '3660',
			'name' => 'Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia.',
			'authors' => 'Wernig-Zorc S, Yadav MP, Kopparapu PK, Bemark M, Kristjansdottir HL, Andersson PO, Kanduri C, Kanduri M',
			'description' => '<p>BACKGROUND: Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic and diagnostic implications for several cancers. However, there is no global study exploring the role of 5-hydroxymethylcytosine (5-hmC) levels in CLL. Herein, using mass spectrometry and hMeDIP-sequencing, we analysed the dynamics of 5-hmC during B cell maturation and CLL pathogenesis. RESULTS: We show that na&iuml;ve B-cells had higher levels of 5-hmC and 5-mC compared to non-class switched and class-switched memory B-cells. We found a significant decrease in global 5-mC levels in CLL patients (n&thinsp;=&thinsp;15) compared to na&iuml;ve and memory B cells, with no changes detected between the CLL prognostic groups. On the other hand, global 5-hmC levels of CLL patients were similar to memory B cells and reduced compared to na&iuml;ve B cells. Interestingly, 5-hmC levels were increased at regulatory regions such as gene-body, CpG island shores and shelves and 5-hmC distribution over the gene-body positively correlated with degree of transcriptional activity. Importantly, CLL samples showed aberrant 5-hmC and 5-mC pattern over gene-body compared to well-defined patterns in normal B-cells. Integrated analysis of 5-hmC and RNA-sequencing from CLL datasets identified three novel oncogenic drivers that could have potential roles in CLL development and progression. CONCLUSIONS: Thus, our study suggests that the global loss of 5-hmC, accompanied by its significant increase at the gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Our combined analysis of 5-mC and 5-hmC sequencing provided insights into the potential role of 5-hmC in modulating gene expression changes during CLL pathogenesis.</p>',
			'date' => '2019-01-07',
			'pmid' => 'http://www.pubmed.gov/30616658',
			'doi' => '10.1186/s13072‑018‑0252‑7',
			'modified' => '2019-07-01 11:46:16',
			'created' => '2019-06-21 14:55:31',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '3396',
			'name' => 'The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity',
			'authors' => 'Domínguez-Andrés Jorge, Novakovic Boris, Li Yang, Scicluna Brendon P., Gresnigt Mark S., Arts Rob J.W., Oosting Marije, Moorlag Simone J.C.F.M., Groh Laszlo A., Zwaag Jelle, Koch Rebecca M., ter Horst Rob, Joosten Leo A.B., Wijmenga Cisca, Michelucci Ales',
			'description' => '<p>Sepsis involves simultaneous hyperactivation of the immune system and immune paralysis, leading to both organ dysfunction and increased susceptibility to secondary infections. Acute activation of myeloid cells induced itaconate synthesis, which subsequently mediated innate immune tolerance in human monocytes. In contrast, induction of trained immunity by b-glucan counteracted tolerance induced in a model of human endotoxemia by inhibiting the expression of immune-responsive gene 1 (IRG1), the enzyme that controls itaconate synthesis. b-Glucan also increased the expression of succinate dehydrogenase (SDH), contributing to the integrity of the TCA cycle and leading to an enhanced innate immune response after secondary stimulation. The role of itaconate was further validated by IRG1 and SDH polymorphisms that modulate induction of tolerance and trained immunity in human monocytes. These data demonstrate the importance of the IRG1-itaconateSDH axis in the development of immune tolerance and training and highlight the potential of b-glucaninduced trained immunity to revert immunoparalysis.</p>',
			'date' => '2018-10-01',
			'pmid' => 'http://www.pubmed.gov/30293776',
			'doi' => '10.1016/j.cmet.2018.09.003',
			'modified' => '2018-11-22 15:18:30',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '3469',
			'name' => 'Increased H3K9 methylation and impaired expression of Protocadherins are associated with the cognitive dysfunctions of the Kleefstra syndrome.',
			'authors' => 'Iacono G, Dubos A, Méziane H, Benevento M, Habibi E, Mandoli A, Riet F, Selloum M, Feil R, Zhou H, Kleefstra T, Kasri NN, van Bokhoven H, Herault Y, Stunnenberg HG',
			'description' => '<p>Kleefstra syndrome, a disease with intellectual disability, autism spectrum disorders and other developmental defects is caused in humans by haploinsufficiency of EHMT1. Although EHMT1 and its paralog EHMT2 were shown to be histone methyltransferases responsible for deposition of the di-methylated H3K9 (H3K9me2), the exact nature of epigenetic dysfunctions in Kleefstra syndrome remains unknown. Here, we found that the epigenome of Ehmt1+/- adult mouse brain displays a marked increase of H3K9me2/3 which correlates with impaired expression of protocadherins, master regulators of neuronal diversity. Increased H3K9me3 was present already at birth, indicating that aberrant methylation patterns are established during embryogenesis. Interestingly, we found that Ehmt2+/- mice do not present neither the marked increase of H3K9me2/3 nor the cognitive deficits found in Ehmt1+/- mice, indicating an evolutionary diversification of functions. Our finding of increased H3K9me3 in Ehmt1+/- mice is the first one supporting the notion that EHMT1 can quench the deposition of tri-methylation by other Histone methyltransferases, ultimately leading to impaired neurocognitive functioning. Our insights into the epigenetic pathophysiology of Kleefstra syndrome may offer guidance for future developments of therapeutic strategies for this disease.</p>',
			'date' => '2018-06-01',
			'pmid' => 'http://www.pubmed.gov/29554304',
			'doi' => '10.1093/nar/gky196',
			'modified' => '2019-02-15 21:04:02',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '3539',
			'name' => 'A long range distal enhancer controls temporal fine-tuning of PAX6 expression in neuronal precursors.',
			'authors' => 'Lacomme M, Medevielle F, Bourbon HM, Thierion E, Kleinjan DJ, Roussat M, Pituello F, Bel-Vialar S',
			'description' => '<p>Proper embryonic development relies on a tight control of spatial and temporal gene expression profiles in a highly regulated manner. One good example is the ON/OFF switching of the transcription factor PAX6 that governs important steps of neurogenesis. In the neural tube PAX6 expression is initiated in neural progenitors through the positive action of retinoic acid signaling and downregulated in neuronal precursors by the bHLH transcription factor NEUROG2. How these two regulatory inputs are integrated at the molecular level to properly fine tune temporal PAX6 expression is not known. In this study we identified and characterized a 940-bp long distal cis-regulatory module (CRM), located far away from the PAX6 transcription unit and which conveys positive input from RA signaling pathway and indirect repressive signal(s) from NEUROG2. These opposing regulatory signals are integrated through HOMZ, a 94 bp core region within E940 which is evolutionarily conserved in distant organisms such as the zebrafish. We show that within HOMZ, NEUROG2 and RA exert their opposite temporal activities through a short 60 bp region containing a functional RA-responsive element (RARE). We propose a model in which retinoic acid receptors (RARs) and NEUROG2 repressive target(s) compete on the same DNA motif to fine tune temporal PAX6 expression during the course of spinal neurogenesis.</p>',
			'date' => '2018-04-15',
			'pmid' => 'http://www.pubmed.gov/29486153',
			'doi' => '10.1016/j.ydbio.2018.02.015',
			'modified' => '2019-02-28 10:42:57',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '3542',
			'name' => 'Inhibition of Methyltransferase Setd7 Allows the In Vitro Expansion of Myogenic Stem Cells with Improved Therapeutic Potential.',
			'authors' => 'Judson RN, Quarta M, Oudhoff MJ, Soliman H, Yi L, Chang CK, Loi G, Vander Werff R, Cait A, Hamer M, Blonigan J, Paine P, Doan LTN, Groppa E, He W, Su L, Zhang RH, Xu P, Eisner C, Low M, Barta I, Lewis CB, Zaph C, Karimi MM, Rando TA, Rossi FM',
			'description' => '<p>The development of cell therapy for repairing damaged or diseased skeletal muscle has been hindered by the inability to significantly expand immature, transplantable myogenic stem cells (MuSCs) in&nbsp;culture. To overcome this limitation, a deeper understanding of the mechanisms regulating the transition between activated, proliferating MuSCs and differentiation-primed, poorly engrafting progenitors is needed. Here, we show that methyltransferase Setd7 facilitates such transition by regulating the nuclear accumulation of &beta;-catenin in proliferating MuSCs. Genetic or pharmacological inhibition of Setd7 promotes in&nbsp;vitro expansion of MuSCs and increases the yield of primary myogenic cell cultures. Upon transplantation, both mouse and human MuSCs expanded with a Setd7 small-molecule inhibitor are better able to repopulate the satellite cell niche, and treated mouse MuSCs show enhanced therapeutic potential in preclinical models of muscular dystrophy. Thus, Setd7 inhibition may help bypass a key obstacle in the translation of cell therapy for muscle disease.</p>',
			'date' => '2018-02-01',
			'pmid' => 'http://www.pubmed.gov/29395054',
			'doi' => '10.1016/j.stem.2017.12.010',
			'modified' => '2019-02-28 10:56:48',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '3446',
			'name' => 'Metabolic Induction of Trained Immunity through the Mevalonate Pathway.',
			'authors' => 'Bekkering S, Arts RJW, Novakovic B, Kourtzelis I, van der Heijden CDCC, Li Y, Popa CD, Ter Horst R, van Tuijl J, Netea-Maier RT, van de Veerdonk FL, Chavakis T, Joosten LAB, van der Meer JWM, Stunnenberg H, Riksen NP, Netea MG',
			'description' => '<p>Innate immune cells can develop long-term memory after stimulation by microbial products during infections or vaccinations. Here, we report that metabolic signals can induce trained immunity. Pharmacological and genetic experiments reveal that activation of the cholesterol synthesis pathway, but not the synthesis of cholesterol itself, is essential for training of myeloid cells. Rather, the metabolite mevalonate is the mediator of training via activation of IGF1-R and mTOR and subsequent histone modifications in inflammatory pathways. Statins, which block mevalonate generation, prevent trained immunity induction. Furthermore, monocytes of patients with hyper immunoglobulin D syndrome (HIDS), who are mevalonate kinase deficient and accumulate mevalonate, have a constitutive trained immunity phenotype at both immunological and epigenetic levels, which could explain the attacks of sterile inflammation that these patients experience. Unraveling the role of mevalonate in trained immunity contributes to our understanding of the pathophysiology of HIDS and identifies novel therapeutic targets for clinical conditions with excessive activation of trained immunity.</p>',
			'date' => '2018-01-11',
			'pmid' => 'http://www.pubmed.gov/29328908',
			'doi' => '10.1016/j.cell.2017.11.025',
			'modified' => '2019-02-15 21:37:39',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '3282',
			'name' => 'Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements',
			'authors' => 'Thierion E. et al.',
			'description' => '<p>Developmental genes can harbour multiple transcriptional enhancers that act simultaneously or in succession to achieve robust and precise spatiotemporal expression. However, the mechanisms underlying cooperation between cis-acting elements are poorly documented, notably in vertebrates. The mouse gene Krox20 encodes a transcription factor required for the specification of two segments (rhombomeres) of the developing hindbrain. In rhombomere 3, Krox20 is subject to direct positive feedback governed by an autoregulatory enhancer, element A. In contrast, a second enhancer, element C, distant by 70 kb, is active from the initiation of transcription independent of the presence of the KROX20 protein. Here, using both enhancer knock-outs and investigations of chromatin organisation, we show that element C possesses a dual activity: besides its classical enhancer function, it is also permanently required in cis to potentiate the autoregulatory activity of element A, by increasing its chromatin accessibility. This work uncovers a novel, asymmetrical, long-range mode of cooperation between cis-acting elements that might be essential to avoid promiscuous activation of positive autoregulatory elements.</p>',
			'date' => '2017-07-27',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28749941',
			'doi' => '',
			'modified' => '2017-10-23 17:38:21',
			'created' => '2017-10-23 17:38:21',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '3084',
			'name' => 'A transcription factor pulse can prime chromatin for heritable transcriptional memory',
			'authors' => 'Iberg-Badeaux A. et al.',
			'description' => '<p>Short-term and long-term transcriptional memory is the phenomenon whereby the kinetics or magnitude of gene induction is enhanced following a prior induction period. Short-term memory persists within one cell generation or in post-mitotic cells, while long-term memory can survive multiple rounds of cell division. We have developed a tissue culture model to study the epigenetic basis for long-term transcriptional memory (LTTM), and subsequently used this model to better understand the epigenetic mechanisms that enable heritable memory of temporary stimuli. We find that a pulse of transcription factor C/EBP&alpha; induces LTTM on a subset of target genes that survives 9 cell divisions. The chromatin landscape at genes that acquire LTTM is more repressed as compared to those genes that do not exhibit memory, akin to a latent state. We show through ChIP and chemical inhibitor studies that Pol II elongation is important for establishing memory in this model, but that Pol II itself is not retained as part of the memory mechanism. More generally, our work reveals that a transcription factor involved in lineage specification can induce LTTM, and that failure to re-repress chromatin is one epigenetic mechanism underlying transcriptional memory.</p>',
			'date' => '2016-12-05',
			'pmid' => 'http://mcb.asm.org/content/early/2016/11/30/MCB.00372-16.abstract',
			'doi' => '',
			'modified' => '2016-12-20 10:33:32',
			'created' => '2016-12-20 10:33:32',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => array(
			'id' => '3103',
			'name' => 'β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance',
			'authors' => 'Novakovic B. et al.',
			'description' => '<p>Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as lipopolysaccharide (LPS). We apply an integrated epigenomic&nbsp;approach to characterize the molecular events involved in LPS-induced tolerance in a time-dependent manner. Mechanistically, LPS-treated monocytes fail to accumulate active histone marks at promoter and enhancers of genes in the lipid metabolism and phagocytic pathways. Transcriptional inactivity in response to a second LPS exposure in tolerized macrophages is accompanied by failure to deposit active histone marks at promoters of tolerized genes. In contrast, &beta;-glucan partially reverses the LPS-induced tolerance in&nbsp;vitro. Importantly, ex&nbsp;vivo &beta;-glucan treatment of monocytes from volunteers with experimental endotoxemia re-instates their capacity for cytokine production. Tolerance is reversed at the level of distal element histone modification and transcriptional reactivation of otherwise unresponsive genes.</p>',
			'date' => '2016-11-17',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27863248',
			'doi' => '',
			'modified' => '2017-01-03 15:31:46',
			'created' => '2017-01-03 15:31:46',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 21 => array(
			'id' => '3015',
			'name' => 'Enhancer decommissioning by Snail1-induced competitive displacement of TCF7L2 and down-regulation of transcriptional activators results in EPHB2 silencing',
			'authors' => 'Schnappauf O et al.',
			'description' => '<p>Transcriptional silencing is a major cause for the inactivation of tumor suppressor genes, however, the underlying mechanisms are only poorly understood. The EPHB2 gene encodes a receptor tyrosine kinase that controls epithelial cell migration and allocation in intestinal crypts. Through its ability to restrict cell spreading, EPHB2 functions as a tumor suppressor in colorectal cancer whose expression is frequently lost as tumors progress to the carcinoma stage. Previously we reported that EPHB2 expression depends on a transcriptional enhancer whose activity is diminished in EPHB2 non-expressing cells. Here we investigated the mechanisms that lead to EPHB2 enhancer inactivation. We show that expression of EPHB2 and SNAIL1 - an inducer of epithelial-mesenchymal transition (EMT) - is anti-correlated in colorectal cancer cell lines and tumors. In a cellular model of Snail1-induced EMT, we observe that features of active chromatin at the EPHB2 enhancer are diminished upon expression of murine Snail1. We identify the transcription factors FOXA1, MYB, CDX2 and TCF7L2 as EPHB2 enhancer factors and demonstrate that Snail1 indirectly inactivates the EPHB2 enhancer by downregulation of FOXA1 and MYB. In addition, Snail1 induces the expression of Lymphoid enhancer factor 1 (LEF1) which competitively displaces TCF7L2 from the EPHB2 enhancer. In contrast to TCF7L2, however, LEF1 appears to repress the EPHB2 enhancer. Our findings underscore the importance of transcriptional enhancers for gene regulation under physiological and pathological conditions and show that SNAIL1 employs a combinatorial mechanism to inactivate the EPHB2 enhancer based on activator deprivation and competitive displacement of transcription factors.</p>',
			'date' => '2016-08-05',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27504909',
			'doi' => '',
			'modified' => '2016-08-31 09:18:03',
			'created' => '2016-08-31 09:18:03',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '2972',
			'name' => 'cChIP-seq: a robust small-scale method for investigation of histone modifications',
			'authors' => 'Valensisi C et al.',
			'description' => '<div id="__sec1" class="sec sec-first">
<h3>Background</h3>
<p id="__p1" class="p p-first-last">ChIP-seq is highly utilized for mapping histone modifications that are informative about gene regulation and genome annotations. For example, applying ChIP-seq to histone modifications such as H3K4me1 has facilitated generating epigenomic maps of putative enhancers. This powerful technology, however, is limited in its application by the large number of cells required. ChIP-seq involves extensive manipulation of sample material and multiple reactions with limited quality control at each step, therefore, scaling down the number of cells required has proven challenging. Recently, several methods have been proposed to overcome this limit but most of these methods require extensive optimization to tailor the protocol to the specific antibody used or number of cells being profiled.</p>
</div>
<div id="__sec2" class="sec">
<h3>Results</h3>
<p id="__p2" class="p p-first-last">Here we describe a robust, yet facile method, which we named carrier ChIP-seq (cChIP-seq), for use on limited cell amounts. cChIP-seq employs a DNA-free histone carrier in order to maintain the working ChIP reaction scale, removing the need to tailor reactions to specific amounts of cells or histone modifications to be assayed. We have applied our method to three different histone modifications, H3K4me3, H3K4me1 and H3K27me3 in the K562 cell line, and H3K4me1 in H1 hESCs. We successfully obtained epigenomic maps for these histone modifications starting with as few as 10,000 cells. We compared cChIP-seq data to data generated as part of the ENCODE project. ENCODE data are the reference standard in the field and have been generated starting from tens of million of cells. Our results show that cChIP-seq successfully recapitulates bulk data. Furthermore, we showed that the differences observed between small-scale ChIP-seq data and ENCODE data are largely to be due to lab-to-lab variability rather than operating on a reduced scale.</p>
</div>
<div id="__sec3" class="sec">
<h3>Conclusions</h3>
<p id="__p3" class="p p-first-last">Data generated using cChIP-seq are equivalent to reference epigenomic maps from three orders of magnitude more cells. Our method offers a robust and straightforward approach to scale down ChIP-seq to as low as 10,000 cells. The underlying principle of our strategy makes it suitable for being applied to a vast range of chromatin modifications without requiring expensive optimization. Furthermore, our strategy of a DNA-free carrier can be adapted to most ChIP-seq protocols.</p>
</div>',
			'date' => '2015-12-21',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687106/',
			'doi' => ' 10.1186/s12864-015-2285-7',
			'modified' => '2016-07-01 10:05:06',
			'created' => '2016-07-01 10:05:06',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '2869',
			'name' => 'C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis',
			'authors' => 'van Oevelen C, Collombet S, Vicent G, Hoogenkamp M, Lepoivre C, Badeaux A, Bussmann L, Sardina JL, Thieffry D, Beato M, Shi Y, Bonifer C, Graf T',
			'description' => '<section id="abs0020" class="articleHighlights">
<h2 class="sectionTitle">Highlights</h2>
<div class="content">
<p></p>
<ul class="ce-list" id="ulist0010">
<li id="u0010">C/EBP&alpha; activates two classes of prospective myeloid enhancers in B cells</li>
<li id="u0015">Pre-existing enhancers are bound by PU.1 and become hyper-activated by C/EBP&alpha;</li>
<li id="u0020">C/EBP&alpha; acts as a pioneer factor with delayed kinetics on de novo enhancers</li>
<li id="u0025">The two types of enhancers direct myeloid cell fate in B cells and hematopoiesis</li>
</ul>
<p></p>
</div>
</section>
<section class="graphical"></section>
<div class="abstract">
<h2 class="sectionTitle">Summary</h2>
<p>Transcription-factor-induced somatic cell conversions are highly relevant for both basic and clinical research yet their mechanism is not fully understood and it is unclear whether they reflect normal differentiation processes. Here we show that during pre-B-cell-to-macrophage transdifferentiation, C/EBP&alpha; binds to two types of myeloid enhancers in B cells: pre-existing enhancers that are bound by PU.1, providing a platform for incoming C/EBP&alpha;; and de novo enhancers that are targeted by C/EBP&alpha;, acting as a pioneer factor for subsequent binding by PU.1. The order of factor binding dictates the upregulation kinetics of nearby genes. Pre-existing enhancers are broadly active throughout the hematopoietic lineage tree, including B cells. In contrast, de novo enhancers are silent in most cell types except in myeloid cells where they become activated by C/EBP factors. Our data suggest that C/EBP&alpha; recapitulates physiological developmental processes by short-circuiting two macrophage enhancer pathways in pre-B cells.</p>
</div>',
			'date' => '2015-08-11',
			'pmid' => 'http://www.cell.com/stem-cell-reports/abstract/S2213-6711%2815%2900188-5',
			'doi' => 'http://dx.doi.org/10.1016/j.stemcr.2015.06.007',
			'modified' => '2016-03-25 10:23:25',
			'created' => '2016-03-25 10:22:05',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => 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) 25 => array(
			'id' => '2228',
			'name' => 'Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping.',
			'authors' => 'Light N, Adoue V, Ge B, Chen SH, Kwan T, Pastinen T',
			'description' => 'Allele-specific (AS) assessment of chromatin has the potential to elucidate specific cis-regulatory mechanisms, which are predicted to underlie the majority of the known genetic associations to complex disease. However, development of chromatin landscapes at allelic resolution has been challenging since sites of variable signal strength require substantial read depths not commonly applied in sequencing based approaches. In this study, we addressed this by performing parallel analyses of input DNA and chromatin immunoprecipitates (ChIP) on high-density Illumina genotyping arrays. Allele-specificity for the histone modifications H3K4me1, H3K4me3, H3K27ac, H3K27me3, and H3K36me3 was assessed using ChIP samples generated from 14 lymphoblast and 6 fibroblast cell lines. AS-ChIP SNPs were combined into domains and validated using high-confidence ChIP-seq sites. We observed characteristic patterns of allelic-imbalance for each histone-modification around allele-specifically expressed transcripts. Notably, we found H3K4me1 to be significantly anti-correlated with allelic expression (AE) at transcription start sites, indicating H3K4me1 allelic imbalance as a marker of AE. We also found that allelic chromatin domains exhibit population and cell-type specificity as well as heritability within trios. Finally, we observed that a subset of allelic chromatin domains is regulated by DNase I-sensitive quantitative trait loci and that these domains are significantly enriched for genome-wide association studies hits, with autoimmune disease associated SNPs specifically enriched in lymphoblasts. This study provides the first genome-wide maps of allelic-imbalance for five histone marks. Our results provide new insights into the role of chromatin in cis-regulation and highlight the need for high-depth sequencing in ChIP-seq studies along with the need to improve allele-specificity of ChIP-enrichment.',
			'date' => '2014-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25055051',
			'doi' => '',
			'modified' => '2015-07-24 15:39:03',
			'created' => '2015-07-24 15:39:03',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 26 => array(
			'id' => '2054',
			'name' => 'Nuclear ARRB1 induces pseudohypoxia and cellular metabolism reprogramming in prostate cancer',
			'authors' => 'Zecchini V, Madhu B, Russell R, Pértega-Gomes N, Warren A, Gaude E, Borlido J, Stark R, Ireland-Zecchini H, Rao R, Scott H, Boren J, Massie C, Asim M, Brindle K, Griffiths J, Frezza C, Neal DE, Mills IG',
			'description' => 'Tumour cells sustain their high proliferation rate through metabolic reprogramming, whereby cellular metabolism shifts from oxidative phosphorylation to aerobic glycolysis, even under normal oxygen levels. Hypoxia-inducible factor 1A (HIF1A) is a major regulator of this process, but its activation under normoxic conditions, termed pseudohypoxia, is not well documented. Here, using an integrative approach combining the first genome-wide mapping of chromatin binding for an endocytic adaptor, ARRB1, both in vitro and in vivo with gene expression profiling, we demonstrate that nuclear ARRB1 contributes to this metabolic shift in prostate cancer cells via regulation of HIF1A transcriptional activity under normoxic conditions through regulation of succinate dehydrogenase A (SDHA) and fumarate hydratase (FH) expression. ARRB1-induced pseudohypoxia may facilitate adaptation of cancer cells to growth in the harsh conditions that are frequently encountered within solid tumours. Our study is the first example of an endocytic adaptor protein regulating metabolic pathways. It implicates ARRB1 as a potential tumour promoter in prostate cancer and highlights the importance of metabolic alterations in prostate cancer.',
			'date' => '2014-05-16',
			'pmid' => 'http://onlinelibrary.wiley.com/doi/10.15252/embj.201386874/full',
			'doi' => '',
			'modified' => '2015-07-24 15:39:02',
			'created' => '2015-07-24 15:39:02',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 27 => array(
			'id' => '1793',
			'name' => 'A novel microscopy-based high-throughput screening method to identify proteins that regulate global histone modification levels.',
			'authors' => 'Baas R, Lelieveld D, van Teeffelen H, Lijnzaad P, Castelijns B, van Schaik FM, Vermeulen M, Egan DA, Timmers HT, de Graaf P',
			'description' => '<p>Posttranslational modifications of histones play an important role in the regulation of gene expression and chromatin structure in eukaryotes. The balance between chromatin factors depositing (writers) and removing (erasers) histone marks regulates the steady-state levels of chromatin modifications. Here we describe a novel microscopy-based screening method to identify proteins that regulate histone modification levels in a high-throughput fashion. We named our method CROSS, for Chromatin Regulation Ontology SiRNA Screening. CROSS is based on an siRNA library targeting the expression of 529 proteins involved in chromatin regulation. As a proof of principle, we used CROSS to identify chromatin factors involved in histone H3 methylation on either lysine-4 or lysine-27. Furthermore, we show that CROSS can be used to identify chromatin factors that affect growth in cancer cell lines. Taken together, CROSS is a powerful method to identify the writers and erasers of novel and known chromatin marks and facilitates the identification of drugs targeting epigenetic modifications.</p>',
			'date' => '2014-02-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24334265',
			'doi' => '',
			'modified' => '2016-04-12 09:46:40',
			'created' => '2015-07-24 15:39:01',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 28 => array(
			'id' => '1577',
			'name' => 'An In-Depth Characterization of the Major Psoriasis Susceptibility Locus Identifies Candidate Susceptibility Alleles within an HLA-C Enhancer Element.',
			'authors' => 'Clop A, Bertoni A, Spain SL, Simpson MA, Pullabhatla V, Tonda R, Hundhausen C, Di Meglio P, De Jong P, Hayday AC, Nestle FO, Barker JN, Bell RJ, Capon F, Trembath RC',
			'description' => 'Psoriasis is an immune-mediated skin disorder that is inherited as a complex genetic trait. Although genome-wide association scans (GWAS) have identified 36 disease susceptibility regions, more than 50% of the genetic variance can be attributed to a single Major Histocompatibility Complex (MHC) locus, known as PSORS1. Genetic studies indicate that HLA-C is the strongest PSORS1 candidate gene, since markers tagging HLA-Cw*0602 consistently generate the most significant association signals in GWAS. However, it is unclear whether HLA-Cw*0602 is itself the causal PSORS1 allele, especially as the role of SNPs that may affect its expression has not been investigated. Here, we have undertaken an in-depth molecular characterization of the PSORS1 interval, with a view to identifying regulatory variants that may contribute to disease susceptibility. By analysing high-density SNP data, we refined PSORS1 to a 179 kb region encompassing HLA-C and the neighbouring HCG27 pseudogene. We compared multiple MHC sequences spanning this refined locus and identified 144 candidate susceptibility variants, which are unique to chromosomes bearing HLA-Cw*0602. In parallel, we investigated the epigenetic profile of the critical PSORS1 interval and uncovered three enhancer elements likely to be active in T lymphocytes. Finally we showed that nine candidate susceptibility SNPs map within a HLA-C enhancer and that three of these variants co-localise with binding sites for immune-related transcription factors. These data indicate that SNPs affecting HLA-Cw*0602 expression are likely to contribute to psoriasis susceptibility and highlight the importance of integrating multiple experimental approaches in the investigation of complex genomic regions such as the MHC.',
			'date' => '2013-08-19',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23990973',
			'doi' => '',
			'modified' => '2015-07-24 15:39:00',
			'created' => '2015-07-24 15:39:00',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 29 => array(
			'id' => '1512',
			'name' => 'Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus.',
			'authors' => 'Miller CL, Anderson DR, Kundu RK, Raiesdana A, Nürnberg ST, Diaz R, Cheng K, Leeper NJ, Chen CH, Chang IS, Schadt EE, Hsiung CA, Assimes TL, Quertermous T',
			'description' => 'Coronary heart disease (CHD) is the leading cause of mortality in both developed and developing countries worldwide. Genome-wide association studies (GWAS) have now identified 46 independent susceptibility loci for CHD, however, the biological and disease-relevant mechanisms for these associations remain elusive. The large-scale meta-analysis of GWAS recently identified in Caucasians a CHD-associated locus at chromosome 6q23.2, a region containing the transcription factor TCF21 gene. TCF21 (Capsulin/Pod1/Epicardin) is a member of the basic-helix-loop-helix (bHLH) transcription factor family, and regulates cell fate decisions and differentiation in the developing coronary vasculature. Herein, we characterize a cis-regulatory mechanism by which the lead polymorphism rs12190287 disrupts an atypical activator protein 1 (AP-1) element, as demonstrated by allele-specific transcriptional regulation, transcription factor binding, and chromatin organization, leading to altered TCF21 expression. Further, this element is shown to mediate signaling through platelet-derived growth factor receptor beta (PDGFR-β) and Wilms tumor 1 (WT1) pathways. A second disease allele identified in East Asians also appears to disrupt an AP-1-like element. Thus, both disease-related growth factor and embryonic signaling pathways may regulate CHD risk through two independent alleles at TCF21.',
			'date' => '2013-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23874238',
			'doi' => '',
			'modified' => '2015-07-24 15:39:00',
			'created' => '2015-07-24 15:39:00',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 30 => array(
			'id' => '1350',
			'name' => 'Balancing of histone H3K4 methylation states by the Kdm5c/SMCX histone demethylase modulates promoter and enhancer function.',
			'authors' => 'Outchkourov NS, Muiño JM, Kaufmann K, van Ijcken WF, Groot Koerkamp MJ, van Leenen D, de Graaf P, Holstege FC, Grosveld FG, Timmers HT',
