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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
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<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
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<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
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<p></p>
<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
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<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>0.2-1.8 μg per ChIP</td>
<td>Fig 1, 2</td>
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<tr>
<td>Immunofluorescence</td>
<td>1:500</td>
<td>Fig 3</td>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP.png" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="288" height="254" /></p>
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-A.png" alt="H3K9me3 Antibody ChIP-seq Grade" caption="false" width="447" height="189" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-B.png" alt="H3K9me3 Antibody for ChIP-seq" caption="false" width="447" height="60" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-C.png" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="447" height="59" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-D.png" alt="H3K9me3 Antibody validated in ChIP-seq" caption="false" width="447" height="66" /></p>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-IF.png" alt="H3K9me3 Antibody validated in Immunofluorescence" caption="false" width="288" height="292" /></p>
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<div class="small-8 columns">
<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
</div>
</div>
<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
<ul>
<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
</ul>
<p></p>
<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
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<p>Diagenode offers huge selection of highly sensitive antibodies validated in IF.</p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15200229-IF.jpg" alt="" height="245" width="256" /></p>
<p><sup><strong>Immunofluorescence using the Diagenode monoclonal antibody directed against CRISPR/Cas9</strong></sup></p>
<p><sup>HeLa cells transfected with a Cas9 expression vector (left) or untransfected cells (right) were fixed in methanol at -20°C, permeabilized with acetone at -20°C and blocked with PBS containing 2% BSA. The cells were stained with the Cas9 C-terminal antibody (Cat. No. C15200229) diluted 1:400, followed by incubation with an anti-mouse secondary antibody coupled to AF488. The bottom images show counter-staining of the nuclei with Hoechst 33342.</sup></p>
<h5><sup>Check our selection of antibodies validated in IF.</sup></h5>',
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<p><span style="font-weight: 400;">Diagenode provides leading solutions for epigenetic research. Because ChIP-seq is a widely-used technique, we validate our antibodies in ChIP and ChIP-seq experiments (in addition to conventional methods like Western blot, Dot blot, ELISA, and immunofluorescence) to provide the highest quality antibody. We standardize our validation and production to guarantee high product quality without technical bias. Diagenode guarantees ChIP-seq grade antibody performance under our suggested conditions.</span></p>
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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 µg of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 µg of the antibody against H3K36me3 (cat. No. C15410192). The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. The figure shows the signal distribution along the complete sequence of human chromosome 3, a zoomin to a 10 Mb region and a further zoomin to a 1.5 Mb region. </small></p>
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<p>Diagenode’s highly validated antibodies:</p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
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'description' => '<p>Histones are the main protein components of chromatin involved in the compaction of DNA into nucleosomes, the basic units of chromatin. A <strong>nucleosome</strong> consists of one pair of each of the core histones (<strong>H2A</strong>, <strong>H2B</strong>, <strong>H3</strong> and <strong>H4</strong>) forming an octameric structure wrapped by 146 base pairs of DNA. The different nucleosomes are linked by the linker histone<strong> H1, </strong>allowing for further condensation of chromatin.</p>
<p>The core histones have a globular structure with large unstructured N-terminal tails protruding from the nucleosome. They can undergo to multiple post-translational modifications (PTM), mainly at the N-terminal tails. These <strong>post-translational modifications </strong>include methylation, acetylation, phosphorylation, ubiquitinylation, citrullination, sumoylation, deamination and crotonylation. The most well characterized PTMs are <strong>methylation,</strong> <strong>acetylation and phosphorylation</strong>. Histone methylation occurs mainly on lysine (K) residues, which can be mono-, di- or tri-methylated, and on arginines (R), which can be mono-methylated and symmetrically or asymmetrically di-methylated. Histone acetylation occurs on lysines and histone phosphorylation mainly on serines (S), threonines (T) and tyrosines (Y).</p>