			'description' => 'The functional organization of eukaryotic genomes correlates with specific patterns of histone methylations. Regulatory regions in genomes such as enhancers and promoters differ in their extent of methylation of histone H3 at lysine-4 (H3K4), but it is largely unknown how the different methylation states are specified and controlled. Here, we show that the Kdm5c/Jarid1c/SMCX member of the Kdm5 family of H3K4 demethylases can be recruited to both enhancer and promoter elements in mouse embryonic stem cells and in neuronal progenitor cells. Knockdown of Kdm5c deregulates transcription via local increases in H3K4me3. Our data indicate that by restricting H3K4me3 modification at core promoters, Kdm5c dampens transcription, but at enhancers Kdm5c stimulates their activity. Remarkably, an impaired enhancer function activates the intrinsic promoter activity of Kdm5c-bound distal elements. Our results demonstrate that the Kdm5c demethylase plays a crucial and dynamic role in the functional discrimination between enhancers and core promoters.',
			'date' => '2013-04-25',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23545502',
			'doi' => '',
			'modified' => '2015-07-24 15:39:00',
			'created' => '2015-07-24 15:39:00',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 31 => array(
			'id' => '592',
			'name' => 'Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.',
			'authors' => 'Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ',
			'description' => 'The H3K9me3 histone modification is often found at promoter regions, where it functions to repress transcription. However, we have previously shown that 3' exons of zinc finger genes (ZNFs) are marked by high levels of H3K9me3. We have now further investigated this unusual location for H3K9me3 in ZNF genes. Neither bioinformatic nor experimental approaches support the hypothesis that the 3' exons of ZNFs are promoters. We further characterized the histone modifications at the 3' ZNF exons and found that these regions also contain H3K36me3, a mark of transcriptional elongation. A genome-wide analysis of ChIP-seq data revealed that ZNFs constitute the majority of genes that have high levels of both H3K9me3 and H3K36me3. These results suggested the possibility that the ZNF genes may be imprinted, with one allele transcribed and one allele repressed. To test the hypothesis that the contradictory modifications are due to imprinting, we used a SNP analysis of RNA-seq data to demonstrate that both alleles of certain ZNF genes having H3K9me3 and H3K36me3 are transcribed. We next analyzed isolated ZNF 3' exons using stably integrated episomes. We found that although the H3K36me3 mark was lost when the 3' ZNF exon was removed from its natural genomic location, the isolated ZNF 3' exons retained the H3K9me3 mark. Thus, the H3K9me3 mark at ZNF 3' exons does not impede transcription and it is regulated independently of the H3K36me3 mark. Finally, we demonstrate a strong relationship between the number of tandemly repeated domains in the 3' exons and the H3K9me3 mark. We suggest that the H3K9me3 at ZNF 3' exons may function to protect the genome from inappropriate recombination rather than to regulate transcription.',
			'date' => '2011-02-15',
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			'description' => '<p>The dynamic modification of DNA and histones plays a key role in transcriptional regulation through - altering the packaging of DNA and modifying the nucleosome surface. These chromatin states, also referred to as the epigenome, are distinctive for different tissues, developmental stages, and disease states and can also be altered by environmental influences. New technologies allow the genome-wide visualization of the information encoded in the epigenome. For example, the chromatin immunoprecipitation (ChIP) assay allows investigators to characterize DNA&ndash;protein interactions in vivo. ChIP followed by hybridization to microarrays (ChIP-chip) or by high-throughput sequencing (ChIP-seq) are both powerful tools to identify genome-wide profiles of transcription factors, histone modifications, DNA methylation, and nucleosome positioning. ChIP-seq technology, which can now interrogate the entire human genome at high resolution with only one lane of sequencing, has recently surpassed ChIP-chip technology for epigenomic analyses. Importantly, for the study of primary cells and tissues, epigenetic profiles can be generated using as little as 1 &mu;g of chromatin. In this chapter, we describe in detail the steps involved in performing ChIP assays (with a focus on characterizing histone modifications in primary cells)either manually or using the IP-Star ChIP robot, followed by a detailed protocol to prepare successful libraries for Illumina sequencing. Critical quality control checkpoints are discussed. Although not a focus of this chapter, we also point the reader to several methods by which massive ChIP-seq data sets can be analyzed to extract the tremendous information contained within.</p>',
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		'description' => '<p><span>Polyclonal antibody raised in rabbit against histone <strong>H3 containing the monomethylated lysine 4</strong> (<strong>H3K4me1</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
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<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
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<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
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<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
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<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_DotBlot.png" alt="H3K4me1 Antibody Dot Blot Validation " /></p>
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<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
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<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
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<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
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<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
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<div class="extra-spaced"></div>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
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<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_DotBlot.png" alt="H3K4me1 Antibody Dot Blot Validation " /></p>
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<div class="small-7 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
</div>
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<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
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<div class="row">
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<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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>ChIP/ChIP-seq <sup>*</sup></td>
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<td>Fig 1, 2</td>
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<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
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<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
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<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
</div>
</div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_DotBlot.png" alt="H3K4me1 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-7 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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>
</div>
</div>',
		'label2' => 'Target Description',
		'info2' => '<p>Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called &ldquo;histone code&rdquo;. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases.</p>',
		'label3' => '',
		'info3' => '',
		'format' => '10 µg',
		'catalog_number' => 'C15410037-10',
		'old_catalog_number' => '',
		'sf_code' => 'C15410037-D001-000582',
		'type' => 'FRE',
		'search_order' => '',
		'price_EUR' => '105',
		'price_USD' => '115',
		'price_GBP' => '100',
		'price_JPY' => '16450',
		'price_CNY' => '',
		'price_AUD' => '288',
		'country' => 'ALL',
		'except_countries' => 'None',
		'quote' => false,
		'in_stock' => false,
		'featured' => false,
		'no_promo' => false,
		'online' => true,
		'master' => false,
		'last_datasheet_update' => 'January 6, 2020',
		'slug' => 'h3k4me1-polyclonal-antibody-classic-10-ug',
		'meta_title' => '',
		'meta_keywords' => '',
		'meta_description' => '',
		'modified' => '2024-01-16 14:13:51',
		'created' => '2017-06-07 16:05:55',
		'locale' => 'jpn'
	),
	'Antibody' => array(
		'host' => '*****',
		'id' => '110',
		'name' => 'H3K4me1 polyclonal antibody ',
		'description' => 'Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases.',
		'clonality' => '',
		'isotype' => '',
		'lot' => 'A1657D',
		'concentration' => '2.9 &micro;g/&micro;l',
		'reactivity' => 'Human, mouse, pig',
		'type' => 'Polyclonal',
		'purity' => 'Affinity purified polyclonal antibody.',
		'classification' => 'Classic',
		'application_table' => '<table>
<thead>
<tr>
<th>Applications</th>
<th>Suggested dilution</th>
<th>References</th>
</tr>
</thead>
<tbody>
<tr>
<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>1-2 &mu;g/IP</td>
<td>Fig 1, 2</td>
</tr>
<tr>
<td>ELISA</td>
<td>1:500</td>
<td>Fig 3</td>
</tr>
<tr>
<td>Dot Blotting</td>
<td>1:10,000</td>
<td>Fig 4</td>
</tr>
<tr>
<td>Western Blotting</td>
<td>1:500</td>
<td>Fig 5</td>
</tr>
<tr>
<td>Immunofluorescence</td>
<td>1:500</td>
<td>Fig 6</td>
</tr>
</tbody>
</table>
<p></p>
<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 &mu;g per IP.</small></p>',
		'storage_conditions' => 'Store at -20°C; for long storage, store at -80°C. Avoid multiple freeze-thaw cycles.',
		'storage_buffer' => 'PBS containing 0.05% azide and 0.05% ProClin 300.',
		'precautions' => 'This product is for research use only. Not for use in diagnostic or therapeutic procedures.',
		'uniprot_acc' => '',
		'slug' => '',
		'meta_keywords' => '',
		'meta_description' => '',
		'modified' => '2022-10-04 15:01:10',
		'created' => '0000-00-00 00:00:00',
		'select_label' => '110 - H3K4me1 polyclonal antibody  (A1657D - 2.9 &micro;g/&micro;l - Human, mouse, pig - Affinity purified polyclonal antibody. - Rabbit)'
	),
	'Slave' => array(),
	'Group' => array(
		'Group' => array(
			'id' => '214',
			'name' => 'C15410037',
			'product_id' => '2202',
			'modified' => '2017-06-07 16:16:20',
			'created' => '2017-06-07 16:16:20'
		),
		'Master' => array(
			'id' => '2202',
			'antibody_id' => '110',
			'name' => 'H3K4me1 Antibody',
			'description' => '<p><span>Polyclonal antibody raised in rabbit against histone <strong>H3 containing the monomethylated lysine 4</strong> (<strong>H3K4me1</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
			'label1' => 'Validation Data',
			'info1' => '<div class="row">
<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
</div>
</div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_DotBlot.png" alt="H3K4me1 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-7 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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>
</div>
</div>',
			'label2' => 'Target Description',
			'info2' => '<p>Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called &ldquo;histone code&rdquo;. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases.</p>',
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			'meta_description' => 'H3K4me1 (Histone H3 monomethylated at lysine 4) Polyclonal Antibody validated  in ChIP-seq, ChIP-qPCR, ELISA, IF, DB and WB. Batch-specific data available on the website. ',
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			'description' => '<p><strong>Western blot</strong> : The quality of antibodies used in this technique is crucial for correct and specific protein identification. Diagenode offers huge selection of highly sensitive and specific western blot-validated antibodies.</p>
<p>Learn more about: <a href="https://www.diagenode.com/applications/western-blot">Loading control, MW marker visualization</a><em>. <br /></em></p>
<p><em></em>Check our selection of antibodies validated in Western blot.</p>',
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			'description' => '<h1><strong>Validated epigenetics antibodies</strong>&nbsp;&ndash; care for a sample?<br />&nbsp;</h1>
<p>Diagenode has partnered with leading epigenetics experts and numerous epigenetics consortiums to bring to you a validated and comprehensive collection of epigenetic antibodies. As an expert in epigenetics, we are committed to offering highly-specific antibodies validated for ChIP/ChIP-seq and many other applications. All batch-specific validation data is available on our website.<br /><a href="../categories/antibodies">Read about our expertise in antibody production</a>.</p>
<ul>
<li><strong>Focused</strong> -&nbsp;Diagenode's selection of antibodies is exclusively dedicated for epigenetic research. <a title="See the full collection." href="../categories/all-antibodies">See the full collection.</a></li>
<li><strong>Strict quality standards</strong>&nbsp;with rigorous QC and validation</li>
<li><strong>Classified</strong>&nbsp;based on level of validation for flexibility of application</li>
</ul>
<p>Existing sample sizes are listed below. We will soon expand our collection. &nbsp;Are you looking for a sample size of another antibody? Just <a href="mailto:agnieszka.zelisko@diagenode.com?Subject=Sample%20Size%20Request" target="_top">Contact us</a>.</p>',
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			'meta_description' => 'Diagenode offers sample volume on selected antibodies for researchers to test, validate and provide confidence and flexibility in choosing from our wide range of antibodies ',
			'meta_title' => 'Sample-size Antibodies | Diagenode',
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			'name' => 'All antibodies',
			'description' => '<p><span style="font-weight: 400;">All Diagenode&rsquo;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&rsquo;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_description' => 'Diagenode Offers Strict quality standards with Rigorous QC and validated Antibodies. Classified based on level of validation for flexibility of Application. Comprehensive selection of histone and non-histone Antibodies',
			'meta_title' => 'Diagenode's selection of Antibodies is exclusively dedicated for Epigenetic Research | Diagenode',
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			'name' => 'ChIP-seq grade antibodies',
			'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 &micro;g of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 &micro;g 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&rsquo;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_description' => 'Diagenode Offers Wide Range of Validated ChIP-Seq Grade Antibodies for Unparalleled ChIP-Seq Results',
			'meta_title' => 'Chromatin Immunoprecipitation ChIP-Seq Grade Antibodies | Diagenode',
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			'name' => 'ChIP-grade antibodies',
			'description' => '<div class="row">
<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
<p></p>
</div>
</div>
<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>).&nbsp;</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" />&nbsp;</div>
<div class="small-12 medium-6 large-6 columns">
<p></p>
<p></p>
<p></p>
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<p></p>
<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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			'meta_description' => 'Diagenode Offers Extensively Validated ChIP-Grade Antibodies, Confirmed for their Specificity, and high level of Performance in Chromatin Immunoprecipitation ChIP',
			'meta_title' => 'Chromatin immunoprecipitation ChIP-grade antibodies | Diagenode',
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			'name' => 'Histone antibodies',
			'description' => '<p>Histones are the main protein components of chromatin involved in the compaction of DNA into nucleosomes, the basic units of chromatin. A <strong>nucleosome</strong> consists of one pair of each of the core histones (<strong>H2A</strong>, <strong>H2B</strong>, <strong>H3</strong> and <strong>H4</strong>) forming an octameric structure wrapped by 146 base pairs of DNA. The different nucleosomes are linked by the linker histone<strong> H1, </strong>allowing for further condensation of chromatin.</p>
<p>The core histones have a globular structure with large unstructured N-terminal tails protruding from the nucleosome.&nbsp; They can undergo to multiple post-translational modifications (PTM), mainly at the N-terminal tails. These <strong>post-translational modifications </strong>include&nbsp; methylation, acetylation, phosphorylation, ubiquitinylation, citrullination, sumoylation, deamination and crotonylation.&nbsp; The most well characterized PTMs are <strong>methylation,</strong> <strong>acetylation and phosphorylation</strong>. Histone methylation occurs mainly on lysine (K) residues, which can be mono-, di- or tri-methylated, and on arginines (R), which can be mono-methylated and symmetrically or asymmetrically di-methylated. Histone acetylation occurs on lysines and histone phosphorylation mainly on serines (S), threonines (T) and tyrosines (Y).</p>
<p>The PTMs of the different residues are involved in numerous processes such as DNA repair, DNA replication and chromosome condensation. They influence the chromatin organization and can be positively or negatively associated with gene expression. Trimethylation of H3K4, H3K36 and H3K79, and lysine acetylation generally result in an open chromatin configuration (figure below) and are therefore associated with <strong>euchromatin</strong> and gene activation. Trimethylation of H3K9, K3K27 and H4K20, on the other hand, is enriched in <strong>heterochromatin </strong>and associated with gene silencing. The combination of different histone modifications is called the "<strong>histone code</strong>&rdquo;, analogous to the genetic code.</p>
<p><img src="https://www.diagenode.com/img/categories/antibodies/histone-marks-illustration.png" /></p>
<p>Diagenode is proud to offer a large range of antibodies against histones and histone modifications. Our&nbsp; antibodies are highly specific and have been validated in many applications, including <strong>ChIP</strong> and <strong>ChIP-seq</strong>.</p>
<p>Diagenode&rsquo;s collection includes antibodies recognizing:</p>
<ul>
<li><strong>Histone H1 variants</strong></li>
<li><strong>Histone H2A, H2A variants and histone H2A</strong> <strong>modifications</strong> (serine phosphorylation, lysine acetylation, lysine ubiquitinylation)</li>
<li><strong>Histone H2B and H2B</strong> <strong>modifications </strong>(serine phosphorylation, lysine acetylation)</li>
<li><strong>Histone H3 and H3 modifications </strong>(lysine methylation (mono-, di- and tri-methylated), lysine acetylation, serine phosphorylation, threonine phosphorylation, arginine methylation (mono-methylated, symmetrically and asymmetrically di-methylated))</li>
<li><strong>Histone H4 and H4 modifications (</strong>lysine methylation (mono-, di- and tri-methylated), lysine acetylation, arginine methylation (mono-methylated and symmetrically di-methylated), serine phosphorylation )</li>
</ul>
<p><span style="font-weight: 400;"><strong>HDAC's HAT's, HMT's and other</strong> <strong>enzymes</strong> which modify histones can be found in the category <a href="../categories/chromatin-modifying-proteins-histone-transferase">Histone modifying enzymes</a><br /></span></p>
<p><span style="font-weight: 400;"> Diagenode&rsquo;s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Expert technical support</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sample sizes available</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 100% satisfaction guarantee</span></li>
</ul>',
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			'meta_keywords' => 'Histone, antibody, histone h1, histone h2, histone h3, histone h4',
			'meta_description' => 'Polyclonal and Monoclonal Antibodies against Histones and their modifications validated for many applications, including Chromatin Immunoprecipitation (ChIP) and ChIP-Sequencing (ChIP-seq)',
			'meta_title' => 'Histone and Modified Histone Antibodies | Diagenode',
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			'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) 1 => 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>',
			'image_id' => null,
			'type' => 'Brochure',
			'url' => 'files/brochures/Epigenetic_Antibodies_Brochure.pdf',
			'slug' => 'epigenetic-antibodies-brochure',
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		(int) 2 => array(
			'id' => '342',
			'name' => 'Datasheet H3K4me1 C15410037',
			'description' => '<p><span>Polyclonal antibody raised in rabbit against histone H3 containing the monomethylated lysine 4 (H3K4me1), using a KLH-conjugated synthetic peptide.</span></p>',
			'image_id' => null,
			'type' => 'Datasheet',
			'url' => 'files/products/antibodies/Datasheet_H3K4me1_C15410037.pdf',
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			'alt' => 'ChIP-seq Grade',
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			'id' => '4977',
			'name' => 'Single-cell multi-omics, spatial transcriptomics and systematic perturbation decode circuitry of neural crest fate decisions',
			'authors' => 'Hu Z. et al.',
			'description' => '<p><span>Cranial neural crest (NC) cells, which can migrate, adopt multiple fates, and form most of the craniofacial skeleton, are an excellent model for studying cell fate decisions. Using time-resolved single-cell multi-omics, spatial transcriptomics, and systematic Perturb-seq, we fully deciphered zebrafish cranial NC programs, including 23 cell states and three spatial trajectories, reconstructed and tested the complete gene regulatory network (GRN). Our GRN model, combined with a novel velocity-embedded simulation method, accurately predicted functions of all major regulons, with over a 3-fold increase in correlation between in vivo and in silico perturbations. Using our new approach based on regulatory synchronization, we discovered a post-epithelial-mesenchymal-transition endothelial-like program crucial for migration, identified motif coordinators for dual-fate priming, and quantified lineage-specific cooperative transcription factor functions. This study provides a comprehensive and validated NC regulatory landscape with unprecedented resolution, offering general regulatory models for cell fate decisions in vertebrates.</span></p>',
			'date' => '2024-09-17',
			'pmid' => 'https://www.biorxiv.org/content/10.1101/2024.09.17.613303v1',
			'doi' => ' https://doi.org/10.1101/2024.09.17.613303',
			'modified' => '2024-09-24 12:23:31',
			'created' => '2024-09-24 12:23:31',
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		(int) 1 => array(
			'id' => '4943',
			'name' => 'KRAS promotes GLI2-dependent transcription during pancreatic carcinogenesis',
			'authors' => 'Sigafoos A.N. et al.',
			'description' => '<p><span>Aberrant activation of GLI transcription factors has been implicated in the pathogenesis of different tumor types including pancreatic ductal adenocarcinoma (PDAC). However, the mechanistic link with established drivers of this disease remains in part elusive. Here, using a new genetically-engineered mouse model overexpressing constitutively active mouse form of GLI2 and a combination of genome wide assays, we provide evidence of a novel mechanism underlying the interplay between KRAS, a major driver of PDAC development, and GLI2 to control oncogenic gene expression. These mice, also expressing KrasG12D, show significantly reduced median survival rate and accelerated tumorigenesis compared to the KrasG12D only expressing mice. Analysis of the mechanism using RNA-seq demonstrate higher levels of GLI2 targets, particularly tumor growth promoting genes including Ccnd1, N-Myc and Bcl2, in KrasG12D mutant cells. Further, ChIP-seq studies showed that in these cells KrasG12D increases the levels of H3K4me3 at the promoter of GLI2 targets without affecting significantly the levels of other major active chromatin marks. Importantly, Gli2 knockdown reduces H3K4me3 enrichment and gene expression induced by mutant Kras. In summary, we demonstrate that Gli2 plays a significant role in pancreatic carcinogenesis by acting as a downstream effector of KrasG12D to control gene expression.</span></p>',
			'date' => '2024-06-24',
			'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38896052/',
			'doi' => '10.1158/2767-9764.CRC-23-0464',
			'modified' => '2024-06-24 17:07:26',
			'created' => '2024-06-24 17:07:26',
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		(int) 2 => array(
			'id' => '4925',
			'name' => 'Chromatin profiling reveals TFAP4 as a critical transcriptional regulator of bovine satellite cell differentiation',
			'authors' => 'Pengcheng Lyu et al.',
			'description' => '<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Background</h3>
<p>Satellite cells are myogenic precursor cells in adult skeletal muscle and play a crucial role in skeletal muscle regeneration, maintenance, and growth. Like embryonic myoblasts, satellite cells have the ability to proliferate, differentiate, and fuse to form multinucleated myofibers. In this study, we aimed to identify additional transcription factors that control gene expression during bovine satellite cell proliferation and differentiation.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Results</h3>
<p>Using chromatin immunoprecipitation followed by sequencing, we identified 56,973 and 54,470 genomic regions marked with both the histone modifications H3K4me1 and H3K27ac, which were considered active enhancers, and 50,956 and 59,174 genomic regions marked with H3K27me3, which were considered repressed enhancers, in proliferating and differentiating bovine satellite cells, respectively. In addition, we identified 1,216 and 1,171 super-enhancers in proliferating and differentiating bovine satellite cells, respectively. Analyzing these enhancers showed that in proliferating bovine satellite cells, active enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation whereas repressed enhancers were associated with genes essential for myoblast differentiation, and that in differentiating satellite cells, active enhancers were associated with genes essential for myoblast differentiation or muscle contraction whereas repressed enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation. Active enhancers in proliferating bovine satellite cells were enriched with binding sites for many transcription factors such as MYF5 and the AP-1 family transcription factors; active enhancers in differentiating bovine satellite cells were enriched with binding sites for many transcription factors such as MYOG and TFAP4; and repressed enhancers in both proliferating and differentiating bovine satellite cells were enriched with binding sites for NF-kB, ZEB-1, and several other transcription factors. The role of TFAP4 in satellite cell or myoblast differentiation was previously unknown, and through gene knockdown and overexpression, we experimentally validated a critical role for TFAP4 in the differentiation and fusion of bovine satellite cells into myofibers.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Conclusions</h3>
<p>Satellite cell proliferation and differentiation are controlled by many transcription factors such as AP-1, TFAP4, NF-kB, and ZEB-1 whose roles in these processes were previously unknown in addition to those transcription factors such as MYF5 and MYOG whose roles in these processes are widely known.</p>',
			'date' => '2024-03-12',
			'pmid' => 'https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10189-2',
			'doi' => 'https://doi.org/10.1186/s12864-024-10189-2',
			'modified' => '2024-03-15 15:06:06',
			'created' => '2024-03-15 15:06:06',
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			'id' => '4822',
			'name' => 'RUNX1 colludes with NOTCH1 to reprogram chromatin in T-cell acutelymphoblastic leukemia',
			'authors' => 'Islam  R. et al.',
			'description' => '<p><span>Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T&nbsp;cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including&nbsp;</span><em>MYC, DTX1, HES4, IL7R,</em><span><span>&nbsp;</span>and<span>&nbsp;</span></span><em>NOTCH3</em><span>. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.</span></p>',
			'date' => '2023-05-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.isci.2023.106795',
			'doi' => '10.1016/j.isci.2023.106795',
			'modified' => '2023-06-19 10:14:27',
			'created' => '2023-06-13 21:11:31',
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			'id' => '4748',
			'name' => 'Incomplete transcriptional dosage compensation of vertebrate sexchromosomes is balanced by post-transcriptional compensation',
			'authors' => 'Lister  N. C. et al.',
			'description' => '<p>Heteromorphic sex chromosomes (XY or ZW) present problems of gene dosage imbalance between the sexes, and with the autosomes. Mammalian X chromosome inactivation was long thought to imply a critical need for dosage compensation in vertebrates. However, the universal importance of sex chromosome dosage compensation was questioned by mRNA abundance measurements that demonstrated sex chromosome transcripts are neither balanced between the sexes or with autosomes in monotreme mammals or birds. Here, we demonstrate unbalanced mRNA levels of X genes in platypus males and females that correlate with differential loading of histone modifications, and confirm that transcripts of Z genes are unbalanced between males and females also in chicken. However, we found that in both species, median male to female protein abundance ratios were 1:1, implying an additional level of post-transcriptional control. We conclude that parity of sex chromosome output is achieved in birds, as well as all mammal groups, by a combination of transcriptional and post-transcriptional control, consistent with an essential role for sex chromosome dosage compensation in vertebrates.</p>',
			'date' => '2023-02-01',
			'pmid' => 'https://doi.org/10.1101%2F2023.02.23.529605',
			'doi' => '10.1101/2023.02.23.529605',
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			'id' => '4605',
			'name' => 'Gene Regulatory Interactions at Lamina-Associated Domains',
			'authors' => 'Madsen-Østerbye  J. et al.',
			'description' => '<p>The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are inactive, over ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to interact with regulatory elements remain unclear. Here, we integrate publicly available enhancer-capture Hi-C data with our own chromatin state and transcriptomic datasets to show that inferred enhancers of active genes in LADs are able to form connections with other enhancers within LADs and outside LADs. Fluorescence in situ hybridization analyses show proximity changes between differentially expressed genes in LADs and distant enhancers upon the induction of adipogenic differentiation. We also provide evidence of involvement of lamin A/C, but not lamin B1, in repressing genes at the border of an in-LAD active region within a topological domain. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with gene expression in this dynamic nuclear compartment.</p>',
			'date' => '2023-01-01',
			'pmid' => 'https://doi.org/10.3390%2Fgenes14020334',
			'doi' => '10.3390/genes14020334',
			'modified' => '2023-04-04 08:57:32',
			'created' => '2023-02-21 09:59:46',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '4490',
			'name' => 'Repression and 3D-restructuring resolves regulatory conflicts inevolutionarily rearranged genomes.',
			'authors' => 'Ringel  A. et al.',
			'description' => '<p>Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36179666',
			'doi' => '10.1016/j.cell.2022.09.006',
			'modified' => '2022-11-18 12:39:16',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '4417',
			'name' => 'HOTAIR interacts with PRC2 complex regulating the regional preadipocytetranscriptome and human fat distribution.',
			'authors' => 'Kuo  Feng-Chih et al.',
			'description' => '<p>Mechanisms governing regional human adipose tissue (AT) development remain undefined. Here, we show that the long non-coding RNA HOTAIR (HOX transcript antisense RNA) is exclusively expressed in gluteofemoral AT, where it is essential for adipocyte development. We find that HOTAIR interacts with polycomb repressive complex 2 (PRC2) and we identify core HOTAIR-PRC2 target genes involved in adipocyte lineage determination. Repression of target genes coincides with PRC2 promoter occupancy and H3K27 trimethylation. HOTAIR is also involved in modifying the gluteal adipocyte transcriptome through alternative splicing. Gluteal-specific expression of HOTAIR is maintained by defined regions of open chromatin across the HOTAIR promoter. HOTAIR expression levels can be modified by hormonal (estrogen, glucocorticoids) and genetic variation (rs1443512 is a HOTAIR eQTL associated with reduced gynoid fat mass). These data identify HOTAIR as a dynamic regulator of the gluteal adipocyte transcriptome and epigenome with functional importance for human regional AT development.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35905723',
			'doi' => '10.1016/j.celrep.2022.111136',
			'modified' => '2022-09-27 14:41:23',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '4524',
			'name' => 'Local euchromatin enrichment in lamina-associated domains anticipatestheir repositioning in the adipogenic lineage.',
			'authors' => 'Madsen-Østerbye  J. et al.',