<p>The PTMs of the different residues are involved in numerous processes such as DNA repair, DNA replication and chromosome condensation. They influence the chromatin organization and can be positively or negatively associated with gene expression. Trimethylation of H3K4, H3K36 and H3K79, and lysine acetylation generally result in an open chromatin configuration (figure below) and are therefore associated with <strong>euchromatin</strong> and gene activation. Trimethylation of H3K9, K3K27 and H4K20, on the other hand, is enriched in <strong>heterochromatin </strong>and associated with gene silencing. The combination of different histone modifications is called the "<strong>histone code</strong>”, analogous to the genetic code.</p>
<p><img src="https://www.diagenode.com/img/categories/antibodies/histone-marks-illustration.png" /></p>
<p>Diagenode is proud to offer a large range of antibodies against histones and histone modifications. Our antibodies are highly specific and have been validated in many applications, including <strong>ChIP</strong> and <strong>ChIP-seq</strong>.</p>
<p>Diagenode’s collection includes antibodies recognizing:</p>
<ul>
<li><strong>Histone H1 variants</strong></li>
<li><strong>Histone H2A, H2A variants and histone H2A</strong> <strong>modifications</strong> (serine phosphorylation, lysine acetylation, lysine ubiquitinylation)</li>
<li><strong>Histone H2B and H2B</strong> <strong>modifications </strong>(serine phosphorylation, lysine acetylation)</li>
<li><strong>Histone H3 and H3 modifications </strong>(lysine methylation (mono-, di- and tri-methylated), lysine acetylation, serine phosphorylation, threonine phosphorylation, arginine methylation (mono-methylated, symmetrically and asymmetrically di-methylated))</li>
<li><strong>Histone H4 and H4 modifications (</strong>lysine methylation (mono-, di- and tri-methylated), lysine acetylation, arginine methylation (mono-methylated and symmetrically di-methylated), serine phosphorylation )</li>
</ul>
<p><span style="font-weight: 400;"><strong>HDAC's HAT's, HMT's and other</strong> <strong>enzymes</strong> which modify histones can be found in the category <a href="../categories/chromatin-modifying-proteins-histone-transferase">Histone modifying enzymes</a><br /></span></p>
<p><span style="font-weight: 400;"> Diagenode’s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> Expert technical support</span></li>
<li><span style="font-weight: 400;"> Sample sizes available</span></li>
<li><span style="font-weight: 400;"> 100% satisfaction guarantee</span></li>
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<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> - 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> with rigorous QC and validation</li>
<li><strong>Classified</strong> 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. 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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<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>). </p>
<div class="row">
<div class="small-12 medium-6 large-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" alt="" width="400" height="315" /> </div>
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<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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'description' => '<p>Activation of interferon genes constitutes an important anticancer pathway able to restrict proliferation of cancer cells. Here, we demonstrate that the H3K9me3 histone methyltransferase (HMT) suppressor of variegation 3-9 homolog 1 (SUV39H1) is required for the proliferation of acute myeloid leukemia (AML) and find that its loss leads to activation of the interferon pathway. Mechanistically, we show that this occurs via destabilization of a complex composed of SUV39H1 and the two H3K9me2 HMTs, G9A and GLP. Indeed, loss of H3K9me2 correlated with the activation of key interferon pathway genes, and interference with the activities of G9A/GLP largely phenocopied loss of SUV39H1. Last, we demonstrate that inhibition of G9A/GLP synergized with DNA demethylating agents and that SUV39H1 constitutes a potential biomarker for the response to hypomethylation treatment. Collectively, we uncovered a clinically relevant role for H3K9me2 in safeguarding cancer cells against activation of the interferon pathway.</p>',
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'description' => '<p>The SUV39 class of methyltransferase enzymes deposits histone H3 lysine 9 di- and trimethylation (H3K9me2/3), the hallmark of constitutive heterochromatin. How these enzymes are regulated to mark specific genomic regions as heterochromatic is poorly understood. Clr4 is the sole H3K9me2/3 methyltransferase in the fission yeast and recent evidence suggests that ubiquitination of lysine 14 on histone H3 (H3K14ub) plays a key role in H3K9 methylation. However, the molecular mechanism of this regulation and its role in heterochromatin formation remain to be determined. Our structure-function approach shows that the H3K14ub substrate binds specifically and tightly to the catalytic domain of Clr4, and thereby stimulates the enzyme by over 250-fold. Mutations that disrupt this mechanism lead to a loss of H3K9me2/3 and abolish heterochromatin silencing similar to deletion. Comparison with mammalian SET domain proteins suggests that the Clr4 SET domain harbors a conserved sensor for H3K14ub, which mediates licensing of heterochromatin formation.</p>',