			'description' => '<p>BACKGROUND: Interactions of chromatin with the nuclear lamina via lamina-associated domains (LADs) confer structural stability to the genome. The dynamics of positioning of LADs during differentiation, and how LADs impinge on developmental gene expression, remains, however, elusive. RESULTS: We examined changes in the association of lamin B1 with the genome in the first 72 h of differentiation of adipose stem cells into adipocytes. We demonstrate a repositioning of entire stand-alone LADs and of LAD edges as a prominent nuclear structural feature of early adipogenesis. Whereas adipogenic genes are released from LADs, LADs sequester downregulated or repressed genes irrelevant for the adipose lineage. However, LAD repositioning only partly concurs with gene expression changes. Differentially expressed genes in LADs, including LADs conserved throughout differentiation, reside in local euchromatic and lamin-depleted sub-domains. In these sub-domains, pre-differentiation histone modification profiles correlate with the LAD versus inter-LAD outcome of these genes during adipogenic commitment. Lastly, we link differentially expressed genes in LADs to short-range enhancers which overall co-partition with these genes in LADs versus inter-LADs during differentiation. CONCLUSIONS: We conclude that LADs are predictable structural features of adipose nuclear architecture that restrain non-adipogenic genes in a repressive environment.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35410387',
			'doi' => '10.1186/s13059-022-02662-6',
			'modified' => '2022-11-24 09:08:01',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '4326',
			'name' => 'Loss of KMT2C reprograms the epigenomic landscape in hPSCsresulting in NODAL overexpression and a failure of hemogenic endotheliumspecification.',
			'authors' => 'Maurya Shailendra et al.',
			'description' => '<p>Germline or somatic variation in the family of KMT2 lysine methyltransferases have been associated with a variety of congenital disorders and cancers. Notably, -fusions are prevalent in 70\% of infant leukaemias but fail to phenocopy short latency leukaemogenesis in mammalian models, suggesting additional factors are necessary for transformation. Given the lack of additional somatic mutation, the role of epigenetic regulation in cell specification, and our prior results of germline variation in infant leukaemia patients, we hypothesized that germline dysfunction of KMT2C altered haematopoietic specification. In isogenic KO hPSCs, we found genome-wide differences in histone modifications at active and poised enhancers, leading to gene expression profiles akin to mesendoderm rather than mesoderm highlighted by a significant increase in NODAL expression and WNT inhibition, ultimately resulting in a lack of hemogenic endothelium specification. These unbiased multi-omic results provide new evidence for germline mechanisms increasing risk of early leukaemogenesis.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://doi.org/10.1080%2F15592294.2021.1954780',
			'doi' => '10.1080/15592294.2021.1954780',
			'modified' => '2022-06-20 09:27:45',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '4196',
			'name' => 'Functional annotations of three domestic animal genomes provide vitalresources for comparative and agricultural research.',
			'authors' => 'Kern C. et al.',
			'description' => '<p>Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken (Gallus gallus), pig (Sus scrofa), and cattle (Bos taurus). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://doi.org/10.1038%2Fs41467-021-22100-8',
			'doi' => '10.1038/s41467-021-22100-8',
			'modified' => '2022-01-06 14:30:41',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '3711',
			'name' => 'Long intergenic non-coding RNAs regulate human lung fibroblast function: Implications for idiopathic pulmonary fibrosis.',
			'authors' => 'Hadjicharalambous MR, Roux BT, Csomor E, Feghali-Bostwick CA, Murray LA, Clarke DL, Lindsay MA',
			'description' => '<p>Phenotypic changes in lung fibroblasts are believed to contribute to the development of Idiopathic Pulmonary Fibrosis (IPF), a progressive and fatal lung disease. Long intergenic non-coding RNAs (lincRNAs) have been identified as novel regulators of gene expression and protein activity. In non-stimulated cells, we observed reduced proliferation and inflammation but no difference in the fibrotic response of IPF fibroblasts. These functional changes in non-stimulated cells were associated with changes in the expression of the histone marks, H3K4me1, H3K4me3 and H3K27ac indicating a possible involvement of epigenetics. Following activation with TGF-&beta;1 and IL-1&beta;, we demonstrated an increased fibrotic but reduced inflammatory response in IPF fibroblasts. There was no significant difference in proliferation following PDGF exposure. The lincRNAs, LINC00960 and LINC01140 were upregulated in IPF fibroblasts. Knockdown studies showed that LINC00960 and LINC01140 were positive regulators of proliferation in both control and IPF fibroblasts but had no effect upon the fibrotic response. Knockdown of LINC01140 but not LINC00960 increased the inflammatory response, which was greater in IPF compared to control fibroblasts. Overall, these studies demonstrate for the first time that lincRNAs are important regulators of proliferation and inflammation in human lung fibroblasts and that these might mediate the reduced inflammatory response observed in IPF-derived fibroblasts.</p>',
			'date' => '2019-04-15',
			'pmid' => 'http://www.pubmed.gov/30988425',
			'doi' => '10.1038/s41598-019-42292-w',
			'modified' => '2019-07-05 14:31:28',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '3660',
			'name' => 'Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia.',
			'authors' => 'Wernig-Zorc S, Yadav MP, Kopparapu PK, Bemark M, Kristjansdottir HL, Andersson PO, Kanduri C, Kanduri M',
			'description' => '<p>BACKGROUND: Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic and diagnostic implications for several cancers. However, there is no global study exploring the role of 5-hydroxymethylcytosine (5-hmC) levels in CLL. Herein, using mass spectrometry and hMeDIP-sequencing, we analysed the dynamics of 5-hmC during B cell maturation and CLL pathogenesis. RESULTS: We show that na&iuml;ve B-cells had higher levels of 5-hmC and 5-mC compared to non-class switched and class-switched memory B-cells. We found a significant decrease in global 5-mC levels in CLL patients (n&thinsp;=&thinsp;15) compared to na&iuml;ve and memory B cells, with no changes detected between the CLL prognostic groups. On the other hand, global 5-hmC levels of CLL patients were similar to memory B cells and reduced compared to na&iuml;ve B cells. Interestingly, 5-hmC levels were increased at regulatory regions such as gene-body, CpG island shores and shelves and 5-hmC distribution over the gene-body positively correlated with degree of transcriptional activity. Importantly, CLL samples showed aberrant 5-hmC and 5-mC pattern over gene-body compared to well-defined patterns in normal B-cells. Integrated analysis of 5-hmC and RNA-sequencing from CLL datasets identified three novel oncogenic drivers that could have potential roles in CLL development and progression. CONCLUSIONS: Thus, our study suggests that the global loss of 5-hmC, accompanied by its significant increase at the gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Our combined analysis of 5-mC and 5-hmC sequencing provided insights into the potential role of 5-hmC in modulating gene expression changes during CLL pathogenesis.</p>',
			'date' => '2019-01-07',
			'pmid' => 'http://www.pubmed.gov/30616658',
			'doi' => '10.1186/s13072‑018‑0252‑7',
			'modified' => '2019-07-01 11:46:16',
			'created' => '2019-06-21 14:55:31',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '3396',
			'name' => 'The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity',
			'authors' => 'Domínguez-Andrés Jorge, Novakovic Boris, Li Yang, Scicluna Brendon P., Gresnigt Mark S., Arts Rob J.W., Oosting Marije, Moorlag Simone J.C.F.M., Groh Laszlo A., Zwaag Jelle, Koch Rebecca M., ter Horst Rob, Joosten Leo A.B., Wijmenga Cisca, Michelucci Ales',
			'description' => '<p>Sepsis involves simultaneous hyperactivation of the immune system and immune paralysis, leading to both organ dysfunction and increased susceptibility to secondary infections. Acute activation of myeloid cells induced itaconate synthesis, which subsequently mediated innate immune tolerance in human monocytes. In contrast, induction of trained immunity by b-glucan counteracted tolerance induced in a model of human endotoxemia by inhibiting the expression of immune-responsive gene 1 (IRG1), the enzyme that controls itaconate synthesis. b-Glucan also increased the expression of succinate dehydrogenase (SDH), contributing to the integrity of the TCA cycle and leading to an enhanced innate immune response after secondary stimulation. The role of itaconate was further validated by IRG1 and SDH polymorphisms that modulate induction of tolerance and trained immunity in human monocytes. These data demonstrate the importance of the IRG1-itaconateSDH axis in the development of immune tolerance and training and highlight the potential of b-glucaninduced trained immunity to revert immunoparalysis.</p>',
			'date' => '2018-10-01',
			'pmid' => 'http://www.pubmed.gov/30293776',
			'doi' => '10.1016/j.cmet.2018.09.003',
			'modified' => '2018-11-22 15:18:30',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '3469',
			'name' => 'Increased H3K9 methylation and impaired expression of Protocadherins are associated with the cognitive dysfunctions of the Kleefstra syndrome.',
			'authors' => 'Iacono G, Dubos A, Méziane H, Benevento M, Habibi E, Mandoli A, Riet F, Selloum M, Feil R, Zhou H, Kleefstra T, Kasri NN, van Bokhoven H, Herault Y, Stunnenberg HG',
			'description' => '<p>Kleefstra syndrome, a disease with intellectual disability, autism spectrum disorders and other developmental defects is caused in humans by haploinsufficiency of EHMT1. Although EHMT1 and its paralog EHMT2 were shown to be histone methyltransferases responsible for deposition of the di-methylated H3K9 (H3K9me2), the exact nature of epigenetic dysfunctions in Kleefstra syndrome remains unknown. Here, we found that the epigenome of Ehmt1+/- adult mouse brain displays a marked increase of H3K9me2/3 which correlates with impaired expression of protocadherins, master regulators of neuronal diversity. Increased H3K9me3 was present already at birth, indicating that aberrant methylation patterns are established during embryogenesis. Interestingly, we found that Ehmt2+/- mice do not present neither the marked increase of H3K9me2/3 nor the cognitive deficits found in Ehmt1+/- mice, indicating an evolutionary diversification of functions. Our finding of increased H3K9me3 in Ehmt1+/- mice is the first one supporting the notion that EHMT1 can quench the deposition of tri-methylation by other Histone methyltransferases, ultimately leading to impaired neurocognitive functioning. Our insights into the epigenetic pathophysiology of Kleefstra syndrome may offer guidance for future developments of therapeutic strategies for this disease.</p>',
			'date' => '2018-06-01',
			'pmid' => 'http://www.pubmed.gov/29554304',
			'doi' => '10.1093/nar/gky196',
			'modified' => '2019-02-15 21:04:02',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '3539',
			'name' => 'A long range distal enhancer controls temporal fine-tuning of PAX6 expression in neuronal precursors.',
			'authors' => 'Lacomme M, Medevielle F, Bourbon HM, Thierion E, Kleinjan DJ, Roussat M, Pituello F, Bel-Vialar S',
			'description' => '<p>Proper embryonic development relies on a tight control of spatial and temporal gene expression profiles in a highly regulated manner. One good example is the ON/OFF switching of the transcription factor PAX6 that governs important steps of neurogenesis. In the neural tube PAX6 expression is initiated in neural progenitors through the positive action of retinoic acid signaling and downregulated in neuronal precursors by the bHLH transcription factor NEUROG2. How these two regulatory inputs are integrated at the molecular level to properly fine tune temporal PAX6 expression is not known. In this study we identified and characterized a 940-bp long distal cis-regulatory module (CRM), located far away from the PAX6 transcription unit and which conveys positive input from RA signaling pathway and indirect repressive signal(s) from NEUROG2. These opposing regulatory signals are integrated through HOMZ, a 94 bp core region within E940 which is evolutionarily conserved in distant organisms such as the zebrafish. We show that within HOMZ, NEUROG2 and RA exert their opposite temporal activities through a short 60 bp region containing a functional RA-responsive element (RARE). We propose a model in which retinoic acid receptors (RARs) and NEUROG2 repressive target(s) compete on the same DNA motif to fine tune temporal PAX6 expression during the course of spinal neurogenesis.</p>',
			'date' => '2018-04-15',
			'pmid' => 'http://www.pubmed.gov/29486153',
			'doi' => '10.1016/j.ydbio.2018.02.015',
			'modified' => '2019-02-28 10:42:57',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '3542',
			'name' => 'Inhibition of Methyltransferase Setd7 Allows the In Vitro Expansion of Myogenic Stem Cells with Improved Therapeutic Potential.',
			'authors' => 'Judson RN, Quarta M, Oudhoff MJ, Soliman H, Yi L, Chang CK, Loi G, Vander Werff R, Cait A, Hamer M, Blonigan J, Paine P, Doan LTN, Groppa E, He W, Su L, Zhang RH, Xu P, Eisner C, Low M, Barta I, Lewis CB, Zaph C, Karimi MM, Rando TA, Rossi FM',
			'description' => '<p>The development of cell therapy for repairing damaged or diseased skeletal muscle has been hindered by the inability to significantly expand immature, transplantable myogenic stem cells (MuSCs) in&nbsp;culture. To overcome this limitation, a deeper understanding of the mechanisms regulating the transition between activated, proliferating MuSCs and differentiation-primed, poorly engrafting progenitors is needed. Here, we show that methyltransferase Setd7 facilitates such transition by regulating the nuclear accumulation of &beta;-catenin in proliferating MuSCs. Genetic or pharmacological inhibition of Setd7 promotes in&nbsp;vitro expansion of MuSCs and increases the yield of primary myogenic cell cultures. Upon transplantation, both mouse and human MuSCs expanded with a Setd7 small-molecule inhibitor are better able to repopulate the satellite cell niche, and treated mouse MuSCs show enhanced therapeutic potential in preclinical models of muscular dystrophy. Thus, Setd7 inhibition may help bypass a key obstacle in the translation of cell therapy for muscle disease.</p>',
			'date' => '2018-02-01',
			'pmid' => 'http://www.pubmed.gov/29395054',
			'doi' => '10.1016/j.stem.2017.12.010',
			'modified' => '2019-02-28 10:56:48',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '3446',
			'name' => 'Metabolic Induction of Trained Immunity through the Mevalonate Pathway.',
			'authors' => 'Bekkering S, Arts RJW, Novakovic B, Kourtzelis I, van der Heijden CDCC, Li Y, Popa CD, Ter Horst R, van Tuijl J, Netea-Maier RT, van de Veerdonk FL, Chavakis T, Joosten LAB, van der Meer JWM, Stunnenberg H, Riksen NP, Netea MG',
			'description' => '<p>Innate immune cells can develop long-term memory after stimulation by microbial products during infections or vaccinations. Here, we report that metabolic signals can induce trained immunity. Pharmacological and genetic experiments reveal that activation of the cholesterol synthesis pathway, but not the synthesis of cholesterol itself, is essential for training of myeloid cells. Rather, the metabolite mevalonate is the mediator of training via activation of IGF1-R and mTOR and subsequent histone modifications in inflammatory pathways. Statins, which block mevalonate generation, prevent trained immunity induction. Furthermore, monocytes of patients with hyper immunoglobulin D syndrome (HIDS), who are mevalonate kinase deficient and accumulate mevalonate, have a constitutive trained immunity phenotype at both immunological and epigenetic levels, which could explain the attacks of sterile inflammation that these patients experience. Unraveling the role of mevalonate in trained immunity contributes to our understanding of the pathophysiology of HIDS and identifies novel therapeutic targets for clinical conditions with excessive activation of trained immunity.</p>',
			'date' => '2018-01-11',
			'pmid' => 'http://www.pubmed.gov/29328908',
			'doi' => '10.1016/j.cell.2017.11.025',
			'modified' => '2019-02-15 21:37:39',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '3282',
			'name' => 'Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements',
			'authors' => 'Thierion E. et al.',
			'description' => '<p>Developmental genes can harbour multiple transcriptional enhancers that act simultaneously or in succession to achieve robust and precise spatiotemporal expression. However, the mechanisms underlying cooperation between cis-acting elements are poorly documented, notably in vertebrates. The mouse gene Krox20 encodes a transcription factor required for the specification of two segments (rhombomeres) of the developing hindbrain. In rhombomere 3, Krox20 is subject to direct positive feedback governed by an autoregulatory enhancer, element A. In contrast, a second enhancer, element C, distant by 70 kb, is active from the initiation of transcription independent of the presence of the KROX20 protein. Here, using both enhancer knock-outs and investigations of chromatin organisation, we show that element C possesses a dual activity: besides its classical enhancer function, it is also permanently required in cis to potentiate the autoregulatory activity of element A, by increasing its chromatin accessibility. This work uncovers a novel, asymmetrical, long-range mode of cooperation between cis-acting elements that might be essential to avoid promiscuous activation of positive autoregulatory elements.</p>',
			'date' => '2017-07-27',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28749941',
			'doi' => '',
			'modified' => '2017-10-23 17:38:21',
			'created' => '2017-10-23 17:38:21',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '3084',
			'name' => 'A transcription factor pulse can prime chromatin for heritable transcriptional memory',
			'authors' => 'Iberg-Badeaux A. et al.',
			'description' => '<p>Short-term and long-term transcriptional memory is the phenomenon whereby the kinetics or magnitude of gene induction is enhanced following a prior induction period. Short-term memory persists within one cell generation or in post-mitotic cells, while long-term memory can survive multiple rounds of cell division. We have developed a tissue culture model to study the epigenetic basis for long-term transcriptional memory (LTTM), and subsequently used this model to better understand the epigenetic mechanisms that enable heritable memory of temporary stimuli. We find that a pulse of transcription factor C/EBP&alpha; induces LTTM on a subset of target genes that survives 9 cell divisions. The chromatin landscape at genes that acquire LTTM is more repressed as compared to those genes that do not exhibit memory, akin to a latent state. We show through ChIP and chemical inhibitor studies that Pol II elongation is important for establishing memory in this model, but that Pol II itself is not retained as part of the memory mechanism. More generally, our work reveals that a transcription factor involved in lineage specification can induce LTTM, and that failure to re-repress chromatin is one epigenetic mechanism underlying transcriptional memory.</p>',
			'date' => '2016-12-05',
			'pmid' => 'http://mcb.asm.org/content/early/2016/11/30/MCB.00372-16.abstract',
			'doi' => '',
			'modified' => '2016-12-20 10:33:32',
			'created' => '2016-12-20 10:33:32',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => array(
			'id' => '3103',
			'name' => 'β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance',
			'authors' => 'Novakovic B. et al.',
			'description' => '<p>Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as lipopolysaccharide (LPS). We apply an integrated epigenomic&nbsp;approach to characterize the molecular events involved in LPS-induced tolerance in a time-dependent manner. Mechanistically, LPS-treated monocytes fail to accumulate active histone marks at promoter and enhancers of genes in the lipid metabolism and phagocytic pathways. Transcriptional inactivity in response to a second LPS exposure in tolerized macrophages is accompanied by failure to deposit active histone marks at promoters of tolerized genes. In contrast, &beta;-glucan partially reverses the LPS-induced tolerance in&nbsp;vitro. Importantly, ex&nbsp;vivo &beta;-glucan treatment of monocytes from volunteers with experimental endotoxemia re-instates their capacity for cytokine production. Tolerance is reversed at the level of distal element histone modification and transcriptional reactivation of otherwise unresponsive genes.</p>',
			'date' => '2016-11-17',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27863248',
			'doi' => '',
			'modified' => '2017-01-03 15:31:46',
			'created' => '2017-01-03 15:31:46',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 21 => array(
			'id' => '3015',
			'name' => 'Enhancer decommissioning by Snail1-induced competitive displacement of TCF7L2 and down-regulation of transcriptional activators results in EPHB2 silencing',
			'authors' => 'Schnappauf O et al.',
			'description' => '<p>Transcriptional silencing is a major cause for the inactivation of tumor suppressor genes, however, the underlying mechanisms are only poorly understood. The EPHB2 gene encodes a receptor tyrosine kinase that controls epithelial cell migration and allocation in intestinal crypts. Through its ability to restrict cell spreading, EPHB2 functions as a tumor suppressor in colorectal cancer whose expression is frequently lost as tumors progress to the carcinoma stage. Previously we reported that EPHB2 expression depends on a transcriptional enhancer whose activity is diminished in EPHB2 non-expressing cells. Here we investigated the mechanisms that lead to EPHB2 enhancer inactivation. We show that expression of EPHB2 and SNAIL1 - an inducer of epithelial-mesenchymal transition (EMT) - is anti-correlated in colorectal cancer cell lines and tumors. In a cellular model of Snail1-induced EMT, we observe that features of active chromatin at the EPHB2 enhancer are diminished upon expression of murine Snail1. We identify the transcription factors FOXA1, MYB, CDX2 and TCF7L2 as EPHB2 enhancer factors and demonstrate that Snail1 indirectly inactivates the EPHB2 enhancer by downregulation of FOXA1 and MYB. In addition, Snail1 induces the expression of Lymphoid enhancer factor 1 (LEF1) which competitively displaces TCF7L2 from the EPHB2 enhancer. In contrast to TCF7L2, however, LEF1 appears to repress the EPHB2 enhancer. Our findings underscore the importance of transcriptional enhancers for gene regulation under physiological and pathological conditions and show that SNAIL1 employs a combinatorial mechanism to inactivate the EPHB2 enhancer based on activator deprivation and competitive displacement of transcription factors.</p>',
			'date' => '2016-08-05',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27504909',
			'doi' => '',
			'modified' => '2016-08-31 09:18:03',
			'created' => '2016-08-31 09:18:03',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '2972',
			'name' => 'cChIP-seq: a robust small-scale method for investigation of histone modifications',
			'authors' => 'Valensisi C et al.',
			'description' => '<div id="__sec1" class="sec sec-first">
<h3>Background</h3>
<p id="__p1" class="p p-first-last">ChIP-seq is highly utilized for mapping histone modifications that are informative about gene regulation and genome annotations. For example, applying ChIP-seq to histone modifications such as H3K4me1 has facilitated generating epigenomic maps of putative enhancers. This powerful technology, however, is limited in its application by the large number of cells required. ChIP-seq involves extensive manipulation of sample material and multiple reactions with limited quality control at each step, therefore, scaling down the number of cells required has proven challenging. Recently, several methods have been proposed to overcome this limit but most of these methods require extensive optimization to tailor the protocol to the specific antibody used or number of cells being profiled.</p>
</div>
<div id="__sec2" class="sec">
<h3>Results</h3>
<p id="__p2" class="p p-first-last">Here we describe a robust, yet facile method, which we named carrier ChIP-seq (cChIP-seq), for use on limited cell amounts. cChIP-seq employs a DNA-free histone carrier in order to maintain the working ChIP reaction scale, removing the need to tailor reactions to specific amounts of cells or histone modifications to be assayed. We have applied our method to three different histone modifications, H3K4me3, H3K4me1 and H3K27me3 in the K562 cell line, and H3K4me1 in H1 hESCs. We successfully obtained epigenomic maps for these histone modifications starting with as few as 10,000 cells. We compared cChIP-seq data to data generated as part of the ENCODE project. ENCODE data are the reference standard in the field and have been generated starting from tens of million of cells. Our results show that cChIP-seq successfully recapitulates bulk data. Furthermore, we showed that the differences observed between small-scale ChIP-seq data and ENCODE data are largely to be due to lab-to-lab variability rather than operating on a reduced scale.</p>
</div>
<div id="__sec3" class="sec">
<h3>Conclusions</h3>
<p id="__p3" class="p p-first-last">Data generated using cChIP-seq are equivalent to reference epigenomic maps from three orders of magnitude more cells. Our method offers a robust and straightforward approach to scale down ChIP-seq to as low as 10,000 cells. The underlying principle of our strategy makes it suitable for being applied to a vast range of chromatin modifications without requiring expensive optimization. Furthermore, our strategy of a DNA-free carrier can be adapted to most ChIP-seq protocols.</p>
</div>',
			'date' => '2015-12-21',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687106/',
			'doi' => ' 10.1186/s12864-015-2285-7',
			'modified' => '2016-07-01 10:05:06',
			'created' => '2016-07-01 10:05:06',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '2869',
			'name' => 'C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis',
			'authors' => 'van Oevelen C, Collombet S, Vicent G, Hoogenkamp M, Lepoivre C, Badeaux A, Bussmann L, Sardina JL, Thieffry D, Beato M, Shi Y, Bonifer C, Graf T',
			'description' => '<section id="abs0020" class="articleHighlights">
<h2 class="sectionTitle">Highlights</h2>
<div class="content">
<p></p>
<ul class="ce-list" id="ulist0010">
<li id="u0010">C/EBP&alpha; activates two classes of prospective myeloid enhancers in B cells</li>
<li id="u0015">Pre-existing enhancers are bound by PU.1 and become hyper-activated by C/EBP&alpha;</li>
<li id="u0020">C/EBP&alpha; acts as a pioneer factor with delayed kinetics on de novo enhancers</li>
<li id="u0025">The two types of enhancers direct myeloid cell fate in B cells and hematopoiesis</li>
</ul>
<p></p>
</div>
</section>
<section class="graphical"></section>
<div class="abstract">
<h2 class="sectionTitle">Summary</h2>
<p>Transcription-factor-induced somatic cell conversions are highly relevant for both basic and clinical research yet their mechanism is not fully understood and it is unclear whether they reflect normal differentiation processes. Here we show that during pre-B-cell-to-macrophage transdifferentiation, C/EBP&alpha; binds to two types of myeloid enhancers in B cells: pre-existing enhancers that are bound by PU.1, providing a platform for incoming C/EBP&alpha;; and de novo enhancers that are targeted by C/EBP&alpha;, acting as a pioneer factor for subsequent binding by PU.1. The order of factor binding dictates the upregulation kinetics of nearby genes. Pre-existing enhancers are broadly active throughout the hematopoietic lineage tree, including B cells. In contrast, de novo enhancers are silent in most cell types except in myeloid cells where they become activated by C/EBP factors. Our data suggest that C/EBP&alpha; recapitulates physiological developmental processes by short-circuiting two macrophage enhancer pathways in pre-B cells.</p>
</div>',
			'date' => '2015-08-11',
			'pmid' => 'http://www.cell.com/stem-cell-reports/abstract/S2213-6711%2815%2900188-5',
			'doi' => 'http://dx.doi.org/10.1016/j.stemcr.2015.06.007',
			'modified' => '2016-03-25 10:23:25',
			'created' => '2016-03-25 10:22:05',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => 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) 25 => array(
			'id' => '2228',
			'name' => 'Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping.',
			'authors' => 'Light N, Adoue V, Ge B, Chen SH, Kwan T, Pastinen T',
			'description' => 'Allele-specific (AS) assessment of chromatin has the potential to elucidate specific cis-regulatory mechanisms, which are predicted to underlie the majority of the known genetic associations to complex disease. However, development of chromatin landscapes at allelic resolution has been challenging since sites of variable signal strength require substantial read depths not commonly applied in sequencing based approaches. In this study, we addressed this by performing parallel analyses of input DNA and chromatin immunoprecipitates (ChIP) on high-density Illumina genotyping arrays. Allele-specificity for the histone modifications H3K4me1, H3K4me3, H3K27ac, H3K27me3, and H3K36me3 was assessed using ChIP samples generated from 14 lymphoblast and 6 fibroblast cell lines. AS-ChIP SNPs were combined into domains and validated using high-confidence ChIP-seq sites. We observed characteristic patterns of allelic-imbalance for each histone-modification around allele-specifically expressed transcripts. Notably, we found H3K4me1 to be significantly anti-correlated with allelic expression (AE) at transcription start sites, indicating H3K4me1 allelic imbalance as a marker of AE. We also found that allelic chromatin domains exhibit population and cell-type specificity as well as heritability within trios. Finally, we observed that a subset of allelic chromatin domains is regulated by DNase I-sensitive quantitative trait loci and that these domains are significantly enriched for genome-wide association studies hits, with autoimmune disease associated SNPs specifically enriched in lymphoblasts. This study provides the first genome-wide maps of allelic-imbalance for five histone marks. Our results provide new insights into the role of chromatin in cis-regulation and highlight the need for high-depth sequencing in ChIP-seq studies along with the need to improve allele-specificity of ChIP-enrichment.',
			'date' => '2014-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25055051',
			'doi' => '',
			'modified' => '2015-07-24 15:39:03',
			'created' => '2015-07-24 15:39:03',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 26 => array(
			'id' => '2054',
			'name' => 'Nuclear ARRB1 induces pseudohypoxia and cellular metabolism reprogramming in prostate cancer',
			'authors' => 'Zecchini V, Madhu B, Russell R, Pértega-Gomes N, Warren A, Gaude E, Borlido J, Stark R, Ireland-Zecchini H, Rao R, Scott H, Boren J, Massie C, Asim M, Brindle K, Griffiths J, Frezza C, Neal DE, Mills IG',
			'description' => 'Tumour cells sustain their high proliferation rate through metabolic reprogramming, whereby cellular metabolism shifts from oxidative phosphorylation to aerobic glycolysis, even under normal oxygen levels. Hypoxia-inducible factor 1A (HIF1A) is a major regulator of this process, but its activation under normoxic conditions, termed pseudohypoxia, is not well documented. Here, using an integrative approach combining the first genome-wide mapping of chromatin binding for an endocytic adaptor, ARRB1, both in vitro and in vivo with gene expression profiling, we demonstrate that nuclear ARRB1 contributes to this metabolic shift in prostate cancer cells via regulation of HIF1A transcriptional activity under normoxic conditions through regulation of succinate dehydrogenase A (SDHA) and fumarate hydratase (FH) expression. ARRB1-induced pseudohypoxia may facilitate adaptation of cancer cells to growth in the harsh conditions that are frequently encountered within solid tumours. Our study is the first example of an endocytic adaptor protein regulating metabolic pathways. It implicates ARRB1 as a potential tumour promoter in prostate cancer and highlights the importance of metabolic alterations in prostate cancer.',
			'date' => '2014-05-16',
			'pmid' => 'http://onlinelibrary.wiley.com/doi/10.15252/embj.201386874/full',
			'doi' => '',
			'modified' => '2015-07-24 15:39:02',
			'created' => '2015-07-24 15:39:02',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 27 => array(
			'id' => '1793',
			'name' => 'A novel microscopy-based high-throughput screening method to identify proteins that regulate global histone modification levels.',
			'authors' => 'Baas R, Lelieveld D, van Teeffelen H, Lijnzaad P, Castelijns B, van Schaik FM, Vermeulen M, Egan DA, Timmers HT, de Graaf P',
			'description' => '<p>Posttranslational modifications of histones play an important role in the regulation of gene expression and chromatin structure in eukaryotes. The balance between chromatin factors depositing (writers) and removing (erasers) histone marks regulates the steady-state levels of chromatin modifications. Here we describe a novel microscopy-based screening method to identify proteins that regulate histone modification levels in a high-throughput fashion. We named our method CROSS, for Chromatin Regulation Ontology SiRNA Screening. CROSS is based on an siRNA library targeting the expression of 529 proteins involved in chromatin regulation. As a proof of principle, we used CROSS to identify chromatin factors involved in histone H3 methylation on either lysine-4 or lysine-27. Furthermore, we show that CROSS can be used to identify chromatin factors that affect growth in cancer cell lines. Taken together, CROSS is a powerful method to identify the writers and erasers of novel and known chromatin marks and facilitates the identification of drugs targeting epigenetic modifications.</p>',
			'date' => '2014-02-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24334265',
			'doi' => '',
			'modified' => '2016-04-12 09:46:40',
			'created' => '2015-07-24 15:39:01',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 28 => array(
			'id' => '1577',
			'name' => 'An In-Depth Characterization of the Major Psoriasis Susceptibility Locus Identifies Candidate Susceptibility Alleles within an HLA-C Enhancer Element.',
			'authors' => 'Clop A, Bertoni A, Spain SL, Simpson MA, Pullabhatla V, Tonda R, Hundhausen C, Di Meglio P, De Jong P, Hayday AC, Nestle FO, Barker JN, Bell RJ, Capon F, Trembath RC',
			'description' => 'Psoriasis is an immune-mediated skin disorder that is inherited as a complex genetic trait. Although genome-wide association scans (GWAS) have identified 36 disease susceptibility regions, more than 50% of the genetic variance can be attributed to a single Major Histocompatibility Complex (MHC) locus, known as PSORS1. Genetic studies indicate that HLA-C is the strongest PSORS1 candidate gene, since markers tagging HLA-Cw*0602 consistently generate the most significant association signals in GWAS. However, it is unclear whether HLA-Cw*0602 is itself the causal PSORS1 allele, especially as the role of SNPs that may affect its expression has not been investigated. Here, we have undertaken an in-depth molecular characterization of the PSORS1 interval, with a view to identifying regulatory variants that may contribute to disease susceptibility. By analysing high-density SNP data, we refined PSORS1 to a 179 kb region encompassing HLA-C and the neighbouring HCG27 pseudogene. We compared multiple MHC sequences spanning this refined locus and identified 144 candidate susceptibility variants, which are unique to chromosomes bearing HLA-Cw*0602. In parallel, we investigated the epigenetic profile of the critical PSORS1 interval and uncovered three enhancer elements likely to be active in T lymphocytes. Finally we showed that nine candidate susceptibility SNPs map within a HLA-C enhancer and that three of these variants co-localise with binding sites for immune-related transcription factors. These data indicate that SNPs affecting HLA-Cw*0602 expression are likely to contribute to psoriasis susceptibility and highlight the importance of integrating multiple experimental approaches in the investigation of complex genomic regions such as the MHC.',
			'date' => '2013-08-19',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23990973',
			'doi' => '',
			'modified' => '2015-07-24 15:39:00',
			'created' => '2015-07-24 15:39:00',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 29 => array(
			'id' => '1512',
			'name' => 'Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus.',
			'authors' => 'Miller CL, Anderson DR, Kundu RK, Raiesdana A, Nürnberg ST, Diaz R, Cheng K, Leeper NJ, Chen CH, Chang IS, Schadt EE, Hsiung CA, Assimes TL, Quertermous T',
			'description' => 'Coronary heart disease (CHD) is the leading cause of mortality in both developed and developing countries worldwide. Genome-wide association studies (GWAS) have now identified 46 independent susceptibility loci for CHD, however, the biological and disease-relevant mechanisms for these associations remain elusive. The large-scale meta-analysis of GWAS recently identified in Caucasians a CHD-associated locus at chromosome 6q23.2, a region containing the transcription factor TCF21 gene. TCF21 (Capsulin/Pod1/Epicardin) is a member of the basic-helix-loop-helix (bHLH) transcription factor family, and regulates cell fate decisions and differentiation in the developing coronary vasculature. Herein, we characterize a cis-regulatory mechanism by which the lead polymorphism rs12190287 disrupts an atypical activator protein 1 (AP-1) element, as demonstrated by allele-specific transcriptional regulation, transcription factor binding, and chromatin organization, leading to altered TCF21 expression. Further, this element is shown to mediate signaling through platelet-derived growth factor receptor beta (PDGFR-β) and Wilms tumor 1 (WT1) pathways. A second disease allele identified in East Asians also appears to disrupt an AP-1-like element. Thus, both disease-related growth factor and embryonic signaling pathways may regulate CHD risk through two independent alleles at TCF21.',
			'date' => '2013-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23874238',
			'doi' => '',
			'modified' => '2015-07-24 15:39:00',
			'created' => '2015-07-24 15:39:00',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 30 => array(
			'id' => '1350',
			'name' => 'Balancing of histone H3K4 methylation states by the Kdm5c/SMCX histone demethylase modulates promoter and enhancer function.',
			'authors' => 'Outchkourov NS, Muiño JM, Kaufmann K, van Ijcken WF, Groot Koerkamp MJ, van Leenen D, de Graaf P, Holstege FC, Grosveld FG, Timmers HT',
			'description' => 'The functional organization of eukaryotic genomes correlates with specific patterns of histone methylations. Regulatory regions in genomes such as enhancers and promoters differ in their extent of methylation of histone H3 at lysine-4 (H3K4), but it is largely unknown how the different methylation states are specified and controlled. Here, we show that the Kdm5c/Jarid1c/SMCX member of the Kdm5 family of H3K4 demethylases can be recruited to both enhancer and promoter elements in mouse embryonic stem cells and in neuronal progenitor cells. Knockdown of Kdm5c deregulates transcription via local increases in H3K4me3. Our data indicate that by restricting H3K4me3 modification at core promoters, Kdm5c dampens transcription, but at enhancers Kdm5c stimulates their activity. Remarkably, an impaired enhancer function activates the intrinsic promoter activity of Kdm5c-bound distal elements. Our results demonstrate that the Kdm5c demethylase plays a crucial and dynamic role in the functional discrimination between enhancers and core promoters.',
			'date' => '2013-04-25',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23545502',
			'doi' => '',
			'modified' => '2015-07-24 15:39:00',
			'created' => '2015-07-24 15:39:00',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 31 => array(
			'id' => '592',
			'name' => 'Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.',
			'authors' => 'Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ',
			'description' => 'The H3K9me3 histone modification is often found at promoter regions, where it functions to repress transcription. However, we have previously shown that 3' exons of zinc finger genes (ZNFs) are marked by high levels of H3K9me3. We have now further investigated this unusual location for H3K9me3 in ZNF genes. Neither bioinformatic nor experimental approaches support the hypothesis that the 3' exons of ZNFs are promoters. We further characterized the histone modifications at the 3' ZNF exons and found that these regions also contain H3K36me3, a mark of transcriptional elongation. A genome-wide analysis of ChIP-seq data revealed that ZNFs constitute the majority of genes that have high levels of both H3K9me3 and H3K36me3. These results suggested the possibility that the ZNF genes may be imprinted, with one allele transcribed and one allele repressed. To test the hypothesis that the contradictory modifications are due to imprinting, we used a SNP analysis of RNA-seq data to demonstrate that both alleles of certain ZNF genes having H3K9me3 and H3K36me3 are transcribed. We next analyzed isolated ZNF 3' exons using stably integrated episomes. We found that although the H3K36me3 mark was lost when the 3' ZNF exon was removed from its natural genomic location, the isolated ZNF 3' exons retained the H3K9me3 mark. Thus, the H3K9me3 mark at ZNF 3' exons does not impede transcription and it is regulated independently of the H3K36me3 mark. Finally, we demonstrate a strong relationship between the number of tandemly repeated domains in the 3' exons and the H3K9me3 mark. We suggest that the H3K9me3 at ZNF 3' exons may function to protect the genome from inappropriate recombination rather than to regulate transcription.',
			'date' => '2011-02-15',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21347206',
			'doi' => '',
			'modified' => '2015-07-24 15:38:58',
			'created' => '2015-07-24 15:38:58',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 32 => array(
			'id' => '261',
			'name' => 'Using ChIP-Seq Technology to Generate High-Resolution Profiles of Histone Modifications ',
			'authors' => 'O’Geen H, Echipare L, Farnham PJ',
			'description' => '<p>The dynamic modification of DNA and histones plays a key role in transcriptional regulation through - altering the packaging of DNA and modifying the nucleosome surface. These chromatin states, also referred to as the epigenome, are distinctive for different tissues, developmental stages, and disease states and can also be altered by environmental influences. New technologies allow the genome-wide visualization of the information encoded in the epigenome. For example, the chromatin immunoprecipitation (ChIP) assay allows investigators to characterize DNA&ndash;protein interactions in vivo. ChIP followed by hybridization to microarrays (ChIP-chip) or by high-throughput sequencing (ChIP-seq) are both powerful tools to identify genome-wide profiles of transcription factors, histone modifications, DNA methylation, and nucleosome positioning. ChIP-seq technology, which can now interrogate the entire human genome at high resolution with only one lane of sequencing, has recently surpassed ChIP-chip technology for epigenomic analyses. Importantly, for the study of primary cells and tissues, epigenetic profiles can be generated using as little as 1 &mu;g of chromatin. In this chapter, we describe in detail the steps involved in performing ChIP assays (with a focus on characterizing histone modifications in primary cells)either manually or using the IP-Star ChIP robot, followed by a detailed protocol to prepare successful libraries for Illumina sequencing. Critical quality control checkpoints are discussed. Although not a focus of this chapter, we also point the reader to several methods by which massive ChIP-seq data sets can be analyzed to extract the tremendous information contained within.</p>',
			'date' => '0000-00-00',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/21913086',
			'doi' => '',
			'modified' => '2016-05-03 12:19:44',
			'created' => '2015-07-24 15:38:57',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		)
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			'language' => 'en',
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			'countries' => 'GB',
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			'created' => '2024-01-16 14:10:50',
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			'created' => '2024-01-16 14:11:11',
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<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
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<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
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<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
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<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
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<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
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<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
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<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
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<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
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<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
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	'description' => '<p>The dynamic modification of DNA and histones plays a key role in transcriptional regulation through - altering the packaging of DNA and modifying the nucleosome surface. These chromatin states, also referred to as the epigenome, are distinctive for different tissues, developmental stages, and disease states and can also be altered by environmental influences. New technologies allow the genome-wide visualization of the information encoded in the epigenome. For example, the chromatin immunoprecipitation (ChIP) assay allows investigators to characterize DNA&ndash;protein interactions in vivo. ChIP followed by hybridization to microarrays (ChIP-chip) or by high-throughput sequencing (ChIP-seq) are both powerful tools to identify genome-wide profiles of transcription factors, histone modifications, DNA methylation, and nucleosome positioning. ChIP-seq technology, which can now interrogate the entire human genome at high resolution with only one lane of sequencing, has recently surpassed ChIP-chip technology for epigenomic analyses. Importantly, for the study of primary cells and tissues, epigenetic profiles can be generated using as little as 1 &mu;g of chromatin. In this chapter, we describe in detail the steps involved in performing ChIP assays (with a focus on characterizing histone modifications in primary cells)either manually or using the IP-Star ChIP robot, followed by a detailed protocol to prepare successful libraries for Illumina sequencing. Critical quality control checkpoints are discussed. Although not a focus of this chapter, we also point the reader to several methods by which massive ChIP-seq data sets can be analyzed to extract the tremendous information contained within.</p>',
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include - APP/View/Products/view.ctp, line 755
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 193
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 118

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<td>ChIP/ChIP-seq <sup>*</sup></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 &mu;g per IP.</small></p>',
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		'name' => 'H3K4me1 polyclonal antibody (sample size)',
		'description' => '<p>Polyclonal antibody raised in rabbit against histone H3 containing the monomethylated lysine 4 (H3K4me1), using a KLH-conjugated synthetic peptide.</p>',
		'label1' => 'Validation Data',
		'info1' => '<div class="row">
<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
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<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
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<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_DotBlot.png" alt="H3K4me1 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-7 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
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<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
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</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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' => 'Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases.',
		'clonality' => '',
		'isotype' => '',
		'lot' => 'A1657D',
		'concentration' => '2.9 &micro;g/&micro;l',
		'reactivity' => 'Human, mouse, pig',
		'type' => 'Polyclonal',
		'purity' => 'Affinity purified polyclonal antibody.',
		'classification' => 'Classic',
		'application_table' => '<table>
<thead>
<tr>
<th>Applications</th>
<th>Suggested dilution</th>
<th>References</th>
</tr>
</thead>
<tbody>
<tr>
<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>1-2 &mu;g/IP</td>
<td>Fig 1, 2</td>
</tr>
<tr>
<td>ELISA</td>
<td>1:500</td>
<td>Fig 3</td>
</tr>
<tr>
<td>Dot Blotting</td>
<td>1:10,000</td>
<td>Fig 4</td>
</tr>
<tr>
<td>Western Blotting</td>
<td>1:500</td>
<td>Fig 5</td>
</tr>
<tr>
<td>Immunofluorescence</td>
<td>1:500</td>
<td>Fig 6</td>
</tr>
</tbody>
</table>
<p></p>
<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 &mu;g per IP.</small></p>',
		'storage_conditions' => 'Store at -20°C; for long storage, store at -80°C. Avoid multiple freeze-thaw cycles.',
		'storage_buffer' => 'PBS containing 0.05% azide and 0.05% ProClin 300.',
		'precautions' => 'This product is for research use only. Not for use in diagnostic or therapeutic procedures.',
		'uniprot_acc' => '',
		'slug' => '',
		'meta_keywords' => '',
		'meta_description' => '',
		'modified' => '2022-10-04 15:01:10',
		'created' => '0000-00-00 00:00:00',
		'select_label' => '110 - H3K4me1 polyclonal antibody  (A1657D - 2.9 &micro;g/&micro;l - Human, mouse, pig - Affinity purified polyclonal antibody. - Rabbit)'
	),
	'Slave' => array(),
	'Group' => array(
		'Group' => array(
			'id' => '214',
			'name' => 'C15410037',
			'product_id' => '2202',
			'modified' => '2017-06-07 16:16:20',
			'created' => '2017-06-07 16:16:20'
		),
		'Master' => array(
			'id' => '2202',
			'antibody_id' => '110',
			'name' => 'H3K4me1 Antibody',
			'description' => '<p><span>Polyclonal antibody raised in rabbit against histone <strong>H3 containing the monomethylated lysine 4</strong> (<strong>H3K4me1</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
			'label1' => 'Validation Data',
			'info1' => '<div class="row">
<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
</div>
</div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_DotBlot.png" alt="H3K4me1 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-7 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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>
</div>
</div>',
			'label2' => 'Target Description',
			'info2' => '<p>Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called &ldquo;histone code&rdquo;. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases.</p>',
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			'catalog_number' => 'C15410037',
			'old_catalog_number' => 'pAb-037-050',
			'sf_code' => 'C15410037-D001-000581',
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			'price_EUR' => '380',
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			'meta_description' => 'H3K4me1 (Histone H3 monomethylated at lysine 4) Polyclonal Antibody validated  in ChIP-seq, ChIP-qPCR, ELISA, IF, DB and WB. Batch-specific data available on the website. ',
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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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			'description' => '<h1><strong>Validated epigenetics antibodies</strong>&nbsp;&ndash; care for a sample?<br />&nbsp;</h1>
<p>Diagenode has partnered with leading epigenetics experts and numerous epigenetics consortiums to bring to you a validated and comprehensive collection of epigenetic antibodies. As an expert in epigenetics, we are committed to offering highly-specific antibodies validated for ChIP/ChIP-seq and many other applications. All batch-specific validation data is available on our website.<br /><a href="../categories/antibodies">Read about our expertise in antibody production</a>.</p>
<ul>
<li><strong>Focused</strong> -&nbsp;Diagenode's selection of antibodies is exclusively dedicated for epigenetic research. <a title="See the full collection." href="../categories/all-antibodies">See the full collection.</a></li>
<li><strong>Strict quality standards</strong>&nbsp;with rigorous QC and validation</li>
<li><strong>Classified</strong>&nbsp;based on level of validation for flexibility of application</li>
</ul>
<p>Existing sample sizes are listed below. We will soon expand our collection. &nbsp;Are you looking for a sample size of another antibody? Just <a href="mailto:agnieszka.zelisko@diagenode.com?Subject=Sample%20Size%20Request" target="_top">Contact us</a>.</p>',
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			'description' => '<p><span style="font-weight: 400;">All Diagenode&rsquo;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&rsquo;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>
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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 &micro;g of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 &micro;g 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&rsquo;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_keywords' => 'ChIP-seq grade antibodies,polyclonal antibody,WB, ELISA, ChIP-seq (ab), ChIP-qPCR (ab)',
			'meta_description' => 'Diagenode Offers Wide Range of Validated ChIP-Seq Grade Antibodies for Unparalleled ChIP-Seq Results',
			'meta_title' => 'Chromatin Immunoprecipitation ChIP-Seq Grade Antibodies | Diagenode',
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			'name' => 'ChIP-grade antibodies',
			'description' => '<div class="row">
<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
<p></p>
</div>
</div>
<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>).&nbsp;</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" />&nbsp;</div>
<div class="small-12 medium-6 large-6 columns">
<p></p>
<p></p>
<p></p>
</div>
</div>
<p></p>
<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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			'meta_description' => 'Diagenode Offers Extensively Validated ChIP-Grade Antibodies, Confirmed for their Specificity, and high level of Performance in Chromatin Immunoprecipitation ChIP',
			'meta_title' => 'Chromatin immunoprecipitation ChIP-grade antibodies | Diagenode',
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			'name' => 'Histone antibodies',
			'description' => '<p>Histones are the main protein components of chromatin involved in the compaction of DNA into nucleosomes, the basic units of chromatin. A <strong>nucleosome</strong> consists of one pair of each of the core histones (<strong>H2A</strong>, <strong>H2B</strong>, <strong>H3</strong> and <strong>H4</strong>) forming an octameric structure wrapped by 146 base pairs of DNA. The different nucleosomes are linked by the linker histone<strong> H1, </strong>allowing for further condensation of chromatin.</p>
<p>The core histones have a globular structure with large unstructured N-terminal tails protruding from the nucleosome.&nbsp; They can undergo to multiple post-translational modifications (PTM), mainly at the N-terminal tails. These <strong>post-translational modifications </strong>include&nbsp; methylation, acetylation, phosphorylation, ubiquitinylation, citrullination, sumoylation, deamination and crotonylation.&nbsp; The most well characterized PTMs are <strong>methylation,</strong> <strong>acetylation and phosphorylation</strong>. Histone methylation occurs mainly on lysine (K) residues, which can be mono-, di- or tri-methylated, and on arginines (R), which can be mono-methylated and symmetrically or asymmetrically di-methylated. Histone acetylation occurs on lysines and histone phosphorylation mainly on serines (S), threonines (T) and tyrosines (Y).</p>
<p>The PTMs of the different residues are involved in numerous processes such as DNA repair, DNA replication and chromosome condensation. They influence the chromatin organization and can be positively or negatively associated with gene expression. Trimethylation of H3K4, H3K36 and H3K79, and lysine acetylation generally result in an open chromatin configuration (figure below) and are therefore associated with <strong>euchromatin</strong> and gene activation. Trimethylation of H3K9, K3K27 and H4K20, on the other hand, is enriched in <strong>heterochromatin </strong>and associated with gene silencing. The combination of different histone modifications is called the "<strong>histone code</strong>&rdquo;, analogous to the genetic code.</p>
<p><img src="https://www.diagenode.com/img/categories/antibodies/histone-marks-illustration.png" /></p>
<p>Diagenode is proud to offer a large range of antibodies against histones and histone modifications. Our&nbsp; antibodies are highly specific and have been validated in many applications, including <strong>ChIP</strong> and <strong>ChIP-seq</strong>.</p>
<p>Diagenode&rsquo;s collection includes antibodies recognizing:</p>
<ul>
<li><strong>Histone H1 variants</strong></li>
<li><strong>Histone H2A, H2A variants and histone H2A</strong> <strong>modifications</strong> (serine phosphorylation, lysine acetylation, lysine ubiquitinylation)</li>
<li><strong>Histone H2B and H2B</strong> <strong>modifications </strong>(serine phosphorylation, lysine acetylation)</li>
<li><strong>Histone H3 and H3 modifications </strong>(lysine methylation (mono-, di- and tri-methylated), lysine acetylation, serine phosphorylation, threonine phosphorylation, arginine methylation (mono-methylated, symmetrically and asymmetrically di-methylated))</li>
<li><strong>Histone H4 and H4 modifications (</strong>lysine methylation (mono-, di- and tri-methylated), lysine acetylation, arginine methylation (mono-methylated and symmetrically di-methylated), serine phosphorylation )</li>
</ul>
<p><span style="font-weight: 400;"><strong>HDAC's HAT's, HMT's and other</strong> <strong>enzymes</strong> which modify histones can be found in the category <a href="../categories/chromatin-modifying-proteins-histone-transferase">Histone modifying enzymes</a><br /></span></p>
<p><span style="font-weight: 400;"> Diagenode&rsquo;s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Expert technical support</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sample sizes available</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 100% satisfaction guarantee</span></li>
</ul>',
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			'meta_keywords' => 'Histone, antibody, histone h1, histone h2, histone h3, histone h4',
			'meta_description' => 'Polyclonal and Monoclonal Antibodies against Histones and their modifications validated for many applications, including Chromatin Immunoprecipitation (ChIP) and ChIP-Sequencing (ChIP-seq)',
			'meta_title' => 'Histone and Modified Histone Antibodies | Diagenode',
			'modified' => '2020-09-17 13:34:56',
			'created' => '2016-04-01 16:01:32',
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			'id' => '11',
			'name' => 'Antibodies you can trust',
			'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
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			'type' => 'Poster',
			'url' => 'files/posters/Antibodies_you_can_trust_Poster.pdf',
			'slug' => 'antibodies-you-can-trust-poster',
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		),
		(int) 1 => 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>',
			'image_id' => null,
			'type' => 'Brochure',
			'url' => 'files/brochures/Epigenetic_Antibodies_Brochure.pdf',
			'slug' => 'epigenetic-antibodies-brochure',
			'meta_keywords' => '',
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			'modified' => '2016-06-15 11:24:06',
			'created' => '2015-07-03 16:05:27',
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		(int) 2 => array(
			'id' => '342',
			'name' => 'Datasheet H3K4me1 C15410037',
			'description' => '<p><span>Polyclonal antibody raised in rabbit against histone H3 containing the monomethylated lysine 4 (H3K4me1), using a KLH-conjugated synthetic peptide.</span></p>',
			'image_id' => null,
			'type' => 'Datasheet',
			'url' => 'files/products/antibodies/Datasheet_H3K4me1_C15410037.pdf',
			'slug' => 'datasheet-h3k4me1-C15410037',
			'meta_keywords' => '',
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			'modified' => '2015-11-20 17:38:09',
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			'alt' => 'ChIP-seq Grade',
			'modified' => '2020-11-27 07:04:40',
			'created' => '2018-03-15 15:54:09',
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	'Publication' => array(
		(int) 0 => array(
			'id' => '4977',
			'name' => 'Single-cell multi-omics, spatial transcriptomics and systematic perturbation decode circuitry of neural crest fate decisions',
			'authors' => 'Hu Z. et al.',
			'description' => '<p><span>Cranial neural crest (NC) cells, which can migrate, adopt multiple fates, and form most of the craniofacial skeleton, are an excellent model for studying cell fate decisions. Using time-resolved single-cell multi-omics, spatial transcriptomics, and systematic Perturb-seq, we fully deciphered zebrafish cranial NC programs, including 23 cell states and three spatial trajectories, reconstructed and tested the complete gene regulatory network (GRN). Our GRN model, combined with a novel velocity-embedded simulation method, accurately predicted functions of all major regulons, with over a 3-fold increase in correlation between in vivo and in silico perturbations. Using our new approach based on regulatory synchronization, we discovered a post-epithelial-mesenchymal-transition endothelial-like program crucial for migration, identified motif coordinators for dual-fate priming, and quantified lineage-specific cooperative transcription factor functions. This study provides a comprehensive and validated NC regulatory landscape with unprecedented resolution, offering general regulatory models for cell fate decisions in vertebrates.</span></p>',
			'date' => '2024-09-17',
			'pmid' => 'https://www.biorxiv.org/content/10.1101/2024.09.17.613303v1',
			'doi' => ' https://doi.org/10.1101/2024.09.17.613303',
			'modified' => '2024-09-24 12:23:31',
			'created' => '2024-09-24 12:23:31',
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			)
		),
		(int) 1 => array(
			'id' => '4943',
			'name' => 'KRAS promotes GLI2-dependent transcription during pancreatic carcinogenesis',
			'authors' => 'Sigafoos A.N. et al.',
			'description' => '<p><span>Aberrant activation of GLI transcription factors has been implicated in the pathogenesis of different tumor types including pancreatic ductal adenocarcinoma (PDAC). However, the mechanistic link with established drivers of this disease remains in part elusive. Here, using a new genetically-engineered mouse model overexpressing constitutively active mouse form of GLI2 and a combination of genome wide assays, we provide evidence of a novel mechanism underlying the interplay between KRAS, a major driver of PDAC development, and GLI2 to control oncogenic gene expression. These mice, also expressing KrasG12D, show significantly reduced median survival rate and accelerated tumorigenesis compared to the KrasG12D only expressing mice. Analysis of the mechanism using RNA-seq demonstrate higher levels of GLI2 targets, particularly tumor growth promoting genes including Ccnd1, N-Myc and Bcl2, in KrasG12D mutant cells. Further, ChIP-seq studies showed that in these cells KrasG12D increases the levels of H3K4me3 at the promoter of GLI2 targets without affecting significantly the levels of other major active chromatin marks. Importantly, Gli2 knockdown reduces H3K4me3 enrichment and gene expression induced by mutant Kras. In summary, we demonstrate that Gli2 plays a significant role in pancreatic carcinogenesis by acting as a downstream effector of KrasG12D to control gene expression.</span></p>',
			'date' => '2024-06-24',
			'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38896052/',
			'doi' => '10.1158/2767-9764.CRC-23-0464',
			'modified' => '2024-06-24 17:07:26',
			'created' => '2024-06-24 17:07:26',
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		),
		(int) 2 => array(
			'id' => '4925',
			'name' => 'Chromatin profiling reveals TFAP4 as a critical transcriptional regulator of bovine satellite cell differentiation',
			'authors' => 'Pengcheng Lyu et al.',
			'description' => '<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Background</h3>
<p>Satellite cells are myogenic precursor cells in adult skeletal muscle and play a crucial role in skeletal muscle regeneration, maintenance, and growth. Like embryonic myoblasts, satellite cells have the ability to proliferate, differentiate, and fuse to form multinucleated myofibers. In this study, we aimed to identify additional transcription factors that control gene expression during bovine satellite cell proliferation and differentiation.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Results</h3>
<p>Using chromatin immunoprecipitation followed by sequencing, we identified 56,973 and 54,470 genomic regions marked with both the histone modifications H3K4me1 and H3K27ac, which were considered active enhancers, and 50,956 and 59,174 genomic regions marked with H3K27me3, which were considered repressed enhancers, in proliferating and differentiating bovine satellite cells, respectively. In addition, we identified 1,216 and 1,171 super-enhancers in proliferating and differentiating bovine satellite cells, respectively. Analyzing these enhancers showed that in proliferating bovine satellite cells, active enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation whereas repressed enhancers were associated with genes essential for myoblast differentiation, and that in differentiating satellite cells, active enhancers were associated with genes essential for myoblast differentiation or muscle contraction whereas repressed enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation. Active enhancers in proliferating bovine satellite cells were enriched with binding sites for many transcription factors such as MYF5 and the AP-1 family transcription factors; active enhancers in differentiating bovine satellite cells were enriched with binding sites for many transcription factors such as MYOG and TFAP4; and repressed enhancers in both proliferating and differentiating bovine satellite cells were enriched with binding sites for NF-kB, ZEB-1, and several other transcription factors. The role of TFAP4 in satellite cell or myoblast differentiation was previously unknown, and through gene knockdown and overexpression, we experimentally validated a critical role for TFAP4 in the differentiation and fusion of bovine satellite cells into myofibers.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Conclusions</h3>