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'description' => '<p>Heterochromatic domains containing histone H3 lysine 9 methylation (H3K9me) can be epigenetically inherited independently of underlying DNA sequence. To gain insight into the mechanisms that mediate epigenetic inheritance, we used a inducible heterochromatin formation system to perform a genetic screen for mutations that abolish heterochromatin inheritance without affecting its establishment. We identified mutations in several pathways, including the conserved and essential Rix1-associated complex (henceforth the rixosome), which contains RNA endonuclease and polynucleotide kinase activities with known roles in ribosomal RNA processing. We show that the rixosome is required for spreading and epigenetic inheritance of heterochromatin in fission yeast. Viable rixosome mutations that disrupt its association with Swi6/HP1 fail to localize to heterochromatin, lead to accumulation of heterochromatic RNAs, and block spreading of H3K9me and silencing into actively transcribed regions. These findings reveal a new pathway for degradation of heterochromatic RNAs with essential roles in heterochromatin spreading and inheritance.</p>',
'date' => '2020-06-03',
'pmid' => 'http://www.pubmed.gov/32491985',
'doi' => '10.7554/eLife.54341',
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'name' => 'Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion.',
'authors' => 'Kurihara M, Kato K, Sanbo C, Shigenobu S, Ohkawa Y, Fuchigami T, Miyanari Y',
'description' => '<p>The promyelocytic leukemia (PML) body is a phase-separated nuclear structure physically associated with chromatin, implying its crucial roles in genome functions. However, its role in transcriptional regulation is largely unknown. We developed APEX-mediated chromatin labeling and purification (ALaP) to identify the genomic regions proximal to PML bodies. We found that PML bodies associate with active regulatory regions across the genome and with ∼300 kb of the short arm of the Y chromosome (YS300) in mouse embryonic stem cells. The PML body association with YS300 is essential for the transcriptional activity of the neighboring Y-linked clustered genes. Mechanistically, PML bodies provide specific nuclear spaces that the de novo DNA methyltransferase DNMT3A cannot access, resulting in the steady maintenance of a hypo-methylated state at Y-linked gene promoters. Our study underscores a new mechanism for gene regulation in the 3D nuclear space and provides insights into the functional properties of nuclear structures for genome function.</p>',
'date' => '2020-04-28',
'pmid' => 'http://www.pubmed.gov/32353257',
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'name' => 'Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin.',
'authors' => 'Dong W, Oya E, Zahedi Y, Prasad P, Svensson JP, Lennartsson A, Ekwall K, Durand-Dubief M',
'description' => '<p>Heterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.</p>',
'date' => '2020-04-08',
'pmid' => 'http://www.pubmed.gov/32269268',
'doi' => '10.1038/s41598-020-63209-y',
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'name' => 'Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance.',
'authors' => 'Iglesias N, Paulo JA, Tatarakis A, Wang X, Edwards AL, Bhanu NV, Garcia BA, Haas W, Gygi SP, Moazed D',
'description' => '<p>Spatially and functionally distinct domains of heterochromatin and euchromatin play important roles in the maintenance of chromosome stability and regulation of gene expression, but a comprehensive knowledge of their composition is lacking. Here, we develop a strategy for the isolation of native Schizosaccharomyces pombe heterochromatin and euchromatin fragments and analyze their composition by using quantitative mass spectrometry. The shared and euchromatin-specific proteomes contain proteins involved in DNA and chromatin metabolism and in transcription, respectively. The heterochromatin-specific proteome includes all proteins with known roles in heterochromatin formation and, in addition, is enriched for subsets of nucleoporins and inner nuclear membrane (INM) proteins, which associate with different chromatin domains. While the INM proteins are required for the integrity of the nucleolus, containing ribosomal DNA repeats, the nucleoporins are required for aggregation of heterochromatic foci and epigenetic inheritance. The results provide a comprehensive picture of heterochromatin-associated proteins and suggest a role for specific nucleoporins in heterochromatin function.</p>',
'date' => '2019-11-07',
'pmid' => 'http://www.pubmed.gov/31784357',
'doi' => '10.1016/j.molcel.2019.10.018',
'modified' => '2020-02-25 13:37:25',
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'name' => 'Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer.',
'authors' => 'Du Q, Bert SA, Armstrong NJ, Caldon CE, Song JZ, Nair SS, Gould CM, Luu PL, Peters T, Khoury A, Qu W, Zotenko E, Stirzaker C, Clark SJ',
'description' => '<p>DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.</p>',
'date' => '2019-01-24',
'pmid' => 'http://www.pubmed.gov/30679435',
'doi' => '10.1038/s41467-019-08302-1',
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'name' => 'Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability.',