<p>Satellite cell proliferation and differentiation are controlled by many transcription factors such as AP-1, TFAP4, NF-kB, and ZEB-1 whose roles in these processes were previously unknown in addition to those transcription factors such as MYF5 and MYOG whose roles in these processes are widely known.</p>',
			'date' => '2024-03-12',
			'pmid' => 'https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10189-2',
			'doi' => 'https://doi.org/10.1186/s12864-024-10189-2',
			'modified' => '2024-03-15 15:06:06',
			'created' => '2024-03-15 15:06:06',
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		),
		(int) 3 => array(
			'id' => '4822',
			'name' => 'RUNX1 colludes with NOTCH1 to reprogram chromatin in T-cell acutelymphoblastic leukemia',
			'authors' => 'Islam  R. et al.',
			'description' => '<p><span>Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T&nbsp;cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including&nbsp;</span><em>MYC, DTX1, HES4, IL7R,</em><span><span>&nbsp;</span>and<span>&nbsp;</span></span><em>NOTCH3</em><span>. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.</span></p>',
			'date' => '2023-05-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.isci.2023.106795',
			'doi' => '10.1016/j.isci.2023.106795',
			'modified' => '2023-06-19 10:14:27',
			'created' => '2023-06-13 21:11:31',
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		),
		(int) 4 => array(
			'id' => '4748',
			'name' => 'Incomplete transcriptional dosage compensation of vertebrate sexchromosomes is balanced by post-transcriptional compensation',
			'authors' => 'Lister  N. C. et al.',
			'description' => '<p>Heteromorphic sex chromosomes (XY or ZW) present problems of gene dosage imbalance between the sexes, and with the autosomes. Mammalian X chromosome inactivation was long thought to imply a critical need for dosage compensation in vertebrates. However, the universal importance of sex chromosome dosage compensation was questioned by mRNA abundance measurements that demonstrated sex chromosome transcripts are neither balanced between the sexes or with autosomes in monotreme mammals or birds. Here, we demonstrate unbalanced mRNA levels of X genes in platypus males and females that correlate with differential loading of histone modifications, and confirm that transcripts of Z genes are unbalanced between males and females also in chicken. However, we found that in both species, median male to female protein abundance ratios were 1:1, implying an additional level of post-transcriptional control. We conclude that parity of sex chromosome output is achieved in birds, as well as all mammal groups, by a combination of transcriptional and post-transcriptional control, consistent with an essential role for sex chromosome dosage compensation in vertebrates.</p>',
			'date' => '2023-02-01',
			'pmid' => 'https://doi.org/10.1101%2F2023.02.23.529605',
			'doi' => '10.1101/2023.02.23.529605',
			'modified' => '2023-06-14 08:59:05',
			'created' => '2023-03-02 17:27:08',
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		),
		(int) 5 => array(
			'id' => '4605',
			'name' => 'Gene Regulatory Interactions at Lamina-Associated Domains',
			'authors' => 'Madsen-Østerbye  J. et al.',
			'description' => '<p>The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are inactive, over ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to interact with regulatory elements remain unclear. Here, we integrate publicly available enhancer-capture Hi-C data with our own chromatin state and transcriptomic datasets to show that inferred enhancers of active genes in LADs are able to form connections with other enhancers within LADs and outside LADs. Fluorescence in situ hybridization analyses show proximity changes between differentially expressed genes in LADs and distant enhancers upon the induction of adipogenic differentiation. We also provide evidence of involvement of lamin A/C, but not lamin B1, in repressing genes at the border of an in-LAD active region within a topological domain. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with gene expression in this dynamic nuclear compartment.</p>',
			'date' => '2023-01-01',
			'pmid' => 'https://doi.org/10.3390%2Fgenes14020334',
			'doi' => '10.3390/genes14020334',
			'modified' => '2023-04-04 08:57:32',
			'created' => '2023-02-21 09:59:46',
			'ProductsPublication' => array(
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			)
		),
		(int) 6 => array(
			'id' => '4490',
			'name' => 'Repression and 3D-restructuring resolves regulatory conflicts inevolutionarily rearranged genomes.',
			'authors' => 'Ringel  A. et al.',
			'description' => '<p>Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36179666',
			'doi' => '10.1016/j.cell.2022.09.006',
			'modified' => '2022-11-18 12:39:16',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '4417',
			'name' => 'HOTAIR interacts with PRC2 complex regulating the regional preadipocytetranscriptome and human fat distribution.',
			'authors' => 'Kuo  Feng-Chih et al.',
			'description' => '<p>Mechanisms governing regional human adipose tissue (AT) development remain undefined. Here, we show that the long non-coding RNA HOTAIR (HOX transcript antisense RNA) is exclusively expressed in gluteofemoral AT, where it is essential for adipocyte development. We find that HOTAIR interacts with polycomb repressive complex 2 (PRC2) and we identify core HOTAIR-PRC2 target genes involved in adipocyte lineage determination. Repression of target genes coincides with PRC2 promoter occupancy and H3K27 trimethylation. HOTAIR is also involved in modifying the gluteal adipocyte transcriptome through alternative splicing. Gluteal-specific expression of HOTAIR is maintained by defined regions of open chromatin across the HOTAIR promoter. HOTAIR expression levels can be modified by hormonal (estrogen, glucocorticoids) and genetic variation (rs1443512 is a HOTAIR eQTL associated with reduced gynoid fat mass). These data identify HOTAIR as a dynamic regulator of the gluteal adipocyte transcriptome and epigenome with functional importance for human regional AT development.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35905723',
			'doi' => '10.1016/j.celrep.2022.111136',
			'modified' => '2022-09-27 14:41:23',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '4524',
			'name' => 'Local euchromatin enrichment in lamina-associated domains anticipatestheir repositioning in the adipogenic lineage.',
			'authors' => 'Madsen-Østerbye  J. et al.',
			'description' => '<p>BACKGROUND: Interactions of chromatin with the nuclear lamina via lamina-associated domains (LADs) confer structural stability to the genome. The dynamics of positioning of LADs during differentiation, and how LADs impinge on developmental gene expression, remains, however, elusive. RESULTS: We examined changes in the association of lamin B1 with the genome in the first 72 h of differentiation of adipose stem cells into adipocytes. We demonstrate a repositioning of entire stand-alone LADs and of LAD edges as a prominent nuclear structural feature of early adipogenesis. Whereas adipogenic genes are released from LADs, LADs sequester downregulated or repressed genes irrelevant for the adipose lineage. However, LAD repositioning only partly concurs with gene expression changes. Differentially expressed genes in LADs, including LADs conserved throughout differentiation, reside in local euchromatic and lamin-depleted sub-domains. In these sub-domains, pre-differentiation histone modification profiles correlate with the LAD versus inter-LAD outcome of these genes during adipogenic commitment. Lastly, we link differentially expressed genes in LADs to short-range enhancers which overall co-partition with these genes in LADs versus inter-LADs during differentiation. CONCLUSIONS: We conclude that LADs are predictable structural features of adipose nuclear architecture that restrain non-adipogenic genes in a repressive environment.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35410387',
			'doi' => '10.1186/s13059-022-02662-6',
			'modified' => '2022-11-24 09:08:01',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
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		),
		(int) 9 => array(
			'id' => '4326',
			'name' => 'Loss of KMT2C reprograms the epigenomic landscape in hPSCsresulting in NODAL overexpression and a failure of hemogenic endotheliumspecification.',
			'authors' => 'Maurya Shailendra et al.',
			'description' => '<p>Germline or somatic variation in the family of KMT2 lysine methyltransferases have been associated with a variety of congenital disorders and cancers. Notably, -fusions are prevalent in 70\% of infant leukaemias but fail to phenocopy short latency leukaemogenesis in mammalian models, suggesting additional factors are necessary for transformation. Given the lack of additional somatic mutation, the role of epigenetic regulation in cell specification, and our prior results of germline variation in infant leukaemia patients, we hypothesized that germline dysfunction of KMT2C altered haematopoietic specification. In isogenic KO hPSCs, we found genome-wide differences in histone modifications at active and poised enhancers, leading to gene expression profiles akin to mesendoderm rather than mesoderm highlighted by a significant increase in NODAL expression and WNT inhibition, ultimately resulting in a lack of hemogenic endothelium specification. These unbiased multi-omic results provide new evidence for germline mechanisms increasing risk of early leukaemogenesis.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://doi.org/10.1080%2F15592294.2021.1954780',
			'doi' => '10.1080/15592294.2021.1954780',
			'modified' => '2022-06-20 09:27:45',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '4196',
			'name' => 'Functional annotations of three domestic animal genomes provide vitalresources for comparative and agricultural research.',
			'authors' => 'Kern C. et al.',
			'description' => '<p>Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken (Gallus gallus), pig (Sus scrofa), and cattle (Bos taurus). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://doi.org/10.1038%2Fs41467-021-22100-8',
			'doi' => '10.1038/s41467-021-22100-8',
			'modified' => '2022-01-06 14:30:41',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '3711',
			'name' => 'Long intergenic non-coding RNAs regulate human lung fibroblast function: Implications for idiopathic pulmonary fibrosis.',
			'authors' => 'Hadjicharalambous MR, Roux BT, Csomor E, Feghali-Bostwick CA, Murray LA, Clarke DL, Lindsay MA',
			'description' => '<p>Phenotypic changes in lung fibroblasts are believed to contribute to the development of Idiopathic Pulmonary Fibrosis (IPF), a progressive and fatal lung disease. Long intergenic non-coding RNAs (lincRNAs) have been identified as novel regulators of gene expression and protein activity. In non-stimulated cells, we observed reduced proliferation and inflammation but no difference in the fibrotic response of IPF fibroblasts. These functional changes in non-stimulated cells were associated with changes in the expression of the histone marks, H3K4me1, H3K4me3 and H3K27ac indicating a possible involvement of epigenetics. Following activation with TGF-&beta;1 and IL-1&beta;, we demonstrated an increased fibrotic but reduced inflammatory response in IPF fibroblasts. There was no significant difference in proliferation following PDGF exposure. The lincRNAs, LINC00960 and LINC01140 were upregulated in IPF fibroblasts. Knockdown studies showed that LINC00960 and LINC01140 were positive regulators of proliferation in both control and IPF fibroblasts but had no effect upon the fibrotic response. Knockdown of LINC01140 but not LINC00960 increased the inflammatory response, which was greater in IPF compared to control fibroblasts. Overall, these studies demonstrate for the first time that lincRNAs are important regulators of proliferation and inflammation in human lung fibroblasts and that these might mediate the reduced inflammatory response observed in IPF-derived fibroblasts.</p>',
			'date' => '2019-04-15',
			'pmid' => 'http://www.pubmed.gov/30988425',
			'doi' => '10.1038/s41598-019-42292-w',
			'modified' => '2019-07-05 14:31:28',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '3660',
			'name' => 'Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia.',
			'authors' => 'Wernig-Zorc S, Yadav MP, Kopparapu PK, Bemark M, Kristjansdottir HL, Andersson PO, Kanduri C, Kanduri M',
			'description' => '<p>BACKGROUND: Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic and diagnostic implications for several cancers. However, there is no global study exploring the role of 5-hydroxymethylcytosine (5-hmC) levels in CLL. Herein, using mass spectrometry and hMeDIP-sequencing, we analysed the dynamics of 5-hmC during B cell maturation and CLL pathogenesis. RESULTS: We show that na&iuml;ve B-cells had higher levels of 5-hmC and 5-mC compared to non-class switched and class-switched memory B-cells. We found a significant decrease in global 5-mC levels in CLL patients (n&thinsp;=&thinsp;15) compared to na&iuml;ve and memory B cells, with no changes detected between the CLL prognostic groups. On the other hand, global 5-hmC levels of CLL patients were similar to memory B cells and reduced compared to na&iuml;ve B cells. Interestingly, 5-hmC levels were increased at regulatory regions such as gene-body, CpG island shores and shelves and 5-hmC distribution over the gene-body positively correlated with degree of transcriptional activity. Importantly, CLL samples showed aberrant 5-hmC and 5-mC pattern over gene-body compared to well-defined patterns in normal B-cells. Integrated analysis of 5-hmC and RNA-sequencing from CLL datasets identified three novel oncogenic drivers that could have potential roles in CLL development and progression. CONCLUSIONS: Thus, our study suggests that the global loss of 5-hmC, accompanied by its significant increase at the gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Our combined analysis of 5-mC and 5-hmC sequencing provided insights into the potential role of 5-hmC in modulating gene expression changes during CLL pathogenesis.</p>',
			'date' => '2019-01-07',
			'pmid' => 'http://www.pubmed.gov/30616658',
			'doi' => '10.1186/s13072‑018‑0252‑7',
			'modified' => '2019-07-01 11:46:16',
			'created' => '2019-06-21 14:55:31',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '3396',
			'name' => 'The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity',
			'authors' => 'Domínguez-Andrés Jorge, Novakovic Boris, Li Yang, Scicluna Brendon P., Gresnigt Mark S., Arts Rob J.W., Oosting Marije, Moorlag Simone J.C.F.M., Groh Laszlo A., Zwaag Jelle, Koch Rebecca M., ter Horst Rob, Joosten Leo A.B., Wijmenga Cisca, Michelucci Ales',
			'description' => '<p>Sepsis involves simultaneous hyperactivation of the immune system and immune paralysis, leading to both organ dysfunction and increased susceptibility to secondary infections. Acute activation of myeloid cells induced itaconate synthesis, which subsequently mediated innate immune tolerance in human monocytes. In contrast, induction of trained immunity by b-glucan counteracted tolerance induced in a model of human endotoxemia by inhibiting the expression of immune-responsive gene 1 (IRG1), the enzyme that controls itaconate synthesis. b-Glucan also increased the expression of succinate dehydrogenase (SDH), contributing to the integrity of the TCA cycle and leading to an enhanced innate immune response after secondary stimulation. The role of itaconate was further validated by IRG1 and SDH polymorphisms that modulate induction of tolerance and trained immunity in human monocytes. These data demonstrate the importance of the IRG1-itaconateSDH axis in the development of immune tolerance and training and highlight the potential of b-glucaninduced trained immunity to revert immunoparalysis.</p>',
			'date' => '2018-10-01',
			'pmid' => 'http://www.pubmed.gov/30293776',
			'doi' => '10.1016/j.cmet.2018.09.003',
			'modified' => '2018-11-22 15:18:30',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '3469',
			'name' => 'Increased H3K9 methylation and impaired expression of Protocadherins are associated with the cognitive dysfunctions of the Kleefstra syndrome.',
			'authors' => 'Iacono G, Dubos A, Méziane H, Benevento M, Habibi E, Mandoli A, Riet F, Selloum M, Feil R, Zhou H, Kleefstra T, Kasri NN, van Bokhoven H, Herault Y, Stunnenberg HG',
			'description' => '<p>Kleefstra syndrome, a disease with intellectual disability, autism spectrum disorders and other developmental defects is caused in humans by haploinsufficiency of EHMT1. Although EHMT1 and its paralog EHMT2 were shown to be histone methyltransferases responsible for deposition of the di-methylated H3K9 (H3K9me2), the exact nature of epigenetic dysfunctions in Kleefstra syndrome remains unknown. Here, we found that the epigenome of Ehmt1+/- adult mouse brain displays a marked increase of H3K9me2/3 which correlates with impaired expression of protocadherins, master regulators of neuronal diversity. Increased H3K9me3 was present already at birth, indicating that aberrant methylation patterns are established during embryogenesis. Interestingly, we found that Ehmt2+/- mice do not present neither the marked increase of H3K9me2/3 nor the cognitive deficits found in Ehmt1+/- mice, indicating an evolutionary diversification of functions. Our finding of increased H3K9me3 in Ehmt1+/- mice is the first one supporting the notion that EHMT1 can quench the deposition of tri-methylation by other Histone methyltransferases, ultimately leading to impaired neurocognitive functioning. Our insights into the epigenetic pathophysiology of Kleefstra syndrome may offer guidance for future developments of therapeutic strategies for this disease.</p>',
			'date' => '2018-06-01',
			'pmid' => 'http://www.pubmed.gov/29554304',
			'doi' => '10.1093/nar/gky196',
			'modified' => '2019-02-15 21:04:02',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '3539',
			'name' => 'A long range distal enhancer controls temporal fine-tuning of PAX6 expression in neuronal precursors.',
			'authors' => 'Lacomme M, Medevielle F, Bourbon HM, Thierion E, Kleinjan DJ, Roussat M, Pituello F, Bel-Vialar S',
			'description' => '<p>Proper embryonic development relies on a tight control of spatial and temporal gene expression profiles in a highly regulated manner. One good example is the ON/OFF switching of the transcription factor PAX6 that governs important steps of neurogenesis. In the neural tube PAX6 expression is initiated in neural progenitors through the positive action of retinoic acid signaling and downregulated in neuronal precursors by the bHLH transcription factor NEUROG2. How these two regulatory inputs are integrated at the molecular level to properly fine tune temporal PAX6 expression is not known. In this study we identified and characterized a 940-bp long distal cis-regulatory module (CRM), located far away from the PAX6 transcription unit and which conveys positive input from RA signaling pathway and indirect repressive signal(s) from NEUROG2. These opposing regulatory signals are integrated through HOMZ, a 94 bp core region within E940 which is evolutionarily conserved in distant organisms such as the zebrafish. We show that within HOMZ, NEUROG2 and RA exert their opposite temporal activities through a short 60 bp region containing a functional RA-responsive element (RARE). We propose a model in which retinoic acid receptors (RARs) and NEUROG2 repressive target(s) compete on the same DNA motif to fine tune temporal PAX6 expression during the course of spinal neurogenesis.</p>',
			'date' => '2018-04-15',
			'pmid' => 'http://www.pubmed.gov/29486153',
			'doi' => '10.1016/j.ydbio.2018.02.015',
			'modified' => '2019-02-28 10:42:57',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '3542',
			'name' => 'Inhibition of Methyltransferase Setd7 Allows the In Vitro Expansion of Myogenic Stem Cells with Improved Therapeutic Potential.',
			'authors' => 'Judson RN, Quarta M, Oudhoff MJ, Soliman H, Yi L, Chang CK, Loi G, Vander Werff R, Cait A, Hamer M, Blonigan J, Paine P, Doan LTN, Groppa E, He W, Su L, Zhang RH, Xu P, Eisner C, Low M, Barta I, Lewis CB, Zaph C, Karimi MM, Rando TA, Rossi FM',
			'description' => '<p>The development of cell therapy for repairing damaged or diseased skeletal muscle has been hindered by the inability to significantly expand immature, transplantable myogenic stem cells (MuSCs) in&nbsp;culture. To overcome this limitation, a deeper understanding of the mechanisms regulating the transition between activated, proliferating MuSCs and differentiation-primed, poorly engrafting progenitors is needed. Here, we show that methyltransferase Setd7 facilitates such transition by regulating the nuclear accumulation of &beta;-catenin in proliferating MuSCs. Genetic or pharmacological inhibition of Setd7 promotes in&nbsp;vitro expansion of MuSCs and increases the yield of primary myogenic cell cultures. Upon transplantation, both mouse and human MuSCs expanded with a Setd7 small-molecule inhibitor are better able to repopulate the satellite cell niche, and treated mouse MuSCs show enhanced therapeutic potential in preclinical models of muscular dystrophy. Thus, Setd7 inhibition may help bypass a key obstacle in the translation of cell therapy for muscle disease.</p>',
			'date' => '2018-02-01',
			'pmid' => 'http://www.pubmed.gov/29395054',
			'doi' => '10.1016/j.stem.2017.12.010',
			'modified' => '2019-02-28 10:56:48',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '3446',
			'name' => 'Metabolic Induction of Trained Immunity through the Mevalonate Pathway.',
			'authors' => 'Bekkering S, Arts RJW, Novakovic B, Kourtzelis I, van der Heijden CDCC, Li Y, Popa CD, Ter Horst R, van Tuijl J, Netea-Maier RT, van de Veerdonk FL, Chavakis T, Joosten LAB, van der Meer JWM, Stunnenberg H, Riksen NP, Netea MG',
			'description' => '<p>Innate immune cells can develop long-term memory after stimulation by microbial products during infections or vaccinations. Here, we report that metabolic signals can induce trained immunity. Pharmacological and genetic experiments reveal that activation of the cholesterol synthesis pathway, but not the synthesis of cholesterol itself, is essential for training of myeloid cells. Rather, the metabolite mevalonate is the mediator of training via activation of IGF1-R and mTOR and subsequent histone modifications in inflammatory pathways. Statins, which block mevalonate generation, prevent trained immunity induction. Furthermore, monocytes of patients with hyper immunoglobulin D syndrome (HIDS), who are mevalonate kinase deficient and accumulate mevalonate, have a constitutive trained immunity phenotype at both immunological and epigenetic levels, which could explain the attacks of sterile inflammation that these patients experience. Unraveling the role of mevalonate in trained immunity contributes to our understanding of the pathophysiology of HIDS and identifies novel therapeutic targets for clinical conditions with excessive activation of trained immunity.</p>',
			'date' => '2018-01-11',
			'pmid' => 'http://www.pubmed.gov/29328908',
			'doi' => '10.1016/j.cell.2017.11.025',
			'modified' => '2019-02-15 21:37:39',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '3282',
			'name' => 'Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements',
			'authors' => 'Thierion E. et al.',
			'description' => '<p>Developmental genes can harbour multiple transcriptional enhancers that act simultaneously or in succession to achieve robust and precise spatiotemporal expression. However, the mechanisms underlying cooperation between cis-acting elements are poorly documented, notably in vertebrates. The mouse gene Krox20 encodes a transcription factor required for the specification of two segments (rhombomeres) of the developing hindbrain. In rhombomere 3, Krox20 is subject to direct positive feedback governed by an autoregulatory enhancer, element A. In contrast, a second enhancer, element C, distant by 70 kb, is active from the initiation of transcription independent of the presence of the KROX20 protein. Here, using both enhancer knock-outs and investigations of chromatin organisation, we show that element C possesses a dual activity: besides its classical enhancer function, it is also permanently required in cis to potentiate the autoregulatory activity of element A, by increasing its chromatin accessibility. This work uncovers a novel, asymmetrical, long-range mode of cooperation between cis-acting elements that might be essential to avoid promiscuous activation of positive autoregulatory elements.</p>',
			'date' => '2017-07-27',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28749941',
			'doi' => '',
			'modified' => '2017-10-23 17:38:21',
			'created' => '2017-10-23 17:38:21',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '3084',
			'name' => 'A transcription factor pulse can prime chromatin for heritable transcriptional memory',
			'authors' => 'Iberg-Badeaux A. et al.',
			'description' => '<p>Short-term and long-term transcriptional memory is the phenomenon whereby the kinetics or magnitude of gene induction is enhanced following a prior induction period. Short-term memory persists within one cell generation or in post-mitotic cells, while long-term memory can survive multiple rounds of cell division. We have developed a tissue culture model to study the epigenetic basis for long-term transcriptional memory (LTTM), and subsequently used this model to better understand the epigenetic mechanisms that enable heritable memory of temporary stimuli. We find that a pulse of transcription factor C/EBP&alpha; induces LTTM on a subset of target genes that survives 9 cell divisions. The chromatin landscape at genes that acquire LTTM is more repressed as compared to those genes that do not exhibit memory, akin to a latent state. We show through ChIP and chemical inhibitor studies that Pol II elongation is important for establishing memory in this model, but that Pol II itself is not retained as part of the memory mechanism. More generally, our work reveals that a transcription factor involved in lineage specification can induce LTTM, and that failure to re-repress chromatin is one epigenetic mechanism underlying transcriptional memory.</p>',
			'date' => '2016-12-05',
			'pmid' => 'http://mcb.asm.org/content/early/2016/11/30/MCB.00372-16.abstract',
			'doi' => '',
			'modified' => '2016-12-20 10:33:32',
			'created' => '2016-12-20 10:33:32',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => array(
			'id' => '3103',
			'name' => 'β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance',
			'authors' => 'Novakovic B. et al.',
			'description' => '<p>Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as lipopolysaccharide (LPS). We apply an integrated epigenomic&nbsp;approach to characterize the molecular events involved in LPS-induced tolerance in a time-dependent manner. Mechanistically, LPS-treated monocytes fail to accumulate active histone marks at promoter and enhancers of genes in the lipid metabolism and phagocytic pathways. Transcriptional inactivity in response to a second LPS exposure in tolerized macrophages is accompanied by failure to deposit active histone marks at promoters of tolerized genes. In contrast, &beta;-glucan partially reverses the LPS-induced tolerance in&nbsp;vitro. Importantly, ex&nbsp;vivo &beta;-glucan treatment of monocytes from volunteers with experimental endotoxemia re-instates their capacity for cytokine production. Tolerance is reversed at the level of distal element histone modification and transcriptional reactivation of otherwise unresponsive genes.</p>',
			'date' => '2016-11-17',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27863248',
			'doi' => '',
			'modified' => '2017-01-03 15:31:46',
			'created' => '2017-01-03 15:31:46',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 21 => array(
			'id' => '3015',
			'name' => 'Enhancer decommissioning by Snail1-induced competitive displacement of TCF7L2 and down-regulation of transcriptional activators results in EPHB2 silencing',
			'authors' => 'Schnappauf O et al.',
			'description' => '<p>Transcriptional silencing is a major cause for the inactivation of tumor suppressor genes, however, the underlying mechanisms are only poorly understood. The EPHB2 gene encodes a receptor tyrosine kinase that controls epithelial cell migration and allocation in intestinal crypts. Through its ability to restrict cell spreading, EPHB2 functions as a tumor suppressor in colorectal cancer whose expression is frequently lost as tumors progress to the carcinoma stage. Previously we reported that EPHB2 expression depends on a transcriptional enhancer whose activity is diminished in EPHB2 non-expressing cells. Here we investigated the mechanisms that lead to EPHB2 enhancer inactivation. We show that expression of EPHB2 and SNAIL1 - an inducer of epithelial-mesenchymal transition (EMT) - is anti-correlated in colorectal cancer cell lines and tumors. In a cellular model of Snail1-induced EMT, we observe that features of active chromatin at the EPHB2 enhancer are diminished upon expression of murine Snail1. We identify the transcription factors FOXA1, MYB, CDX2 and TCF7L2 as EPHB2 enhancer factors and demonstrate that Snail1 indirectly inactivates the EPHB2 enhancer by downregulation of FOXA1 and MYB. In addition, Snail1 induces the expression of Lymphoid enhancer factor 1 (LEF1) which competitively displaces TCF7L2 from the EPHB2 enhancer. In contrast to TCF7L2, however, LEF1 appears to repress the EPHB2 enhancer. Our findings underscore the importance of transcriptional enhancers for gene regulation under physiological and pathological conditions and show that SNAIL1 employs a combinatorial mechanism to inactivate the EPHB2 enhancer based on activator deprivation and competitive displacement of transcription factors.</p>',
			'date' => '2016-08-05',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27504909',
			'doi' => '',
			'modified' => '2016-08-31 09:18:03',
			'created' => '2016-08-31 09:18:03',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '2972',
			'name' => 'cChIP-seq: a robust small-scale method for investigation of histone modifications',
			'authors' => 'Valensisi C et al.',
			'description' => '<div id="__sec1" class="sec sec-first">
<h3>Background</h3>
<p id="__p1" class="p p-first-last">ChIP-seq is highly utilized for mapping histone modifications that are informative about gene regulation and genome annotations. For example, applying ChIP-seq to histone modifications such as H3K4me1 has facilitated generating epigenomic maps of putative enhancers. This powerful technology, however, is limited in its application by the large number of cells required. ChIP-seq involves extensive manipulation of sample material and multiple reactions with limited quality control at each step, therefore, scaling down the number of cells required has proven challenging. Recently, several methods have been proposed to overcome this limit but most of these methods require extensive optimization to tailor the protocol to the specific antibody used or number of cells being profiled.</p>
</div>
<div id="__sec2" class="sec">
<h3>Results</h3>
<p id="__p2" class="p p-first-last">Here we describe a robust, yet facile method, which we named carrier ChIP-seq (cChIP-seq), for use on limited cell amounts. cChIP-seq employs a DNA-free histone carrier in order to maintain the working ChIP reaction scale, removing the need to tailor reactions to specific amounts of cells or histone modifications to be assayed. We have applied our method to three different histone modifications, H3K4me3, H3K4me1 and H3K27me3 in the K562 cell line, and H3K4me1 in H1 hESCs. We successfully obtained epigenomic maps for these histone modifications starting with as few as 10,000 cells. We compared cChIP-seq data to data generated as part of the ENCODE project. ENCODE data are the reference standard in the field and have been generated starting from tens of million of cells. Our results show that cChIP-seq successfully recapitulates bulk data. Furthermore, we showed that the differences observed between small-scale ChIP-seq data and ENCODE data are largely to be due to lab-to-lab variability rather than operating on a reduced scale.</p>
</div>
<div id="__sec3" class="sec">
<h3>Conclusions</h3>
<p id="__p3" class="p p-first-last">Data generated using cChIP-seq are equivalent to reference epigenomic maps from three orders of magnitude more cells. Our method offers a robust and straightforward approach to scale down ChIP-seq to as low as 10,000 cells. The underlying principle of our strategy makes it suitable for being applied to a vast range of chromatin modifications without requiring expensive optimization. Furthermore, our strategy of a DNA-free carrier can be adapted to most ChIP-seq protocols.</p>
</div>',
			'date' => '2015-12-21',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687106/',
			'doi' => ' 10.1186/s12864-015-2285-7',
			'modified' => '2016-07-01 10:05:06',
			'created' => '2016-07-01 10:05:06',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '2869',
			'name' => 'C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis',
			'authors' => 'van Oevelen C, Collombet S, Vicent G, Hoogenkamp M, Lepoivre C, Badeaux A, Bussmann L, Sardina JL, Thieffry D, Beato M, Shi Y, Bonifer C, Graf T',
			'description' => '<section id="abs0020" class="articleHighlights">
<h2 class="sectionTitle">Highlights</h2>
<div class="content">
<p></p>
<ul class="ce-list" id="ulist0010">
<li id="u0010">C/EBP&alpha; activates two classes of prospective myeloid enhancers in B cells</li>
<li id="u0015">Pre-existing enhancers are bound by PU.1 and become hyper-activated by C/EBP&alpha;</li>
<li id="u0020">C/EBP&alpha; acts as a pioneer factor with delayed kinetics on de novo enhancers</li>
<li id="u0025">The two types of enhancers direct myeloid cell fate in B cells and hematopoiesis</li>
</ul>
<p></p>
</div>
</section>
<section class="graphical"></section>
<div class="abstract">
<h2 class="sectionTitle">Summary</h2>
<p>Transcription-factor-induced somatic cell conversions are highly relevant for both basic and clinical research yet their mechanism is not fully understood and it is unclear whether they reflect normal differentiation processes. Here we show that during pre-B-cell-to-macrophage transdifferentiation, C/EBP&alpha; binds to two types of myeloid enhancers in B cells: pre-existing enhancers that are bound by PU.1, providing a platform for incoming C/EBP&alpha;; and de novo enhancers that are targeted by C/EBP&alpha;, acting as a pioneer factor for subsequent binding by PU.1. The order of factor binding dictates the upregulation kinetics of nearby genes. Pre-existing enhancers are broadly active throughout the hematopoietic lineage tree, including B cells. In contrast, de novo enhancers are silent in most cell types except in myeloid cells where they become activated by C/EBP factors. Our data suggest that C/EBP&alpha; recapitulates physiological developmental processes by short-circuiting two macrophage enhancer pathways in pre-B cells.</p>
</div>',
			'date' => '2015-08-11',
			'pmid' => 'http://www.cell.com/stem-cell-reports/abstract/S2213-6711%2815%2900188-5',
			'doi' => 'http://dx.doi.org/10.1016/j.stemcr.2015.06.007',
			'modified' => '2016-03-25 10:23:25',
			'created' => '2016-03-25 10:22:05',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => 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) 25 => array(
			'id' => '2228',
			'name' => 'Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping.',
			'authors' => 'Light N, Adoue V, Ge B, Chen SH, Kwan T, Pastinen T',
			'description' => 'Allele-specific (AS) assessment of chromatin has the potential to elucidate specific cis-regulatory mechanisms, which are predicted to underlie the majority of the known genetic associations to complex disease. However, development of chromatin landscapes at allelic resolution has been challenging since sites of variable signal strength require substantial read depths not commonly applied in sequencing based approaches. In this study, we addressed this by performing parallel analyses of input DNA and chromatin immunoprecipitates (ChIP) on high-density Illumina genotyping arrays. Allele-specificity for the histone modifications H3K4me1, H3K4me3, H3K27ac, H3K27me3, and H3K36me3 was assessed using ChIP samples generated from 14 lymphoblast and 6 fibroblast cell lines. AS-ChIP SNPs were combined into domains and validated using high-confidence ChIP-seq sites. We observed characteristic patterns of allelic-imbalance for each histone-modification around allele-specifically expressed transcripts. Notably, we found H3K4me1 to be significantly anti-correlated with allelic expression (AE) at transcription start sites, indicating H3K4me1 allelic imbalance as a marker of AE. We also found that allelic chromatin domains exhibit population and cell-type specificity as well as heritability within trios. Finally, we observed that a subset of allelic chromatin domains is regulated by DNase I-sensitive quantitative trait loci and that these domains are significantly enriched for genome-wide association studies hits, with autoimmune disease associated SNPs specifically enriched in lymphoblasts. This study provides the first genome-wide maps of allelic-imbalance for five histone marks. Our results provide new insights into the role of chromatin in cis-regulation and highlight the need for high-depth sequencing in ChIP-seq studies along with the need to improve allele-specificity of ChIP-enrichment.',
			'date' => '2014-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25055051',
			'doi' => '',
			'modified' => '2015-07-24 15:39:03',
			'created' => '2015-07-24 15:39:03',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 26 => array(
			'id' => '2054',
			'name' => 'Nuclear ARRB1 induces pseudohypoxia and cellular metabolism reprogramming in prostate cancer',
			'authors' => 'Zecchini V, Madhu B, Russell R, Pértega-Gomes N, Warren A, Gaude E, Borlido J, Stark R, Ireland-Zecchini H, Rao R, Scott H, Boren J, Massie C, Asim M, Brindle K, Griffiths J, Frezza C, Neal DE, Mills IG',
			'description' => 'Tumour cells sustain their high proliferation rate through metabolic reprogramming, whereby cellular metabolism shifts from oxidative phosphorylation to aerobic glycolysis, even under normal oxygen levels. Hypoxia-inducible factor 1A (HIF1A) is a major regulator of this process, but its activation under normoxic conditions, termed pseudohypoxia, is not well documented. Here, using an integrative approach combining the first genome-wide mapping of chromatin binding for an endocytic adaptor, ARRB1, both in vitro and in vivo with gene expression profiling, we demonstrate that nuclear ARRB1 contributes to this metabolic shift in prostate cancer cells via regulation of HIF1A transcriptional activity under normoxic conditions through regulation of succinate dehydrogenase A (SDHA) and fumarate hydratase (FH) expression. ARRB1-induced pseudohypoxia may facilitate adaptation of cancer cells to growth in the harsh conditions that are frequently encountered within solid tumours. Our study is the first example of an endocytic adaptor protein regulating metabolic pathways. It implicates ARRB1 as a potential tumour promoter in prostate cancer and highlights the importance of metabolic alterations in prostate cancer.',
			'date' => '2014-05-16',
			'pmid' => 'http://onlinelibrary.wiley.com/doi/10.15252/embj.201386874/full',
			'doi' => '',
			'modified' => '2015-07-24 15:39:02',
			'created' => '2015-07-24 15:39:02',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 27 => array(
			'id' => '1793',
			'name' => 'A novel microscopy-based high-throughput screening method to identify proteins that regulate global histone modification levels.',
			'authors' => 'Baas R, Lelieveld D, van Teeffelen H, Lijnzaad P, Castelijns B, van Schaik FM, Vermeulen M, Egan DA, Timmers HT, de Graaf P',
			'description' => '<p>Posttranslational modifications of histones play an important role in the regulation of gene expression and chromatin structure in eukaryotes. The balance between chromatin factors depositing (writers) and removing (erasers) histone marks regulates the steady-state levels of chromatin modifications. Here we describe a novel microscopy-based screening method to identify proteins that regulate histone modification levels in a high-throughput fashion. We named our method CROSS, for Chromatin Regulation Ontology SiRNA Screening. CROSS is based on an siRNA library targeting the expression of 529 proteins involved in chromatin regulation. As a proof of principle, we used CROSS to identify chromatin factors involved in histone H3 methylation on either lysine-4 or lysine-27. Furthermore, we show that CROSS can be used to identify chromatin factors that affect growth in cancer cell lines. Taken together, CROSS is a powerful method to identify the writers and erasers of novel and known chromatin marks and facilitates the identification of drugs targeting epigenetic modifications.</p>',
			'date' => '2014-02-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24334265',
			'doi' => '',
			'modified' => '2016-04-12 09:46:40',
			'created' => '2015-07-24 15:39:01',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 28 => array(
			'id' => '1577',
			'name' => 'An In-Depth Characterization of the Major Psoriasis Susceptibility Locus Identifies Candidate Susceptibility Alleles within an HLA-C Enhancer Element.',
			'authors' => 'Clop A, Bertoni A, Spain SL, Simpson MA, Pullabhatla V, Tonda R, Hundhausen C, Di Meglio P, De Jong P, Hayday AC, Nestle FO, Barker JN, Bell RJ, Capon F, Trembath RC',
			'description' => 'Psoriasis is an immune-mediated skin disorder that is inherited as a complex genetic trait. Although genome-wide association scans (GWAS) have identified 36 disease susceptibility regions, more than 50% of the genetic variance can be attributed to a single Major Histocompatibility Complex (MHC) locus, known as PSORS1. Genetic studies indicate that HLA-C is the strongest PSORS1 candidate gene, since markers tagging HLA-Cw*0602 consistently generate the most significant association signals in GWAS. However, it is unclear whether HLA-Cw*0602 is itself the causal PSORS1 allele, especially as the role of SNPs that may affect its expression has not been investigated. Here, we have undertaken an in-depth molecular characterization of the PSORS1 interval, with a view to identifying regulatory variants that may contribute to disease susceptibility. By analysing high-density SNP data, we refined PSORS1 to a 179 kb region encompassing HLA-C and the neighbouring HCG27 pseudogene. We compared multiple MHC sequences spanning this refined locus and identified 144 candidate susceptibility variants, which are unique to chromosomes bearing HLA-Cw*0602. In parallel, we investigated the epigenetic profile of the critical PSORS1 interval and uncovered three enhancer elements likely to be active in T lymphocytes. Finally we showed that nine candidate susceptibility SNPs map within a HLA-C enhancer and that three of these variants co-localise with binding sites for immune-related transcription factors. These data indicate that SNPs affecting HLA-Cw*0602 expression are likely to contribute to psoriasis susceptibility and highlight the importance of integrating multiple experimental approaches in the investigation of complex genomic regions such as the MHC.',
			'date' => '2013-08-19',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23990973',
			'doi' => '',
			'modified' => '2015-07-24 15:39:00',
			'created' => '2015-07-24 15:39:00',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 29 => array(
			'id' => '1512',
			'name' => 'Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus.',
			'authors' => 'Miller CL, Anderson DR, Kundu RK, Raiesdana A, Nürnberg ST, Diaz R, Cheng K, Leeper NJ, Chen CH, Chang IS, Schadt EE, Hsiung CA, Assimes TL, Quertermous T',
			'description' => 'Coronary heart disease (CHD) is the leading cause of mortality in both developed and developing countries worldwide. Genome-wide association studies (GWAS) have now identified 46 independent susceptibility loci for CHD, however, the biological and disease-relevant mechanisms for these associations remain elusive. The large-scale meta-analysis of GWAS recently identified in Caucasians a CHD-associated locus at chromosome 6q23.2, a region containing the transcription factor TCF21 gene. TCF21 (Capsulin/Pod1/Epicardin) is a member of the basic-helix-loop-helix (bHLH) transcription factor family, and regulates cell fate decisions and differentiation in the developing coronary vasculature. Herein, we characterize a cis-regulatory mechanism by which the lead polymorphism rs12190287 disrupts an atypical activator protein 1 (AP-1) element, as demonstrated by allele-specific transcriptional regulation, transcription factor binding, and chromatin organization, leading to altered TCF21 expression. Further, this element is shown to mediate signaling through platelet-derived growth factor receptor beta (PDGFR-β) and Wilms tumor 1 (WT1) pathways. A second disease allele identified in East Asians also appears to disrupt an AP-1-like element. Thus, both disease-related growth factor and embryonic signaling pathways may regulate CHD risk through two independent alleles at TCF21.',
			'date' => '2013-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23874238',
			'doi' => '',
			'modified' => '2015-07-24 15:39:00',
			'created' => '2015-07-24 15:39:00',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 30 => array(
			'id' => '1350',
			'name' => 'Balancing of histone H3K4 methylation states by the Kdm5c/SMCX histone demethylase modulates promoter and enhancer function.',
			'authors' => 'Outchkourov NS, Muiño JM, Kaufmann K, van Ijcken WF, Groot Koerkamp MJ, van Leenen D, de Graaf P, Holstege FC, Grosveld FG, Timmers HT',
			'description' => 'The functional organization of eukaryotic genomes correlates with specific patterns of histone methylations. Regulatory regions in genomes such as enhancers and promoters differ in their extent of methylation of histone H3 at lysine-4 (H3K4), but it is largely unknown how the different methylation states are specified and controlled. Here, we show that the Kdm5c/Jarid1c/SMCX member of the Kdm5 family of H3K4 demethylases can be recruited to both enhancer and promoter elements in mouse embryonic stem cells and in neuronal progenitor cells. Knockdown of Kdm5c deregulates transcription via local increases in H3K4me3. Our data indicate that by restricting H3K4me3 modification at core promoters, Kdm5c dampens transcription, but at enhancers Kdm5c stimulates their activity. Remarkably, an impaired enhancer function activates the intrinsic promoter activity of Kdm5c-bound distal elements. Our results demonstrate that the Kdm5c demethylase plays a crucial and dynamic role in the functional discrimination between enhancers and core promoters.',
			'date' => '2013-04-25',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23545502',
			'doi' => '',
			'modified' => '2015-07-24 15:39:00',
			'created' => '2015-07-24 15:39:00',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 31 => array(
			'id' => '592',
			'name' => 'Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.',
			'authors' => 'Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ',
			'description' => 'The H3K9me3 histone modification is often found at promoter regions, where it functions to repress transcription. However, we have previously shown that 3' exons of zinc finger genes (ZNFs) are marked by high levels of H3K9me3. We have now further investigated this unusual location for H3K9me3 in ZNF genes. Neither bioinformatic nor experimental approaches support the hypothesis that the 3' exons of ZNFs are promoters. We further characterized the histone modifications at the 3' ZNF exons and found that these regions also contain H3K36me3, a mark of transcriptional elongation. A genome-wide analysis of ChIP-seq data revealed that ZNFs constitute the majority of genes that have high levels of both H3K9me3 and H3K36me3. These results suggested the possibility that the ZNF genes may be imprinted, with one allele transcribed and one allele repressed. To test the hypothesis that the contradictory modifications are due to imprinting, we used a SNP analysis of RNA-seq data to demonstrate that both alleles of certain ZNF genes having H3K9me3 and H3K36me3 are transcribed. We next analyzed isolated ZNF 3' exons using stably integrated episomes. We found that although the H3K36me3 mark was lost when the 3' ZNF exon was removed from its natural genomic location, the isolated ZNF 3' exons retained the H3K9me3 mark. Thus, the H3K9me3 mark at ZNF 3' exons does not impede transcription and it is regulated independently of the H3K36me3 mark. Finally, we demonstrate a strong relationship between the number of tandemly repeated domains in the 3' exons and the H3K9me3 mark. We suggest that the H3K9me3 at ZNF 3' exons may function to protect the genome from inappropriate recombination rather than to regulate transcription.',
			'date' => '2011-02-15',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21347206',
			'doi' => '',
			'modified' => '2015-07-24 15:38:58',
			'created' => '2015-07-24 15:38:58',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 32 => array(
			'id' => '261',
			'name' => 'Using ChIP-Seq Technology to Generate High-Resolution Profiles of Histone Modifications ',
			'authors' => 'O’Geen H, Echipare L, Farnham PJ',
			'description' => '<p>The dynamic modification of DNA and histones plays a key role in transcriptional regulation through - altering the packaging of DNA and modifying the nucleosome surface. These chromatin states, also referred to as the epigenome, are distinctive for different tissues, developmental stages, and disease states and can also be altered by environmental influences. New technologies allow the genome-wide visualization of the information encoded in the epigenome. For example, the chromatin immunoprecipitation (ChIP) assay allows investigators to characterize DNA&ndash;protein interactions in vivo. ChIP followed by hybridization to microarrays (ChIP-chip) or by high-throughput sequencing (ChIP-seq) are both powerful tools to identify genome-wide profiles of transcription factors, histone modifications, DNA methylation, and nucleosome positioning. ChIP-seq technology, which can now interrogate the entire human genome at high resolution with only one lane of sequencing, has recently surpassed ChIP-chip technology for epigenomic analyses. Importantly, for the study of primary cells and tissues, epigenetic profiles can be generated using as little as 1 &mu;g of chromatin. In this chapter, we describe in detail the steps involved in performing ChIP assays (with a focus on characterizing histone modifications in primary cells)either manually or using the IP-Star ChIP robot, followed by a detailed protocol to prepare successful libraries for Illumina sequencing. Critical quality control checkpoints are discussed. Although not a focus of this chapter, we also point the reader to several methods by which massive ChIP-seq data sets can be analyzed to extract the tremendous information contained within.</p>',
			'date' => '0000-00-00',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/21913086',
			'doi' => '',
			'modified' => '2016-05-03 12:19:44',
			'created' => '2015-07-24 15:38:57',
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		'id' => '2202',
		'antibody_id' => '110',
		'name' => 'H3K4me1 Antibody',
		'description' => '<p><span>Polyclonal antibody raised in rabbit against histone <strong>H3 containing the monomethylated lysine 4</strong> (<strong>H3K4me1</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
		'label1' => 'Validation Data',
		'info1' => '<div class="row">
<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
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<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
</div>
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<div class="row">
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<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
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<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
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<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
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<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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	'description' => '<p><span>Polyclonal antibody raised in rabbit against histone <strong>H3 containing the monomethylated lysine 4</strong> (<strong>H3K4me1</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
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<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
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<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
<div class="extra-spaced"></div>
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<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
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</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
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<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
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<div class="small-7 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
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<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
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<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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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include - APP/View/Products/view.ctp, line 755
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 193
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
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<td>1:500</td>
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		'name' => 'H3K4me1 polyclonal antibody (sample size)',
		'description' => '<p>Polyclonal antibody raised in rabbit against histone H3 containing the monomethylated lysine 4 (H3K4me1), using a KLH-conjugated synthetic peptide.</p>',
		'label1' => 'Validation Data',
		'info1' => '<div class="row">
<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
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<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
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<div class="extra-spaced"></div>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
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<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_DotBlot.png" alt="H3K4me1 Antibody Dot Blot Validation " /></p>
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<div class="small-7 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
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<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
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</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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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		'classification' => 'Classic',
		'application_table' => '<table>
<thead>
<tr>
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<th>Suggested dilution</th>
<th>References</th>
</tr>
</thead>
<tbody>
<tr>
<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>1-2 &mu;g/IP</td>
<td>Fig 1, 2</td>
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<tr>
<td>ELISA</td>
<td>1:500</td>
<td>Fig 3</td>
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<tr>
<td>Dot Blotting</td>
<td>1:10,000</td>
<td>Fig 4</td>
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<tr>
<td>Western Blotting</td>
<td>1:500</td>
<td>Fig 5</td>
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<tr>
<td>Immunofluorescence</td>
<td>1:500</td>
<td>Fig 6</td>
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<p></p>
<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 &mu;g per IP.</small></p>',
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			'description' => '<p><span>Polyclonal antibody raised in rabbit against histone <strong>H3 containing the monomethylated lysine 4</strong> (<strong>H3K4me1</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
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<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
</div>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
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<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
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<div class="row">
<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_DotBlot.png" alt="H3K4me1 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-7 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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>Learn more about: <a href="https://www.diagenode.com/applications/western-blot">Loading control, MW marker visualization</a><em>. <br /></em></p>
<p><em></em>Check our selection of antibodies validated in Western blot.</p>',
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			'description' => '<h1><strong>Validated epigenetics antibodies</strong>&nbsp;&ndash; care for a sample?<br />&nbsp;</h1>
<p>Diagenode has partnered with leading epigenetics experts and numerous epigenetics consortiums to bring to you a validated and comprehensive collection of epigenetic antibodies. As an expert in epigenetics, we are committed to offering highly-specific antibodies validated for ChIP/ChIP-seq and many other applications. All batch-specific validation data is available on our website.<br /><a href="../categories/antibodies">Read about our expertise in antibody production</a>.</p>
<ul>
<li><strong>Focused</strong> -&nbsp;Diagenode's selection of antibodies is exclusively dedicated for epigenetic research. <a title="See the full collection." href="../categories/all-antibodies">See the full collection.</a></li>
<li><strong>Strict quality standards</strong>&nbsp;with rigorous QC and validation</li>
<li><strong>Classified</strong>&nbsp;based on level of validation for flexibility of application</li>
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<p>Existing sample sizes are listed below. We will soon expand our collection. &nbsp;Are you looking for a sample size of another antibody? Just <a href="mailto:agnieszka.zelisko@diagenode.com?Subject=Sample%20Size%20Request" target="_top">Contact us</a>.</p>',
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			'description' => '<p><span style="font-weight: 400;">All Diagenode&rsquo;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&rsquo;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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			'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>
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<div class="small-12 medium-9 large-9 columns">
<p><strong>ChIP-seq profile</strong> of active (H3K4me3 and H3K36me3) and inactive (H3K27me3) marks using Diagenode antibodies.</p>
<img src="https://www.diagenode.com/img/categories/antibodies/chip-seq-grade-antibodies.png" /></div>
<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 &micro;g of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 &micro;g 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&rsquo;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_description' => 'Diagenode Offers Wide Range of Validated ChIP-Seq Grade Antibodies for Unparalleled ChIP-Seq Results',
			'meta_title' => 'Chromatin Immunoprecipitation ChIP-Seq Grade Antibodies | Diagenode',
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			'name' => 'ChIP-grade antibodies',
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<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
<p></p>
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<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>).&nbsp;</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" />&nbsp;</div>
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<p></p>
<p></p>
<p></p>
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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' => 'Histone antibodies',
			'description' => '<p>Histones are the main protein components of chromatin involved in the compaction of DNA into nucleosomes, the basic units of chromatin. A <strong>nucleosome</strong> consists of one pair of each of the core histones (<strong>H2A</strong>, <strong>H2B</strong>, <strong>H3</strong> and <strong>H4</strong>) forming an octameric structure wrapped by 146 base pairs of DNA. The different nucleosomes are linked by the linker histone<strong> H1, </strong>allowing for further condensation of chromatin.</p>
<p>The core histones have a globular structure with large unstructured N-terminal tails protruding from the nucleosome.&nbsp; They can undergo to multiple post-translational modifications (PTM), mainly at the N-terminal tails. These <strong>post-translational modifications </strong>include&nbsp; methylation, acetylation, phosphorylation, ubiquitinylation, citrullination, sumoylation, deamination and crotonylation.&nbsp; The most well characterized PTMs are <strong>methylation,</strong> <strong>acetylation and phosphorylation</strong>. Histone methylation occurs mainly on lysine (K) residues, which can be mono-, di- or tri-methylated, and on arginines (R), which can be mono-methylated and symmetrically or asymmetrically di-methylated. Histone acetylation occurs on lysines and histone phosphorylation mainly on serines (S), threonines (T) and tyrosines (Y).</p>
<p>The PTMs of the different residues are involved in numerous processes such as DNA repair, DNA replication and chromosome condensation. They influence the chromatin organization and can be positively or negatively associated with gene expression. Trimethylation of H3K4, H3K36 and H3K79, and lysine acetylation generally result in an open chromatin configuration (figure below) and are therefore associated with <strong>euchromatin</strong> and gene activation. Trimethylation of H3K9, K3K27 and H4K20, on the other hand, is enriched in <strong>heterochromatin </strong>and associated with gene silencing. The combination of different histone modifications is called the "<strong>histone code</strong>&rdquo;, analogous to the genetic code.</p>
<p><img src="https://www.diagenode.com/img/categories/antibodies/histone-marks-illustration.png" /></p>
<p>Diagenode is proud to offer a large range of antibodies against histones and histone modifications. Our&nbsp; antibodies are highly specific and have been validated in many applications, including <strong>ChIP</strong> and <strong>ChIP-seq</strong>.</p>
<p>Diagenode&rsquo;s collection includes antibodies recognizing:</p>
<ul>
<li><strong>Histone H1 variants</strong></li>
<li><strong>Histone H2A, H2A variants and histone H2A</strong> <strong>modifications</strong> (serine phosphorylation, lysine acetylation, lysine ubiquitinylation)</li>
<li><strong>Histone H2B and H2B</strong> <strong>modifications </strong>(serine phosphorylation, lysine acetylation)</li>
<li><strong>Histone H3 and H3 modifications </strong>(lysine methylation (mono-, di- and tri-methylated), lysine acetylation, serine phosphorylation, threonine phosphorylation, arginine methylation (mono-methylated, symmetrically and asymmetrically di-methylated))</li>
<li><strong>Histone H4 and H4 modifications (</strong>lysine methylation (mono-, di- and tri-methylated), lysine acetylation, arginine methylation (mono-methylated and symmetrically di-methylated), serine phosphorylation )</li>
</ul>
<p><span style="font-weight: 400;"><strong>HDAC's HAT's, HMT's and other</strong> <strong>enzymes</strong> which modify histones can be found in the category <a href="../categories/chromatin-modifying-proteins-histone-transferase">Histone modifying enzymes</a><br /></span></p>
<p><span style="font-weight: 400;"> Diagenode&rsquo;s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Expert technical support</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sample sizes available</span></li>
<li><span style="font-weight: 400;"> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 100% satisfaction guarantee</span></li>
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			'meta_keywords' => 'Histone, antibody, histone h1, histone h2, histone h3, histone h4',
			'meta_description' => 'Polyclonal and Monoclonal Antibodies against Histones and their modifications validated for many applications, including Chromatin Immunoprecipitation (ChIP) and ChIP-Sequencing (ChIP-seq)',
			'meta_title' => 'Histone and Modified Histone Antibodies | Diagenode',
			'modified' => '2020-09-17 13:34:56',
			'created' => '2016-04-01 16:01:32',
			'ProductsCategory' => array(
				[maximum depth reached]
			),
			'CookiesTag' => array([maximum depth reached])
		)
	),
	'Document' => array(
		(int) 0 => array(
			'id' => '11',
			'name' => 'Antibodies you can trust',
			'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
			'image_id' => null,
			'type' => 'Poster',
			'url' => 'files/posters/Antibodies_you_can_trust_Poster.pdf',
			'slug' => 'antibodies-you-can-trust-poster',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2015-10-01 20:18:31',
			'created' => '2015-07-03 16:05:15',
			'ProductsDocument' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => 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>',
			'image_id' => null,
			'type' => 'Brochure',
			'url' => 'files/brochures/Epigenetic_Antibodies_Brochure.pdf',
			'slug' => 'epigenetic-antibodies-brochure',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2016-06-15 11:24:06',
			'created' => '2015-07-03 16:05:27',
			'ProductsDocument' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '342',
			'name' => 'Datasheet H3K4me1 C15410037',
			'description' => '<p><span>Polyclonal antibody raised in rabbit against histone H3 containing the monomethylated lysine 4 (H3K4me1), using a KLH-conjugated synthetic peptide.</span></p>',
			'image_id' => null,
			'type' => 'Datasheet',
			'url' => 'files/products/antibodies/Datasheet_H3K4me1_C15410037.pdf',
			'slug' => 'datasheet-h3k4me1-C15410037',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2015-11-20 17:38:09',
			'created' => '2015-07-07 11:47:44',
			'ProductsDocument' => array(
				[maximum depth reached]
			)
		)
	),
	'Feature' => array(),
	'Image' => array(
		(int) 0 => array(
			'id' => '1783',
			'name' => 'product/antibodies/chipseq-grade-ab-icon.png',
			'alt' => 'ChIP-seq Grade',
			'modified' => '2020-11-27 07:04:40',
			'created' => '2018-03-15 15:54:09',
			'ProductsImage' => array(
				[maximum depth reached]
			)
		)
	),
	'Promotion' => array(),
	'Protocol' => array(),
	'Publication' => array(
		(int) 0 => array(
			'id' => '4977',
			'name' => 'Single-cell multi-omics, spatial transcriptomics and systematic perturbation decode circuitry of neural crest fate decisions',
			'authors' => 'Hu Z. et al.',