'authors' => 'Iglesias N, Currie MA, Jih G, Paulo JA, Siuti N, Kalocsay M, Gygi SP, Moazed D',
'description' => '<p>Histone H3 lysine 9 methylation (H3K9me) mediates heterochromatic gene silencing and is important for genome stability and the regulation of gene expression. The establishment and epigenetic maintenance of heterochromatin involve the recruitment of H3K9 methyltransferases to specific sites on DNA, followed by the recognition of pre-existing H3K9me by the methyltransferase and methylation of proximal histone H3. This positive feedback loop must be tightly regulated to prevent deleterious epigenetic gene silencing. Extrinsic anti-silencing mechanisms involving histone demethylation or boundary elements help to limit the spread of inappropriate H3K9me. However, how H3K9 methyltransferase activity is locally restricted or prevented from initiating random H3K9me-which would lead to aberrant gene silencing and epigenetic instability-is not fully understood. Here we reveal an autoinhibited conformation in the conserved H3K9 methyltransferase Clr4 (also known as Suv39h) of the fission yeast Schizosaccharomyces pombe that has a critical role in preventing aberrant heterochromatin formation. Biochemical and X-ray crystallographic data show that an internal loop in Clr4 inhibits the catalytic activity of this enzyme by blocking the histone H3K9 substrate-binding pocket, and that automethylation of specific lysines in this loop promotes a conformational switch that enhances the H3K9me activity of Clr4. Mutations that are predicted to disrupt this regulation lead to aberrant H3K9me, loss of heterochromatin domains and inhibition of growth, demonstrating the importance of the intrinsic inhibition and auto-activation of Clr4 in regulating the deposition of H3K9me and in preventing epigenetic instability. Conservation of the Clr4 autoregulatory loop in other H3K9 methyltransferases and the automethylation of a corresponding lysine in the human SUV39H2 homologue suggest that the mechanism described here is broadly conserved.</p>',
'date' => '2018-08-01',
'pmid' => 'http://www.pubmed.gov/30051891',
'doi' => '10.1038/s41586-018-0398-2',
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'name' => 'Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation.',
'authors' => 'Yu R, Wang X, Moazed D',
'description' => '<p>Histone post-translational modifications (PTMs) are associated with epigenetic states that form the basis for cell-type-specific gene expression. Once established, histone PTMs can be maintained by positive feedback involving enzymes that recognize a pre-existing histone modification and catalyse the same modification on newly deposited histones. Recent studies suggest that in wild-type cells, histone PTM-based positive feedback is too weak to mediate epigenetic inheritance in the absence of other inputs. RNA interference (RNAi)-mediated histone H3 lysine 9 methylation (H3K9me) and heterochromatin formation define a potential epigenetic inheritance mechanism in which positive feedback involving short interfering RNA (siRNA) amplification can be directly coupled to histone PTM positive feedback. However, it is not known whether the coupling of these two feedback loops can maintain epigenetic silencing independently of DNA sequence and in the absence of enabling mutations that disrupt genome-wide chromatin structure or transcription. Here, using the fission yeast Schizosaccharomyces pombe, we show that siRNA-induced H3K9me and silencing of a euchromatic gene can be epigenetically inherited in cis during multiple mitotic and meiotic cell divisions in wild-type cells. This inheritance involves the spreading of secondary siRNAs and H3K9me3 to the targeted gene and surrounding areas, and requires both RNAi and H3K9me, suggesting that the siRNA and H3K9me positive-feedback loops act synergistically to maintain silencing. By contrast, when maintained solely by histone PTM positive feedback, silencing is erased by H3K9 demethylation promoted by Epe1, or by interallelic interactions that occur after mating to cells containing an expressed allele even in the absence of Epe1. These findings demonstrate that the RNAi machinery can mediate transgenerational epigenetic inheritance independently of DNA sequence or enabling mutations, and reveal a role for the coupling of the siRNA and H3K9me positive-feedback loops in the protection of epigenetic alleles from erasure.</p>',
'date' => '2018-06-20',
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'name' => 'Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription',
'authors' => 'Jih G. et al.',