			'description' => '<p><span>Cranial neural crest (NC) cells, which can migrate, adopt multiple fates, and form most of the craniofacial skeleton, are an excellent model for studying cell fate decisions. Using time-resolved single-cell multi-omics, spatial transcriptomics, and systematic Perturb-seq, we fully deciphered zebrafish cranial NC programs, including 23 cell states and three spatial trajectories, reconstructed and tested the complete gene regulatory network (GRN). Our GRN model, combined with a novel velocity-embedded simulation method, accurately predicted functions of all major regulons, with over a 3-fold increase in correlation between in vivo and in silico perturbations. Using our new approach based on regulatory synchronization, we discovered a post-epithelial-mesenchymal-transition endothelial-like program crucial for migration, identified motif coordinators for dual-fate priming, and quantified lineage-specific cooperative transcription factor functions. This study provides a comprehensive and validated NC regulatory landscape with unprecedented resolution, offering general regulatory models for cell fate decisions in vertebrates.</span></p>',
			'date' => '2024-09-17',
			'pmid' => 'https://www.biorxiv.org/content/10.1101/2024.09.17.613303v1',
			'doi' => ' https://doi.org/10.1101/2024.09.17.613303',
			'modified' => '2024-09-24 12:23:31',
			'created' => '2024-09-24 12:23:31',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'id' => '4943',
			'name' => 'KRAS promotes GLI2-dependent transcription during pancreatic carcinogenesis',
			'authors' => 'Sigafoos A.N. et al.',
			'description' => '<p><span>Aberrant activation of GLI transcription factors has been implicated in the pathogenesis of different tumor types including pancreatic ductal adenocarcinoma (PDAC). However, the mechanistic link with established drivers of this disease remains in part elusive. Here, using a new genetically-engineered mouse model overexpressing constitutively active mouse form of GLI2 and a combination of genome wide assays, we provide evidence of a novel mechanism underlying the interplay between KRAS, a major driver of PDAC development, and GLI2 to control oncogenic gene expression. These mice, also expressing KrasG12D, show significantly reduced median survival rate and accelerated tumorigenesis compared to the KrasG12D only expressing mice. Analysis of the mechanism using RNA-seq demonstrate higher levels of GLI2 targets, particularly tumor growth promoting genes including Ccnd1, N-Myc and Bcl2, in KrasG12D mutant cells. Further, ChIP-seq studies showed that in these cells KrasG12D increases the levels of H3K4me3 at the promoter of GLI2 targets without affecting significantly the levels of other major active chromatin marks. Importantly, Gli2 knockdown reduces H3K4me3 enrichment and gene expression induced by mutant Kras. In summary, we demonstrate that Gli2 plays a significant role in pancreatic carcinogenesis by acting as a downstream effector of KrasG12D to control gene expression.</span></p>',
			'date' => '2024-06-24',
			'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/38896052/',
			'doi' => '10.1158/2767-9764.CRC-23-0464',
			'modified' => '2024-06-24 17:07:26',
			'created' => '2024-06-24 17:07:26',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '4925',
			'name' => 'Chromatin profiling reveals TFAP4 as a critical transcriptional regulator of bovine satellite cell differentiation',
			'authors' => 'Pengcheng Lyu et al.',
			'description' => '<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Background</h3>
<p>Satellite cells are myogenic precursor cells in adult skeletal muscle and play a crucial role in skeletal muscle regeneration, maintenance, and growth. Like embryonic myoblasts, satellite cells have the ability to proliferate, differentiate, and fuse to form multinucleated myofibers. In this study, we aimed to identify additional transcription factors that control gene expression during bovine satellite cell proliferation and differentiation.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Results</h3>
<p>Using chromatin immunoprecipitation followed by sequencing, we identified 56,973 and 54,470 genomic regions marked with both the histone modifications H3K4me1 and H3K27ac, which were considered active enhancers, and 50,956 and 59,174 genomic regions marked with H3K27me3, which were considered repressed enhancers, in proliferating and differentiating bovine satellite cells, respectively. In addition, we identified 1,216 and 1,171 super-enhancers in proliferating and differentiating bovine satellite cells, respectively. Analyzing these enhancers showed that in proliferating bovine satellite cells, active enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation whereas repressed enhancers were associated with genes essential for myoblast differentiation, and that in differentiating satellite cells, active enhancers were associated with genes essential for myoblast differentiation or muscle contraction whereas repressed enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation. Active enhancers in proliferating bovine satellite cells were enriched with binding sites for many transcription factors such as MYF5 and the AP-1 family transcription factors; active enhancers in differentiating bovine satellite cells were enriched with binding sites for many transcription factors such as MYOG and TFAP4; and repressed enhancers in both proliferating and differentiating bovine satellite cells were enriched with binding sites for NF-kB, ZEB-1, and several other transcription factors. The role of TFAP4 in satellite cell or myoblast differentiation was previously unknown, and through gene knockdown and overexpression, we experimentally validated a critical role for TFAP4 in the differentiation and fusion of bovine satellite cells into myofibers.</p>
<h3 class="c-article__sub-heading" data-test="abstract-sub-heading">Conclusions</h3>
<p>Satellite cell proliferation and differentiation are controlled by many transcription factors such as AP-1, TFAP4, NF-kB, and ZEB-1 whose roles in these processes were previously unknown in addition to those transcription factors such as MYF5 and MYOG whose roles in these processes are widely known.</p>',
			'date' => '2024-03-12',
			'pmid' => 'https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10189-2',
			'doi' => 'https://doi.org/10.1186/s12864-024-10189-2',
			'modified' => '2024-03-15 15:06:06',
			'created' => '2024-03-15 15:06:06',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'id' => '4822',
			'name' => 'RUNX1 colludes with NOTCH1 to reprogram chromatin in T-cell acutelymphoblastic leukemia',
			'authors' => 'Islam  R. et al.',
			'description' => '<p><span>Runt-related transcription factor 1 (RUNX1) is oncogenic in diverse types of leukemia and epithelial cancers where its expression is associated with poor prognosis. Current models suggest that RUNX1 cooperates with other oncogenic factors (e.g., NOTCH1, TAL1) to drive the expression of proto-oncogenes in T&nbsp;cell acute lymphoblastic leukemia (T-ALL) but the molecular mechanisms controlled by RUNX1 and its cooperation with other factors remain unclear. Integrative chromatin and transcriptional analysis following inhibition of RUNX1 and NOTCH1 revealed a surprisingly widespread role of RUNX1 in the establishment of global H3K27ac levels and that RUNX1 is required by NOTCH1 for cooperative transcription activation of key NOTCH1 target genes including&nbsp;</span><em>MYC, DTX1, HES4, IL7R,</em><span><span>&nbsp;</span>and<span>&nbsp;</span></span><em>NOTCH3</em><span>. Super-enhancers were preferentially sensitive to RUNX1 knockdown and RUNX1-dependent super-enhancers were disrupted following the treatment of a pan-BET inhibitor, I-BET151.</span></p>',
			'date' => '2023-05-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.isci.2023.106795',
			'doi' => '10.1016/j.isci.2023.106795',
			'modified' => '2023-06-19 10:14:27',
			'created' => '2023-06-13 21:11:31',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 4 => array(
			'id' => '4748',
			'name' => 'Incomplete transcriptional dosage compensation of vertebrate sexchromosomes is balanced by post-transcriptional compensation',
			'authors' => 'Lister  N. C. et al.',
			'description' => '<p>Heteromorphic sex chromosomes (XY or ZW) present problems of gene dosage imbalance between the sexes, and with the autosomes. Mammalian X chromosome inactivation was long thought to imply a critical need for dosage compensation in vertebrates. However, the universal importance of sex chromosome dosage compensation was questioned by mRNA abundance measurements that demonstrated sex chromosome transcripts are neither balanced between the sexes or with autosomes in monotreme mammals or birds. Here, we demonstrate unbalanced mRNA levels of X genes in platypus males and females that correlate with differential loading of histone modifications, and confirm that transcripts of Z genes are unbalanced between males and females also in chicken. However, we found that in both species, median male to female protein abundance ratios were 1:1, implying an additional level of post-transcriptional control. We conclude that parity of sex chromosome output is achieved in birds, as well as all mammal groups, by a combination of transcriptional and post-transcriptional control, consistent with an essential role for sex chromosome dosage compensation in vertebrates.</p>',
			'date' => '2023-02-01',
			'pmid' => 'https://doi.org/10.1101%2F2023.02.23.529605',
			'doi' => '10.1101/2023.02.23.529605',
			'modified' => '2023-06-14 08:59:05',
			'created' => '2023-03-02 17:27:08',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '4605',
			'name' => 'Gene Regulatory Interactions at Lamina-Associated Domains',
			'authors' => 'Madsen-Østerbye  J. et al.',
			'description' => '<p>The nuclear lamina provides a repressive chromatin environment at the nuclear periphery. However, whereas most genes in lamina-associated domains (LADs) are inactive, over ten percent reside in local euchromatic contexts and are expressed. How these genes are regulated and whether they are able to interact with regulatory elements remain unclear. Here, we integrate publicly available enhancer-capture Hi-C data with our own chromatin state and transcriptomic datasets to show that inferred enhancers of active genes in LADs are able to form connections with other enhancers within LADs and outside LADs. Fluorescence in situ hybridization analyses show proximity changes between differentially expressed genes in LADs and distant enhancers upon the induction of adipogenic differentiation. We also provide evidence of involvement of lamin A/C, but not lamin B1, in repressing genes at the border of an in-LAD active region within a topological domain. Our data favor a model where the spatial topology of chromatin at the nuclear lamina is compatible with gene expression in this dynamic nuclear compartment.</p>',
			'date' => '2023-01-01',
			'pmid' => 'https://doi.org/10.3390%2Fgenes14020334',
			'doi' => '10.3390/genes14020334',
			'modified' => '2023-04-04 08:57:32',
			'created' => '2023-02-21 09:59:46',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '4490',
			'name' => 'Repression and 3D-restructuring resolves regulatory conflicts inevolutionarily rearranged genomes.',
			'authors' => 'Ringel  A. et al.',
			'description' => '<p>Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36179666',
			'doi' => '10.1016/j.cell.2022.09.006',
			'modified' => '2022-11-18 12:39:16',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '4417',
			'name' => 'HOTAIR interacts with PRC2 complex regulating the regional preadipocytetranscriptome and human fat distribution.',
			'authors' => 'Kuo  Feng-Chih et al.',
			'description' => '<p>Mechanisms governing regional human adipose tissue (AT) development remain undefined. Here, we show that the long non-coding RNA HOTAIR (HOX transcript antisense RNA) is exclusively expressed in gluteofemoral AT, where it is essential for adipocyte development. We find that HOTAIR interacts with polycomb repressive complex 2 (PRC2) and we identify core HOTAIR-PRC2 target genes involved in adipocyte lineage determination. Repression of target genes coincides with PRC2 promoter occupancy and H3K27 trimethylation. HOTAIR is also involved in modifying the gluteal adipocyte transcriptome through alternative splicing. Gluteal-specific expression of HOTAIR is maintained by defined regions of open chromatin across the HOTAIR promoter. HOTAIR expression levels can be modified by hormonal (estrogen, glucocorticoids) and genetic variation (rs1443512 is a HOTAIR eQTL associated with reduced gynoid fat mass). These data identify HOTAIR as a dynamic regulator of the gluteal adipocyte transcriptome and epigenome with functional importance for human regional AT development.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35905723',
			'doi' => '10.1016/j.celrep.2022.111136',
			'modified' => '2022-09-27 14:41:23',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '4524',
			'name' => 'Local euchromatin enrichment in lamina-associated domains anticipatestheir repositioning in the adipogenic lineage.',
			'authors' => 'Madsen-Østerbye  J. et al.',
			'description' => '<p>BACKGROUND: Interactions of chromatin with the nuclear lamina via lamina-associated domains (LADs) confer structural stability to the genome. The dynamics of positioning of LADs during differentiation, and how LADs impinge on developmental gene expression, remains, however, elusive. RESULTS: We examined changes in the association of lamin B1 with the genome in the first 72 h of differentiation of adipose stem cells into adipocytes. We demonstrate a repositioning of entire stand-alone LADs and of LAD edges as a prominent nuclear structural feature of early adipogenesis. Whereas adipogenic genes are released from LADs, LADs sequester downregulated or repressed genes irrelevant for the adipose lineage. However, LAD repositioning only partly concurs with gene expression changes. Differentially expressed genes in LADs, including LADs conserved throughout differentiation, reside in local euchromatic and lamin-depleted sub-domains. In these sub-domains, pre-differentiation histone modification profiles correlate with the LAD versus inter-LAD outcome of these genes during adipogenic commitment. Lastly, we link differentially expressed genes in LADs to short-range enhancers which overall co-partition with these genes in LADs versus inter-LADs during differentiation. CONCLUSIONS: We conclude that LADs are predictable structural features of adipose nuclear architecture that restrain non-adipogenic genes in a repressive environment.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35410387',
			'doi' => '10.1186/s13059-022-02662-6',
			'modified' => '2022-11-24 09:08:01',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '4326',
			'name' => 'Loss of KMT2C reprograms the epigenomic landscape in hPSCsresulting in NODAL overexpression and a failure of hemogenic endotheliumspecification.',
			'authors' => 'Maurya Shailendra et al.',
			'description' => '<p>Germline or somatic variation in the family of KMT2 lysine methyltransferases have been associated with a variety of congenital disorders and cancers. Notably, -fusions are prevalent in 70\% of infant leukaemias but fail to phenocopy short latency leukaemogenesis in mammalian models, suggesting additional factors are necessary for transformation. Given the lack of additional somatic mutation, the role of epigenetic regulation in cell specification, and our prior results of germline variation in infant leukaemia patients, we hypothesized that germline dysfunction of KMT2C altered haematopoietic specification. In isogenic KO hPSCs, we found genome-wide differences in histone modifications at active and poised enhancers, leading to gene expression profiles akin to mesendoderm rather than mesoderm highlighted by a significant increase in NODAL expression and WNT inhibition, ultimately resulting in a lack of hemogenic endothelium specification. These unbiased multi-omic results provide new evidence for germline mechanisms increasing risk of early leukaemogenesis.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://doi.org/10.1080%2F15592294.2021.1954780',
			'doi' => '10.1080/15592294.2021.1954780',
			'modified' => '2022-06-20 09:27:45',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '4196',
			'name' => 'Functional annotations of three domestic animal genomes provide vitalresources for comparative and agricultural research.',
			'authors' => 'Kern C. et al.',
			'description' => '<p>Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight diverse tissues in three important agricultural species: chicken (Gallus gallus), pig (Sus scrofa), and cattle (Bos taurus). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of divergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://doi.org/10.1038%2Fs41467-021-22100-8',
			'doi' => '10.1038/s41467-021-22100-8',
			'modified' => '2022-01-06 14:30:41',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '3711',
			'name' => 'Long intergenic non-coding RNAs regulate human lung fibroblast function: Implications for idiopathic pulmonary fibrosis.',
			'authors' => 'Hadjicharalambous MR, Roux BT, Csomor E, Feghali-Bostwick CA, Murray LA, Clarke DL, Lindsay MA',
			'description' => '<p>Phenotypic changes in lung fibroblasts are believed to contribute to the development of Idiopathic Pulmonary Fibrosis (IPF), a progressive and fatal lung disease. Long intergenic non-coding RNAs (lincRNAs) have been identified as novel regulators of gene expression and protein activity. In non-stimulated cells, we observed reduced proliferation and inflammation but no difference in the fibrotic response of IPF fibroblasts. These functional changes in non-stimulated cells were associated with changes in the expression of the histone marks, H3K4me1, H3K4me3 and H3K27ac indicating a possible involvement of epigenetics. Following activation with TGF-&beta;1 and IL-1&beta;, we demonstrated an increased fibrotic but reduced inflammatory response in IPF fibroblasts. There was no significant difference in proliferation following PDGF exposure. The lincRNAs, LINC00960 and LINC01140 were upregulated in IPF fibroblasts. Knockdown studies showed that LINC00960 and LINC01140 were positive regulators of proliferation in both control and IPF fibroblasts but had no effect upon the fibrotic response. Knockdown of LINC01140 but not LINC00960 increased the inflammatory response, which was greater in IPF compared to control fibroblasts. Overall, these studies demonstrate for the first time that lincRNAs are important regulators of proliferation and inflammation in human lung fibroblasts and that these might mediate the reduced inflammatory response observed in IPF-derived fibroblasts.</p>',
			'date' => '2019-04-15',
			'pmid' => 'http://www.pubmed.gov/30988425',
			'doi' => '10.1038/s41598-019-42292-w',
			'modified' => '2019-07-05 14:31:28',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '3660',
			'name' => 'Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia.',
			'authors' => 'Wernig-Zorc S, Yadav MP, Kopparapu PK, Bemark M, Kristjansdottir HL, Andersson PO, Kanduri C, Kanduri M',
			'description' => '<p>BACKGROUND: Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic and diagnostic implications for several cancers. However, there is no global study exploring the role of 5-hydroxymethylcytosine (5-hmC) levels in CLL. Herein, using mass spectrometry and hMeDIP-sequencing, we analysed the dynamics of 5-hmC during B cell maturation and CLL pathogenesis. RESULTS: We show that na&iuml;ve B-cells had higher levels of 5-hmC and 5-mC compared to non-class switched and class-switched memory B-cells. We found a significant decrease in global 5-mC levels in CLL patients (n&thinsp;=&thinsp;15) compared to na&iuml;ve and memory B cells, with no changes detected between the CLL prognostic groups. On the other hand, global 5-hmC levels of CLL patients were similar to memory B cells and reduced compared to na&iuml;ve B cells. Interestingly, 5-hmC levels were increased at regulatory regions such as gene-body, CpG island shores and shelves and 5-hmC distribution over the gene-body positively correlated with degree of transcriptional activity. Importantly, CLL samples showed aberrant 5-hmC and 5-mC pattern over gene-body compared to well-defined patterns in normal B-cells. Integrated analysis of 5-hmC and RNA-sequencing from CLL datasets identified three novel oncogenic drivers that could have potential roles in CLL development and progression. CONCLUSIONS: Thus, our study suggests that the global loss of 5-hmC, accompanied by its significant increase at the gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Our combined analysis of 5-mC and 5-hmC sequencing provided insights into the potential role of 5-hmC in modulating gene expression changes during CLL pathogenesis.</p>',
			'date' => '2019-01-07',
			'pmid' => 'http://www.pubmed.gov/30616658',
			'doi' => '10.1186/s13072‑018‑0252‑7',
			'modified' => '2019-07-01 11:46:16',
			'created' => '2019-06-21 14:55:31',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '3396',
			'name' => 'The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity',
			'authors' => 'Domínguez-Andrés Jorge, Novakovic Boris, Li Yang, Scicluna Brendon P., Gresnigt Mark S., Arts Rob J.W., Oosting Marije, Moorlag Simone J.C.F.M., Groh Laszlo A., Zwaag Jelle, Koch Rebecca M., ter Horst Rob, Joosten Leo A.B., Wijmenga Cisca, Michelucci Ales',
			'description' => '<p>Sepsis involves simultaneous hyperactivation of the immune system and immune paralysis, leading to both organ dysfunction and increased susceptibility to secondary infections. Acute activation of myeloid cells induced itaconate synthesis, which subsequently mediated innate immune tolerance in human monocytes. In contrast, induction of trained immunity by b-glucan counteracted tolerance induced in a model of human endotoxemia by inhibiting the expression of immune-responsive gene 1 (IRG1), the enzyme that controls itaconate synthesis. b-Glucan also increased the expression of succinate dehydrogenase (SDH), contributing to the integrity of the TCA cycle and leading to an enhanced innate immune response after secondary stimulation. The role of itaconate was further validated by IRG1 and SDH polymorphisms that modulate induction of tolerance and trained immunity in human monocytes. These data demonstrate the importance of the IRG1-itaconateSDH axis in the development of immune tolerance and training and highlight the potential of b-glucaninduced trained immunity to revert immunoparalysis.</p>',
			'date' => '2018-10-01',
			'pmid' => 'http://www.pubmed.gov/30293776',
			'doi' => '10.1016/j.cmet.2018.09.003',
			'modified' => '2018-11-22 15:18:30',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '3469',
			'name' => 'Increased H3K9 methylation and impaired expression of Protocadherins are associated with the cognitive dysfunctions of the Kleefstra syndrome.',
			'authors' => 'Iacono G, Dubos A, Méziane H, Benevento M, Habibi E, Mandoli A, Riet F, Selloum M, Feil R, Zhou H, Kleefstra T, Kasri NN, van Bokhoven H, Herault Y, Stunnenberg HG',
			'description' => '<p>Kleefstra syndrome, a disease with intellectual disability, autism spectrum disorders and other developmental defects is caused in humans by haploinsufficiency of EHMT1. Although EHMT1 and its paralog EHMT2 were shown to be histone methyltransferases responsible for deposition of the di-methylated H3K9 (H3K9me2), the exact nature of epigenetic dysfunctions in Kleefstra syndrome remains unknown. Here, we found that the epigenome of Ehmt1+/- adult mouse brain displays a marked increase of H3K9me2/3 which correlates with impaired expression of protocadherins, master regulators of neuronal diversity. Increased H3K9me3 was present already at birth, indicating that aberrant methylation patterns are established during embryogenesis. Interestingly, we found that Ehmt2+/- mice do not present neither the marked increase of H3K9me2/3 nor the cognitive deficits found in Ehmt1+/- mice, indicating an evolutionary diversification of functions. Our finding of increased H3K9me3 in Ehmt1+/- mice is the first one supporting the notion that EHMT1 can quench the deposition of tri-methylation by other Histone methyltransferases, ultimately leading to impaired neurocognitive functioning. Our insights into the epigenetic pathophysiology of Kleefstra syndrome may offer guidance for future developments of therapeutic strategies for this disease.</p>',
			'date' => '2018-06-01',
			'pmid' => 'http://www.pubmed.gov/29554304',
			'doi' => '10.1093/nar/gky196',
			'modified' => '2019-02-15 21:04:02',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '3539',
			'name' => 'A long range distal enhancer controls temporal fine-tuning of PAX6 expression in neuronal precursors.',
			'authors' => 'Lacomme M, Medevielle F, Bourbon HM, Thierion E, Kleinjan DJ, Roussat M, Pituello F, Bel-Vialar S',
			'description' => '<p>Proper embryonic development relies on a tight control of spatial and temporal gene expression profiles in a highly regulated manner. One good example is the ON/OFF switching of the transcription factor PAX6 that governs important steps of neurogenesis. In the neural tube PAX6 expression is initiated in neural progenitors through the positive action of retinoic acid signaling and downregulated in neuronal precursors by the bHLH transcription factor NEUROG2. How these two regulatory inputs are integrated at the molecular level to properly fine tune temporal PAX6 expression is not known. In this study we identified and characterized a 940-bp long distal cis-regulatory module (CRM), located far away from the PAX6 transcription unit and which conveys positive input from RA signaling pathway and indirect repressive signal(s) from NEUROG2. These opposing regulatory signals are integrated through HOMZ, a 94 bp core region within E940 which is evolutionarily conserved in distant organisms such as the zebrafish. We show that within HOMZ, NEUROG2 and RA exert their opposite temporal activities through a short 60 bp region containing a functional RA-responsive element (RARE). We propose a model in which retinoic acid receptors (RARs) and NEUROG2 repressive target(s) compete on the same DNA motif to fine tune temporal PAX6 expression during the course of spinal neurogenesis.</p>',
			'date' => '2018-04-15',
			'pmid' => 'http://www.pubmed.gov/29486153',
			'doi' => '10.1016/j.ydbio.2018.02.015',
			'modified' => '2019-02-28 10:42:57',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '3542',
			'name' => 'Inhibition of Methyltransferase Setd7 Allows the In Vitro Expansion of Myogenic Stem Cells with Improved Therapeutic Potential.',
			'authors' => 'Judson RN, Quarta M, Oudhoff MJ, Soliman H, Yi L, Chang CK, Loi G, Vander Werff R, Cait A, Hamer M, Blonigan J, Paine P, Doan LTN, Groppa E, He W, Su L, Zhang RH, Xu P, Eisner C, Low M, Barta I, Lewis CB, Zaph C, Karimi MM, Rando TA, Rossi FM',
			'description' => '<p>The development of cell therapy for repairing damaged or diseased skeletal muscle has been hindered by the inability to significantly expand immature, transplantable myogenic stem cells (MuSCs) in&nbsp;culture. To overcome this limitation, a deeper understanding of the mechanisms regulating the transition between activated, proliferating MuSCs and differentiation-primed, poorly engrafting progenitors is needed. Here, we show that methyltransferase Setd7 facilitates such transition by regulating the nuclear accumulation of &beta;-catenin in proliferating MuSCs. Genetic or pharmacological inhibition of Setd7 promotes in&nbsp;vitro expansion of MuSCs and increases the yield of primary myogenic cell cultures. Upon transplantation, both mouse and human MuSCs expanded with a Setd7 small-molecule inhibitor are better able to repopulate the satellite cell niche, and treated mouse MuSCs show enhanced therapeutic potential in preclinical models of muscular dystrophy. Thus, Setd7 inhibition may help bypass a key obstacle in the translation of cell therapy for muscle disease.</p>',
			'date' => '2018-02-01',
			'pmid' => 'http://www.pubmed.gov/29395054',
			'doi' => '10.1016/j.stem.2017.12.010',
			'modified' => '2019-02-28 10:56:48',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '3446',
			'name' => 'Metabolic Induction of Trained Immunity through the Mevalonate Pathway.',
			'authors' => 'Bekkering S, Arts RJW, Novakovic B, Kourtzelis I, van der Heijden CDCC, Li Y, Popa CD, Ter Horst R, van Tuijl J, Netea-Maier RT, van de Veerdonk FL, Chavakis T, Joosten LAB, van der Meer JWM, Stunnenberg H, Riksen NP, Netea MG',
			'description' => '<p>Innate immune cells can develop long-term memory after stimulation by microbial products during infections or vaccinations. Here, we report that metabolic signals can induce trained immunity. Pharmacological and genetic experiments reveal that activation of the cholesterol synthesis pathway, but not the synthesis of cholesterol itself, is essential for training of myeloid cells. Rather, the metabolite mevalonate is the mediator of training via activation of IGF1-R and mTOR and subsequent histone modifications in inflammatory pathways. Statins, which block mevalonate generation, prevent trained immunity induction. Furthermore, monocytes of patients with hyper immunoglobulin D syndrome (HIDS), who are mevalonate kinase deficient and accumulate mevalonate, have a constitutive trained immunity phenotype at both immunological and epigenetic levels, which could explain the attacks of sterile inflammation that these patients experience. Unraveling the role of mevalonate in trained immunity contributes to our understanding of the pathophysiology of HIDS and identifies novel therapeutic targets for clinical conditions with excessive activation of trained immunity.</p>',
			'date' => '2018-01-11',
			'pmid' => 'http://www.pubmed.gov/29328908',
			'doi' => '10.1016/j.cell.2017.11.025',
			'modified' => '2019-02-15 21:37:39',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '3282',
			'name' => 'Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements',
			'authors' => 'Thierion E. et al.',
			'description' => '<p>Developmental genes can harbour multiple transcriptional enhancers that act simultaneously or in succession to achieve robust and precise spatiotemporal expression. However, the mechanisms underlying cooperation between cis-acting elements are poorly documented, notably in vertebrates. The mouse gene Krox20 encodes a transcription factor required for the specification of two segments (rhombomeres) of the developing hindbrain. In rhombomere 3, Krox20 is subject to direct positive feedback governed by an autoregulatory enhancer, element A. In contrast, a second enhancer, element C, distant by 70 kb, is active from the initiation of transcription independent of the presence of the KROX20 protein. Here, using both enhancer knock-outs and investigations of chromatin organisation, we show that element C possesses a dual activity: besides its classical enhancer function, it is also permanently required in cis to potentiate the autoregulatory activity of element A, by increasing its chromatin accessibility. This work uncovers a novel, asymmetrical, long-range mode of cooperation between cis-acting elements that might be essential to avoid promiscuous activation of positive autoregulatory elements.</p>',
			'date' => '2017-07-27',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28749941',
			'doi' => '',
			'modified' => '2017-10-23 17:38:21',
			'created' => '2017-10-23 17:38:21',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '3084',
			'name' => 'A transcription factor pulse can prime chromatin for heritable transcriptional memory',
			'authors' => 'Iberg-Badeaux A. et al.',
			'description' => '<p>Short-term and long-term transcriptional memory is the phenomenon whereby the kinetics or magnitude of gene induction is enhanced following a prior induction period. Short-term memory persists within one cell generation or in post-mitotic cells, while long-term memory can survive multiple rounds of cell division. We have developed a tissue culture model to study the epigenetic basis for long-term transcriptional memory (LTTM), and subsequently used this model to better understand the epigenetic mechanisms that enable heritable memory of temporary stimuli. We find that a pulse of transcription factor C/EBP&alpha; induces LTTM on a subset of target genes that survives 9 cell divisions. The chromatin landscape at genes that acquire LTTM is more repressed as compared to those genes that do not exhibit memory, akin to a latent state. We show through ChIP and chemical inhibitor studies that Pol II elongation is important for establishing memory in this model, but that Pol II itself is not retained as part of the memory mechanism. More generally, our work reveals that a transcription factor involved in lineage specification can induce LTTM, and that failure to re-repress chromatin is one epigenetic mechanism underlying transcriptional memory.</p>',
			'date' => '2016-12-05',
			'pmid' => 'http://mcb.asm.org/content/early/2016/11/30/MCB.00372-16.abstract',
			'doi' => '',
			'modified' => '2016-12-20 10:33:32',
			'created' => '2016-12-20 10:33:32',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => array(
			'id' => '3103',
			'name' => 'β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance',
			'authors' => 'Novakovic B. et al.',