'description' => '<p>Heterochromatic DNA domains have important roles in the regulation of gene expression and maintenance of genome stability by silencing repetitive DNA elements and transposons. From fission yeast to mammals, heterochromatin assembly at DNA repeats involves the activity of small noncoding RNAs (sRNAs) associated with the RNA interference (RNAi) pathway. Typically, sRNAs, originating from long noncoding RNAs, guide Argonaute-containing effector complexes to complementary nascent RNAs to initiate histone H3 lysine 9 di- and trimethylation (H3K9me2 and H3K9me3, respectively) and the formation of heterochromatin. H3K9me is in turn required for the recruitment of RNAi to chromatin to promote the amplification of sRNA. Yet, how heterochromatin formation, which silences transcription, can proceed by a co-transcriptional mechanism that also promotes sRNA generation remains paradoxical. Here, using Clr4, the fission yeast Schizosaccharomyces pombe homologue of mammalian SUV39H H3K9 methyltransferases, we design active-site mutations that block H3K9me3, but allow H3K9me2 catalysis. We show that H3K9me2 defines a functionally distinct heterochromatin state that is sufficient for RNAi-dependent co-transcriptional gene silencing at pericentromeric DNA repeats. Unlike H3K9me3 domains, which are transcriptionally silent, H3K9me2 domains are transcriptionally active, contain modifications associated with euchromatic transcription, and couple RNAi-mediated transcript degradation to the establishment of H3K9me domains. The two H3K9me states recruit reader proteins with different efficiencies, explaining their different downstream silencing functions. Furthermore, the transition from H3K9me2 to H3K9me3 is required for RNAi-independent epigenetic inheritance of H3K9me domains. Our findings demonstrate that H3K9me2 and H3K9me3 define functionally distinct chromatin states and uncover a mechanism for the formation of transcriptionally permissive heterochromatin that is compatible with its broadly conserved role in sRNA-mediated genome defence.</p>',
'date' => '2017-07-27',
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'description' => '<p><span>Diagenode is pleased to offer the first recombinant antibody against <strong>H3K9me3</strong>. It has has been selected using tailored phage-display libraries, and produced in </span><em>E.coli</em><span> eliminating animals from the antibody-production process. This recombinant antibody shows superior specificity and affinity as well as no lot-to-lot variation.</span></p>',
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP.png" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="288" height="254" /></p>
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-A.png" alt="H3K9me3 Antibody ChIP-seq Grade" caption="false" width="447" height="189" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-B.png" alt="H3K9me3 Antibody for ChIP-seq" caption="false" width="447" height="60" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-C.png" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="447" height="59" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-D.png" alt="H3K9me3 Antibody validated in ChIP-seq" caption="false" width="447" height="66" /></p>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-IF.png" alt="H3K9me3 Antibody validated in Immunofluorescence" caption="false" width="288" height="292" /></p>
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<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
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<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
<ul>
<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
</ul>
<p></p>
<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
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'description' => '<p><span>Diagenode is pleased to offer the first recombinant antibody against <strong>H3K9me3</strong>. It has has been selected using tailored phage-display libraries, and produced in </span><em>E.coli</em><span> eliminating animals from the antibody-production process. This recombinant antibody shows superior specificity and affinity as well as no lot-to-lot variation.</span></p>',
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP.png" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="288" height="254" /></p>
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-A.png" alt="H3K9me3 Antibody ChIP-seq Grade" caption="false" width="447" height="189" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-B.png" alt="H3K9me3 Antibody for ChIP-seq" caption="false" width="447" height="60" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-C.png" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="447" height="59" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-D.png" alt="H3K9me3 Antibody validated in ChIP-seq" caption="false" width="447" height="66" /></p>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-IF.png" alt="H3K9me3 Antibody validated in Immunofluorescence" caption="false" width="288" height="292" /></p>
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<div class="small-8 columns">
<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
</div>
</div>
<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
<ul>
<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
</ul>
<p></p>
<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
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'meta_description' => 'Diagenode offers a wide range of antibodies and technical support for ChIP-qPCR applications',
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'name' => 'Datasheet H3K9me3 C15500003',
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'name' => 'Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription',
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'description' => '<p>Heterochromatic DNA domains have important roles in the regulation of gene expression and maintenance of genome stability by silencing repetitive DNA elements and transposons. From fission yeast to mammals, heterochromatin assembly at DNA repeats involves the activity of small noncoding RNAs (sRNAs) associated with the RNA interference (RNAi) pathway. Typically, sRNAs, originating from long noncoding RNAs, guide Argonaute-containing effector complexes to complementary nascent RNAs to initiate histone H3 lysine 9 di- and trimethylation (H3K9me2 and H3K9me3, respectively) and the formation of heterochromatin. H3K9me is in turn required for the recruitment of RNAi to chromatin to promote the amplification of sRNA. Yet, how heterochromatin formation, which silences transcription, can proceed by a co-transcriptional mechanism that also promotes sRNA generation remains paradoxical. Here, using Clr4, the fission yeast Schizosaccharomyces pombe homologue of mammalian SUV39H H3K9 methyltransferases, we design active-site mutations that block H3K9me3, but allow H3K9me2 catalysis. We show that H3K9me2 defines a functionally distinct heterochromatin state that is sufficient for RNAi-dependent co-transcriptional gene silencing at pericentromeric DNA repeats. Unlike H3K9me3 domains, which are transcriptionally silent, H3K9me2 domains are transcriptionally active, contain modifications associated with euchromatic transcription, and couple RNAi-mediated transcript degradation to the establishment of H3K9me domains. The two H3K9me states recruit reader proteins with different efficiencies, explaining their different downstream silencing functions. Furthermore, the transition from H3K9me2 to H3K9me3 is required for RNAi-independent epigenetic inheritance of H3K9me domains. Our findings demonstrate that H3K9me2 and H3K9me3 define functionally distinct chromatin states and uncover a mechanism for the formation of transcriptionally permissive heterochromatin that is compatible with its broadly conserved role in sRNA-mediated genome defence.</p>',
'date' => '2017-07-27',
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<thead>
<tr>
<th>Applications</th>
<th>Suggested dilution/amount</th>
<th>References</th>
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<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>0.2-1.8 μg per ChIP</td>
<td>Fig 1, 2</td>
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<tr>
<td>Immunofluorescence</td>
<td>1:500</td>
<td>Fig 3</td>
</tr>
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<p><small><sup>*</sup> Please note that the optimal antibody amount per IP should be determined by the end-user. We recommend testing 0.5-5 μg per IP.</small></p>',
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP.png" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="288" height="254" /></p>
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-A.png" alt="H3K9me3 Antibody ChIP-seq Grade" caption="false" width="447" height="189" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-B.png" alt="H3K9me3 Antibody for ChIP-seq" caption="false" width="447" height="60" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-C.png" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="447" height="59" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-D.png" alt="H3K9me3 Antibody validated in ChIP-seq" caption="false" width="447" height="66" /></p>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-IF.png" alt="H3K9me3 Antibody validated in Immunofluorescence" caption="false" width="288" height="292" /></p>
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<div class="small-8 columns">
<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
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<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
<ul>
<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
</ul>
<p></p>
<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
'label2' => 'Target Description',
'info2' => '<p>Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Trimethylation of histone H3K9 is associated with imprinted regions, satellite repeats and ZNF repeat genes.</p>',
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'slug' => 'h3k9me3-recombinant-antibody-and-negative-control-classic-10-ug',
'meta_title' => 'H3K9me3 Antibody - ChIP-seq Grade (C15500003) | Diagenode',
'meta_keywords' => 'H3K9me3 recombinant antibody,Chromatin immunoprecipitation sequencing(ChIP-seq)',
'meta_description' => 'H3K9me3 Recombinant Antibody and negative control validated in ChIP-seq, ChIP-qPCR and IF. Batch-specific data available on the website. Sample size available.',
'modified' => '2022-02-09 09:45:49',
'created' => '2016-07-12 10:34:24',
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'description' => 'Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Trimethylation of histone H3K9 is associated with imprinted regions, satellite repeats and ZNF repeat genes.',
'clonality' => '',
'isotype' => '',
'lot' => '001',
'concentration' => '0.25 µg/µl',
'reactivity' => 'Human, mouse, drosophila, yeast',
'type' => 'Monoclonal, Recombinant',
'purity' => 'affinity purified',
'classification' => '',
'application_table' => '<table>
<thead>
<tr>
<th>Applications</th>
<th>Suggested dilution/amount</th>
<th>References</th>
</tr>
</thead>
<tbody>
<tr>
<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>0.2-1.8 μg per ChIP</td>
<td>Fig 1, 2</td>
</tr>
<tr>
<td>Immunofluorescence</td>
<td>1:500</td>
<td>Fig 3</td>
</tr>
</tbody>
</table>
<p><small><sup>*</sup> Please note that the optimal antibody amount per IP should be determined by the end-user. We recommend testing 0.5-5 μg per IP.</small></p>',