			'description' => '<p>Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to microbial components such as lipopolysaccharide (LPS). We apply an integrated epigenomic&nbsp;approach to characterize the molecular events involved in LPS-induced tolerance in a time-dependent manner. Mechanistically, LPS-treated monocytes fail to accumulate active histone marks at promoter and enhancers of genes in the lipid metabolism and phagocytic pathways. Transcriptional inactivity in response to a second LPS exposure in tolerized macrophages is accompanied by failure to deposit active histone marks at promoters of tolerized genes. In contrast, &beta;-glucan partially reverses the LPS-induced tolerance in&nbsp;vitro. Importantly, ex&nbsp;vivo &beta;-glucan treatment of monocytes from volunteers with experimental endotoxemia re-instates their capacity for cytokine production. Tolerance is reversed at the level of distal element histone modification and transcriptional reactivation of otherwise unresponsive genes.</p>',
			'date' => '2016-11-17',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27863248',
			'doi' => '',
			'modified' => '2017-01-03 15:31:46',
			'created' => '2017-01-03 15:31:46',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 21 => array(
			'id' => '3015',
			'name' => 'Enhancer decommissioning by Snail1-induced competitive displacement of TCF7L2 and down-regulation of transcriptional activators results in EPHB2 silencing',
			'authors' => 'Schnappauf O et al.',
			'description' => '<p>Transcriptional silencing is a major cause for the inactivation of tumor suppressor genes, however, the underlying mechanisms are only poorly understood. The EPHB2 gene encodes a receptor tyrosine kinase that controls epithelial cell migration and allocation in intestinal crypts. Through its ability to restrict cell spreading, EPHB2 functions as a tumor suppressor in colorectal cancer whose expression is frequently lost as tumors progress to the carcinoma stage. Previously we reported that EPHB2 expression depends on a transcriptional enhancer whose activity is diminished in EPHB2 non-expressing cells. Here we investigated the mechanisms that lead to EPHB2 enhancer inactivation. We show that expression of EPHB2 and SNAIL1 - an inducer of epithelial-mesenchymal transition (EMT) - is anti-correlated in colorectal cancer cell lines and tumors. In a cellular model of Snail1-induced EMT, we observe that features of active chromatin at the EPHB2 enhancer are diminished upon expression of murine Snail1. We identify the transcription factors FOXA1, MYB, CDX2 and TCF7L2 as EPHB2 enhancer factors and demonstrate that Snail1 indirectly inactivates the EPHB2 enhancer by downregulation of FOXA1 and MYB. In addition, Snail1 induces the expression of Lymphoid enhancer factor 1 (LEF1) which competitively displaces TCF7L2 from the EPHB2 enhancer. In contrast to TCF7L2, however, LEF1 appears to repress the EPHB2 enhancer. Our findings underscore the importance of transcriptional enhancers for gene regulation under physiological and pathological conditions and show that SNAIL1 employs a combinatorial mechanism to inactivate the EPHB2 enhancer based on activator deprivation and competitive displacement of transcription factors.</p>',
			'date' => '2016-08-05',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27504909',
			'doi' => '',
			'modified' => '2016-08-31 09:18:03',
			'created' => '2016-08-31 09:18:03',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '2972',
			'name' => 'cChIP-seq: a robust small-scale method for investigation of histone modifications',
			'authors' => 'Valensisi C et al.',
			'description' => '<div id="__sec1" class="sec sec-first">
<h3>Background</h3>
<p id="__p1" class="p p-first-last">ChIP-seq is highly utilized for mapping histone modifications that are informative about gene regulation and genome annotations. For example, applying ChIP-seq to histone modifications such as H3K4me1 has facilitated generating epigenomic maps of putative enhancers. This powerful technology, however, is limited in its application by the large number of cells required. ChIP-seq involves extensive manipulation of sample material and multiple reactions with limited quality control at each step, therefore, scaling down the number of cells required has proven challenging. Recently, several methods have been proposed to overcome this limit but most of these methods require extensive optimization to tailor the protocol to the specific antibody used or number of cells being profiled.</p>
</div>
<div id="__sec2" class="sec">
<h3>Results</h3>
<p id="__p2" class="p p-first-last">Here we describe a robust, yet facile method, which we named carrier ChIP-seq (cChIP-seq), for use on limited cell amounts. cChIP-seq employs a DNA-free histone carrier in order to maintain the working ChIP reaction scale, removing the need to tailor reactions to specific amounts of cells or histone modifications to be assayed. We have applied our method to three different histone modifications, H3K4me3, H3K4me1 and H3K27me3 in the K562 cell line, and H3K4me1 in H1 hESCs. We successfully obtained epigenomic maps for these histone modifications starting with as few as 10,000 cells. We compared cChIP-seq data to data generated as part of the ENCODE project. ENCODE data are the reference standard in the field and have been generated starting from tens of million of cells. Our results show that cChIP-seq successfully recapitulates bulk data. Furthermore, we showed that the differences observed between small-scale ChIP-seq data and ENCODE data are largely to be due to lab-to-lab variability rather than operating on a reduced scale.</p>
</div>
<div id="__sec3" class="sec">
<h3>Conclusions</h3>
<p id="__p3" class="p p-first-last">Data generated using cChIP-seq are equivalent to reference epigenomic maps from three orders of magnitude more cells. Our method offers a robust and straightforward approach to scale down ChIP-seq to as low as 10,000 cells. The underlying principle of our strategy makes it suitable for being applied to a vast range of chromatin modifications without requiring expensive optimization. Furthermore, our strategy of a DNA-free carrier can be adapted to most ChIP-seq protocols.</p>
</div>',
			'date' => '2015-12-21',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687106/',
			'doi' => ' 10.1186/s12864-015-2285-7',
			'modified' => '2016-07-01 10:05:06',
			'created' => '2016-07-01 10:05:06',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '2869',
			'name' => 'C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis',
			'authors' => 'van Oevelen C, Collombet S, Vicent G, Hoogenkamp M, Lepoivre C, Badeaux A, Bussmann L, Sardina JL, Thieffry D, Beato M, Shi Y, Bonifer C, Graf T',
			'description' => '<section id="abs0020" class="articleHighlights">
<h2 class="sectionTitle">Highlights</h2>
<div class="content">
<p></p>
<ul class="ce-list" id="ulist0010">
<li id="u0010">C/EBP&alpha; activates two classes of prospective myeloid enhancers in B cells</li>
<li id="u0015">Pre-existing enhancers are bound by PU.1 and become hyper-activated by C/EBP&alpha;</li>
<li id="u0020">C/EBP&alpha; acts as a pioneer factor with delayed kinetics on de novo enhancers</li>
<li id="u0025">The two types of enhancers direct myeloid cell fate in B cells and hematopoiesis</li>
</ul>
<p></p>
</div>
</section>
<section class="graphical"></section>
<div class="abstract">
<h2 class="sectionTitle">Summary</h2>
<p>Transcription-factor-induced somatic cell conversions are highly relevant for both basic and clinical research yet their mechanism is not fully understood and it is unclear whether they reflect normal differentiation processes. Here we show that during pre-B-cell-to-macrophage transdifferentiation, C/EBP&alpha; binds to two types of myeloid enhancers in B cells: pre-existing enhancers that are bound by PU.1, providing a platform for incoming C/EBP&alpha;; and de novo enhancers that are targeted by C/EBP&alpha;, acting as a pioneer factor for subsequent binding by PU.1. The order of factor binding dictates the upregulation kinetics of nearby genes. Pre-existing enhancers are broadly active throughout the hematopoietic lineage tree, including B cells. In contrast, de novo enhancers are silent in most cell types except in myeloid cells where they become activated by C/EBP factors. Our data suggest that C/EBP&alpha; recapitulates physiological developmental processes by short-circuiting two macrophage enhancer pathways in pre-B cells.</p>
</div>',
			'date' => '2015-08-11',
			'pmid' => 'http://www.cell.com/stem-cell-reports/abstract/S2213-6711%2815%2900188-5',
			'doi' => 'http://dx.doi.org/10.1016/j.stemcr.2015.06.007',
			'modified' => '2016-03-25 10:23:25',
			'created' => '2016-03-25 10:22:05',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => 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) 25 => array(
			'id' => '2228',
			'name' => 'Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping.',
			'authors' => 'Light N, Adoue V, Ge B, Chen SH, Kwan T, Pastinen T',
			'description' => 'Allele-specific (AS) assessment of chromatin has the potential to elucidate specific cis-regulatory mechanisms, which are predicted to underlie the majority of the known genetic associations to complex disease. However, development of chromatin landscapes at allelic resolution has been challenging since sites of variable signal strength require substantial read depths not commonly applied in sequencing based approaches. In this study, we addressed this by performing parallel analyses of input DNA and chromatin immunoprecipitates (ChIP) on high-density Illumina genotyping arrays. Allele-specificity for the histone modifications H3K4me1, H3K4me3, H3K27ac, H3K27me3, and H3K36me3 was assessed using ChIP samples generated from 14 lymphoblast and 6 fibroblast cell lines. AS-ChIP SNPs were combined into domains and validated using high-confidence ChIP-seq sites. We observed characteristic patterns of allelic-imbalance for each histone-modification around allele-specifically expressed transcripts. Notably, we found H3K4me1 to be significantly anti-correlated with allelic expression (AE) at transcription start sites, indicating H3K4me1 allelic imbalance as a marker of AE. We also found that allelic chromatin domains exhibit population and cell-type specificity as well as heritability within trios. Finally, we observed that a subset of allelic chromatin domains is regulated by DNase I-sensitive quantitative trait loci and that these domains are significantly enriched for genome-wide association studies hits, with autoimmune disease associated SNPs specifically enriched in lymphoblasts. This study provides the first genome-wide maps of allelic-imbalance for five histone marks. Our results provide new insights into the role of chromatin in cis-regulation and highlight the need for high-depth sequencing in ChIP-seq studies along with the need to improve allele-specificity of ChIP-enrichment.',
			'date' => '2014-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25055051',
			'doi' => '',
			'modified' => '2015-07-24 15:39:03',
			'created' => '2015-07-24 15:39:03',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 26 => array(
			'id' => '2054',
			'name' => 'Nuclear ARRB1 induces pseudohypoxia and cellular metabolism reprogramming in prostate cancer',
			'authors' => 'Zecchini V, Madhu B, Russell R, Pértega-Gomes N, Warren A, Gaude E, Borlido J, Stark R, Ireland-Zecchini H, Rao R, Scott H, Boren J, Massie C, Asim M, Brindle K, Griffiths J, Frezza C, Neal DE, Mills IG',
			'description' => 'Tumour cells sustain their high proliferation rate through metabolic reprogramming, whereby cellular metabolism shifts from oxidative phosphorylation to aerobic glycolysis, even under normal oxygen levels. Hypoxia-inducible factor 1A (HIF1A) is a major regulator of this process, but its activation under normoxic conditions, termed pseudohypoxia, is not well documented. Here, using an integrative approach combining the first genome-wide mapping of chromatin binding for an endocytic adaptor, ARRB1, both in vitro and in vivo with gene expression profiling, we demonstrate that nuclear ARRB1 contributes to this metabolic shift in prostate cancer cells via regulation of HIF1A transcriptional activity under normoxic conditions through regulation of succinate dehydrogenase A (SDHA) and fumarate hydratase (FH) expression. ARRB1-induced pseudohypoxia may facilitate adaptation of cancer cells to growth in the harsh conditions that are frequently encountered within solid tumours. Our study is the first example of an endocytic adaptor protein regulating metabolic pathways. It implicates ARRB1 as a potential tumour promoter in prostate cancer and highlights the importance of metabolic alterations in prostate cancer.',
			'date' => '2014-05-16',
			'pmid' => 'http://onlinelibrary.wiley.com/doi/10.15252/embj.201386874/full',
			'doi' => '',
			'modified' => '2015-07-24 15:39:02',
			'created' => '2015-07-24 15:39:02',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 27 => array(
			'id' => '1793',
			'name' => 'A novel microscopy-based high-throughput screening method to identify proteins that regulate global histone modification levels.',
			'authors' => 'Baas R, Lelieveld D, van Teeffelen H, Lijnzaad P, Castelijns B, van Schaik FM, Vermeulen M, Egan DA, Timmers HT, de Graaf P',
			'description' => '<p>Posttranslational modifications of histones play an important role in the regulation of gene expression and chromatin structure in eukaryotes. The balance between chromatin factors depositing (writers) and removing (erasers) histone marks regulates the steady-state levels of chromatin modifications. Here we describe a novel microscopy-based screening method to identify proteins that regulate histone modification levels in a high-throughput fashion. We named our method CROSS, for Chromatin Regulation Ontology SiRNA Screening. CROSS is based on an siRNA library targeting the expression of 529 proteins involved in chromatin regulation. As a proof of principle, we used CROSS to identify chromatin factors involved in histone H3 methylation on either lysine-4 or lysine-27. Furthermore, we show that CROSS can be used to identify chromatin factors that affect growth in cancer cell lines. Taken together, CROSS is a powerful method to identify the writers and erasers of novel and known chromatin marks and facilitates the identification of drugs targeting epigenetic modifications.</p>',
			'date' => '2014-02-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24334265',
			'doi' => '',
			'modified' => '2016-04-12 09:46:40',
			'created' => '2015-07-24 15:39:01',
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		(int) 28 => array(
			'id' => '1577',
			'name' => 'An In-Depth Characterization of the Major Psoriasis Susceptibility Locus Identifies Candidate Susceptibility Alleles within an HLA-C Enhancer Element.',
			'authors' => 'Clop A, Bertoni A, Spain SL, Simpson MA, Pullabhatla V, Tonda R, Hundhausen C, Di Meglio P, De Jong P, Hayday AC, Nestle FO, Barker JN, Bell RJ, Capon F, Trembath RC',
			'description' => 'Psoriasis is an immune-mediated skin disorder that is inherited as a complex genetic trait. Although genome-wide association scans (GWAS) have identified 36 disease susceptibility regions, more than 50% of the genetic variance can be attributed to a single Major Histocompatibility Complex (MHC) locus, known as PSORS1. Genetic studies indicate that HLA-C is the strongest PSORS1 candidate gene, since markers tagging HLA-Cw*0602 consistently generate the most significant association signals in GWAS. However, it is unclear whether HLA-Cw*0602 is itself the causal PSORS1 allele, especially as the role of SNPs that may affect its expression has not been investigated. Here, we have undertaken an in-depth molecular characterization of the PSORS1 interval, with a view to identifying regulatory variants that may contribute to disease susceptibility. By analysing high-density SNP data, we refined PSORS1 to a 179 kb region encompassing HLA-C and the neighbouring HCG27 pseudogene. We compared multiple MHC sequences spanning this refined locus and identified 144 candidate susceptibility variants, which are unique to chromosomes bearing HLA-Cw*0602. In parallel, we investigated the epigenetic profile of the critical PSORS1 interval and uncovered three enhancer elements likely to be active in T lymphocytes. Finally we showed that nine candidate susceptibility SNPs map within a HLA-C enhancer and that three of these variants co-localise with binding sites for immune-related transcription factors. These data indicate that SNPs affecting HLA-Cw*0602 expression are likely to contribute to psoriasis susceptibility and highlight the importance of integrating multiple experimental approaches in the investigation of complex genomic regions such as the MHC.',
			'date' => '2013-08-19',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23990973',
			'doi' => '',
			'modified' => '2015-07-24 15:39:00',
			'created' => '2015-07-24 15:39:00',
			'ProductsPublication' => array(
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		(int) 29 => array(
			'id' => '1512',
			'name' => 'Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus.',
			'authors' => 'Miller CL, Anderson DR, Kundu RK, Raiesdana A, Nürnberg ST, Diaz R, Cheng K, Leeper NJ, Chen CH, Chang IS, Schadt EE, Hsiung CA, Assimes TL, Quertermous T',
			'description' => 'Coronary heart disease (CHD) is the leading cause of mortality in both developed and developing countries worldwide. Genome-wide association studies (GWAS) have now identified 46 independent susceptibility loci for CHD, however, the biological and disease-relevant mechanisms for these associations remain elusive. The large-scale meta-analysis of GWAS recently identified in Caucasians a CHD-associated locus at chromosome 6q23.2, a region containing the transcription factor TCF21 gene. TCF21 (Capsulin/Pod1/Epicardin) is a member of the basic-helix-loop-helix (bHLH) transcription factor family, and regulates cell fate decisions and differentiation in the developing coronary vasculature. Herein, we characterize a cis-regulatory mechanism by which the lead polymorphism rs12190287 disrupts an atypical activator protein 1 (AP-1) element, as demonstrated by allele-specific transcriptional regulation, transcription factor binding, and chromatin organization, leading to altered TCF21 expression. Further, this element is shown to mediate signaling through platelet-derived growth factor receptor beta (PDGFR-β) and Wilms tumor 1 (WT1) pathways. A second disease allele identified in East Asians also appears to disrupt an AP-1-like element. Thus, both disease-related growth factor and embryonic signaling pathways may regulate CHD risk through two independent alleles at TCF21.',
			'date' => '2013-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23874238',
			'doi' => '',
			'modified' => '2015-07-24 15:39:00',
			'created' => '2015-07-24 15:39:00',
			'ProductsPublication' => array(
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		(int) 30 => array(
			'id' => '1350',
			'name' => 'Balancing of histone H3K4 methylation states by the Kdm5c/SMCX histone demethylase modulates promoter and enhancer function.',
			'authors' => 'Outchkourov NS, Muiño JM, Kaufmann K, van Ijcken WF, Groot Koerkamp MJ, van Leenen D, de Graaf P, Holstege FC, Grosveld FG, Timmers HT',
			'description' => 'The functional organization of eukaryotic genomes correlates with specific patterns of histone methylations. Regulatory regions in genomes such as enhancers and promoters differ in their extent of methylation of histone H3 at lysine-4 (H3K4), but it is largely unknown how the different methylation states are specified and controlled. Here, we show that the Kdm5c/Jarid1c/SMCX member of the Kdm5 family of H3K4 demethylases can be recruited to both enhancer and promoter elements in mouse embryonic stem cells and in neuronal progenitor cells. Knockdown of Kdm5c deregulates transcription via local increases in H3K4me3. Our data indicate that by restricting H3K4me3 modification at core promoters, Kdm5c dampens transcription, but at enhancers Kdm5c stimulates their activity. Remarkably, an impaired enhancer function activates the intrinsic promoter activity of Kdm5c-bound distal elements. Our results demonstrate that the Kdm5c demethylase plays a crucial and dynamic role in the functional discrimination between enhancers and core promoters.',
			'date' => '2013-04-25',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/23545502',
			'doi' => '',
			'modified' => '2015-07-24 15:39:00',
			'created' => '2015-07-24 15:39:00',
			'ProductsPublication' => array(
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		(int) 31 => array(
			'id' => '592',
			'name' => 'Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.',
			'authors' => 'Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ',
			'description' => 'The H3K9me3 histone modification is often found at promoter regions, where it functions to repress transcription. However, we have previously shown that 3' exons of zinc finger genes (ZNFs) are marked by high levels of H3K9me3. We have now further investigated this unusual location for H3K9me3 in ZNF genes. Neither bioinformatic nor experimental approaches support the hypothesis that the 3' exons of ZNFs are promoters. We further characterized the histone modifications at the 3' ZNF exons and found that these regions also contain H3K36me3, a mark of transcriptional elongation. A genome-wide analysis of ChIP-seq data revealed that ZNFs constitute the majority of genes that have high levels of both H3K9me3 and H3K36me3. These results suggested the possibility that the ZNF genes may be imprinted, with one allele transcribed and one allele repressed. To test the hypothesis that the contradictory modifications are due to imprinting, we used a SNP analysis of RNA-seq data to demonstrate that both alleles of certain ZNF genes having H3K9me3 and H3K36me3 are transcribed. We next analyzed isolated ZNF 3' exons using stably integrated episomes. We found that although the H3K36me3 mark was lost when the 3' ZNF exon was removed from its natural genomic location, the isolated ZNF 3' exons retained the H3K9me3 mark. Thus, the H3K9me3 mark at ZNF 3' exons does not impede transcription and it is regulated independently of the H3K36me3 mark. Finally, we demonstrate a strong relationship between the number of tandemly repeated domains in the 3' exons and the H3K9me3 mark. We suggest that the H3K9me3 at ZNF 3' exons may function to protect the genome from inappropriate recombination rather than to regulate transcription.',
			'date' => '2011-02-15',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21347206',
			'doi' => '',
			'modified' => '2015-07-24 15:38:58',
			'created' => '2015-07-24 15:38:58',
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			'id' => '261',
			'name' => 'Using ChIP-Seq Technology to Generate High-Resolution Profiles of Histone Modifications ',
			'authors' => 'O’Geen H, Echipare L, Farnham PJ',
			'description' => '<p>The dynamic modification of DNA and histones plays a key role in transcriptional regulation through - altering the packaging of DNA and modifying the nucleosome surface. These chromatin states, also referred to as the epigenome, are distinctive for different tissues, developmental stages, and disease states and can also be altered by environmental influences. New technologies allow the genome-wide visualization of the information encoded in the epigenome. For example, the chromatin immunoprecipitation (ChIP) assay allows investigators to characterize DNA&ndash;protein interactions in vivo. ChIP followed by hybridization to microarrays (ChIP-chip) or by high-throughput sequencing (ChIP-seq) are both powerful tools to identify genome-wide profiles of transcription factors, histone modifications, DNA methylation, and nucleosome positioning. ChIP-seq technology, which can now interrogate the entire human genome at high resolution with only one lane of sequencing, has recently surpassed ChIP-chip technology for epigenomic analyses. Importantly, for the study of primary cells and tissues, epigenetic profiles can be generated using as little as 1 &mu;g of chromatin. In this chapter, we describe in detail the steps involved in performing ChIP assays (with a focus on characterizing histone modifications in primary cells)either manually or using the IP-Star ChIP robot, followed by a detailed protocol to prepare successful libraries for Illumina sequencing. Critical quality control checkpoints are discussed. Although not a focus of this chapter, we also point the reader to several methods by which massive ChIP-seq data sets can be analyzed to extract the tremendous information contained within.</p>',
			'date' => '0000-00-00',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/21913086',
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	(int) 0 => array(
		'id' => '2202',
		'antibody_id' => '110',
		'name' => 'H3K4me1 Antibody',
		'description' => '<p><span>Polyclonal antibody raised in rabbit against histone <strong>H3 containing the monomethylated lysine 4</strong> (<strong>H3K4me1</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
		'label1' => 'Validation Data',
		'info1' => '<div class="row">
<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
</div>
</div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_DotBlot.png" alt="H3K4me1 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-7 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 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>
</div>
</div>',
		'label2' => 'Target Description',
		'info2' => '<p>Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called &ldquo;histone code&rdquo;. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases.</p>',
		'label3' => '',
		'info3' => '',
		'format' => '50 µg',
		'catalog_number' => 'C15410037',
		'old_catalog_number' => 'pAb-037-050',
		'sf_code' => 'C15410037-D001-000581',
		'type' => 'FRE',
		'search_order' => '03-Antibody',
		'price_EUR' => '380',
		'price_USD' => '380',
		'price_GBP' => '340',
		'price_JPY' => '59525',
		'price_CNY' => '',
		'price_AUD' => '950',
		'country' => 'ALL',
		'except_countries' => 'None',
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		'last_datasheet_update' => 'January 6, 2020',
		'slug' => 'h3k4me1-polyclonal-antibody-classic-50-ug-18-ul',
		'meta_title' => 'H3K4me1 Antibody - ChIP-seq Grade (C15410037) | Diagenode',
		'meta_keywords' => '',
		'meta_description' => 'H3K4me1 (Histone H3 monomethylated at lysine 4) Polyclonal Antibody validated  in ChIP-seq, ChIP-qPCR, ELISA, IF, DB and WB. Batch-specific data available on the website. ',
		'modified' => '2024-11-19 16:55:49',
		'created' => '2015-06-29 14:08:20'
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	'id' => '2202',
	'antibody_id' => '110',
	'name' => 'H3K4me1 Antibody',
	'description' => '<p><span>Polyclonal antibody raised in rabbit against histone <strong>H3 containing the monomethylated lysine 4</strong> (<strong>H3K4me1</strong>), using a KLH-conjugated synthetic peptide.</span></p>',
	'label1' => 'Validation Data',
	'info1' => '<div class="row">
<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP.png" alt="H3K4me1 Antibody ChIP Grade" style="border: 1px solid black;" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-2.png" alt="H3K4me1 Antibody for ChIP" style="border: 1px solid black;" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed with the Diagenode antibody against H3K4me1 (cat. No. C15410037) on sheared chromatin from 500,000 HeLaS3 cells using the &ldquo;iDeal ChIP-seq&rdquo; kit (cat. No. C01010051). The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation (SNAP-ChIP K-MetStat Panel, Epicypher). A titration of the antibody consisting of 0.5, 1, 2 and 5 &micro;g per ChIP experiment was analysed. IgG (2 &micro;g/IP) was used as negative IP control. <strong>Figure 1A.</strong> Quantitative PCR was performed with primers for a region surrounding the ACTB and GAS2L1 genes, used as positive controls, and for the promoters of the GAPDH and EIF4A2 genes, used as negative controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). <strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K27me1, H3K36me1, H4K20me1 and the unmodified H3K4 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K4me1 modification. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-A.png" alt="H3K4me1 Antibody ChIP-seq Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-B.png" alt="H3K4me1 Antibody for ChIP-seq" /></p>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-C.png" alt="H3K4me1 Antibody validated in ChIP-seq" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410037_ChIP-seq-D.png" alt="H3K4me1 Antibody for ChIP-seq assay" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K4me1</strong><br /> ChIP was performed as described above with 1 &micro;g of the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The IP&rsquo;d DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer&rsquo;s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2A and B show the enrichment in chromosomal regions surrounding the ACTB and GAS2L1 positive control genes. The position of the amplicon used in the qPCR validation is indicated by an arrow. Figure 2C and D show the H3K4me1 signal in two 1 Mb regions of chromosome 5 and X, respectively. </small></p>
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</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_ELISA.png" alt="H3K4me1 Antibody ELISA Validation" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 3. Determination of the titer</strong><br /> To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K4me1 (Cat. No. C15410037) in antigen coated wells. The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 3), the titer of the antibody was estimated to be 1:20,100. </small></p>
</div>
</div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-5 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_DotBlot.png" alt="H3K4me1 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-7 columns">
<p><small><strong>Figure 4. Cross reactivity tests using the Diagenode antibody directed against H3K4me1</strong><br /> A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K4me1 (Cat. No. C15410037) with peptides containing other modifications or unmodified sequences of histone H3 and H4. One hundred to 0.2 pmol of the respective peptides were spotted on a membrane. The antibody was used at a dilution of 1:10,000. Figure 4 shows a high specificity of the antibody for the modification of interest. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_WB.png" alt="H3K4me1 Antibody validated in Western Blot" /></p>
</div>
<div class="small-8 columns">
<p><small><strong>Figure 5. Western blot analysis using the Diagenode antibody directed against H3K4me1</strong><br /> Western blot was performed on whole cell (25 &micro;g, lane 1) and histone extracts (15 &micro;g, lane 2) from HeLa cells, and on 1 &micro;g of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K4me1 (Cat. No. C15410037). The antibody was diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is shown on the right, the marker (in kDa) is shown on the left. </small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410037_IF.png" alt="H3K4me1 Antibody for Immunofluorescence " /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 6. Immunofluorescence using the Diagenode antibody directed against H3K4me1</strong><br /> HeLa cells were stained with the Diagenode antibody against H3K4me1 (cat. C15410037) and with DAPI. Cells were fixed with 4% formaldehyde for 10&rsquo; and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labeled with the H3K4me1 antibody (left) diluted 1:500 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right. </small></p>
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	'description' => '<p>The dynamic modification of DNA and histones plays a key role in transcriptional regulation through - altering the packaging of DNA and modifying the nucleosome surface. These chromatin states, also referred to as the epigenome, are distinctive for different tissues, developmental stages, and disease states and can also be altered by environmental influences. New technologies allow the genome-wide visualization of the information encoded in the epigenome. For example, the chromatin immunoprecipitation (ChIP) assay allows investigators to characterize DNA&ndash;protein interactions in vivo. ChIP followed by hybridization to microarrays (ChIP-chip) or by high-throughput sequencing (ChIP-seq) are both powerful tools to identify genome-wide profiles of transcription factors, histone modifications, DNA methylation, and nucleosome positioning. ChIP-seq technology, which can now interrogate the entire human genome at high resolution with only one lane of sequencing, has recently surpassed ChIP-chip technology for epigenomic analyses. Importantly, for the study of primary cells and tissues, epigenetic profiles can be generated using as little as 1 &mu;g of chromatin. In this chapter, we describe in detail the steps involved in performing ChIP assays (with a focus on characterizing histone modifications in primary cells)either manually or using the IP-Star ChIP robot, followed by a detailed protocol to prepare successful libraries for Illumina sequencing. Critical quality control checkpoints are discussed. Although not a focus of this chapter, we also point the reader to several methods by which massive ChIP-seq data sets can be analyzed to extract the tremendous information contained within.</p>',
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	'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/21913086',
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Antibodies you can trust POSTER Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of lar...	Download
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Datasheet H3K4me1 C15410037 DATASHEET Polyclonal antibody raised in rabbit against histone H3 containing the monomethylated lysine 4 (H...	Download

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