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'precautions' => 'This product is for research use only. Not for use in diagnostic or therapeutic procedures.',
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'name' => 'H3K9me3 recombinant antibody and negative control',
'description' => '<p><span>Diagenode is pleased to offer the first recombinant antibody against <strong>H3K9me3</strong>. It has has been selected using tailored phage-display libraries, and produced in </span><em>E.coli</em><span> eliminating animals from the antibody-production process. This recombinant antibody shows superior specificity and affinity as well as no lot-to-lot variation.</span></p>',
'label1' => 'Validation Data',
'info1' => '<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP.png" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="288" height="254" /></p>
</div>
<div class="small-8 columns">
<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-A.png" alt="H3K9me3 Antibody ChIP-seq Grade" caption="false" width="447" height="189" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-B.png" alt="H3K9me3 Antibody for ChIP-seq" caption="false" width="447" height="60" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-C.png" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="447" height="59" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-D.png" alt="H3K9me3 Antibody validated in ChIP-seq" caption="false" width="447" height="66" /></p>
</div>
<div class="small-6 columns">
<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-IF.png" alt="H3K9me3 Antibody validated in Immunofluorescence" caption="false" width="288" height="292" /></p>
</div>
<div class="small-8 columns">
<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
</div>
</div>
<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
<ul>
<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
</ul>
<p></p>
<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
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<p>Diagenode offers huge selection of highly sensitive antibodies validated in IF.</p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15200229-IF.jpg" alt="" height="245" width="256" /></p>
<p><sup><strong>Immunofluorescence using the Diagenode monoclonal antibody directed against CRISPR/Cas9</strong></sup></p>
<p><sup>HeLa cells transfected with a Cas9 expression vector (left) or untransfected cells (right) were fixed in methanol at -20°C, permeabilized with acetone at -20°C and blocked with PBS containing 2% BSA. The cells were stained with the Cas9 C-terminal antibody (Cat. No. C15200229) diluted 1:400, followed by incubation with an anti-mouse secondary antibody coupled to AF488. The bottom images show counter-staining of the nuclei with Hoechst 33342.</sup></p>
<h5><sup>Check our selection of antibodies validated in IF.</sup></h5>',
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<p><span style="font-weight: 400;">Diagenode provides leading solutions for epigenetic research. Because ChIP-seq is a widely-used technique, we validate our antibodies in ChIP and ChIP-seq experiments (in addition to conventional methods like Western blot, Dot blot, ELISA, and immunofluorescence) to provide the highest quality antibody. We standardize our validation and production to guarantee high product quality without technical bias. Diagenode guarantees ChIP-seq grade antibody performance under our suggested conditions.</span></p>
<div class="row">
<div class="small-12 medium-9 large-9 columns">
<p><strong>ChIP-seq profile</strong> of active (H3K4me3 and H3K36me3) and inactive (H3K27me3) marks using Diagenode antibodies.</p>
<img src="https://www.diagenode.com/img/categories/antibodies/chip-seq-grade-antibodies.png" /></div>
<div class="small-12 medium-3 large-3 columns">
<p><small> ChIP was performed on sheared chromatin from 100,000 K562 cells using iDeal ChIP-seq kit for Histones (cat. No. C01010051) with 1 µg of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 µg of the antibody against H3K36me3 (cat. No. C15410192). The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. The figure shows the signal distribution along the complete sequence of human chromosome 3, a zoomin to a 10 Mb region and a further zoomin to a 1.5 Mb region. </small></p>
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<p>Diagenode’s highly validated antibodies:</p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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'description' => '<p>Histones are the main protein components of chromatin involved in the compaction of DNA into nucleosomes, the basic units of chromatin. A <strong>nucleosome</strong> consists of one pair of each of the core histones (<strong>H2A</strong>, <strong>H2B</strong>, <strong>H3</strong> and <strong>H4</strong>) forming an octameric structure wrapped by 146 base pairs of DNA. The different nucleosomes are linked by the linker histone<strong> H1, </strong>allowing for further condensation of chromatin.</p>
<p>The core histones have a globular structure with large unstructured N-terminal tails protruding from the nucleosome. They can undergo to multiple post-translational modifications (PTM), mainly at the N-terminal tails. These <strong>post-translational modifications </strong>include methylation, acetylation, phosphorylation, ubiquitinylation, citrullination, sumoylation, deamination and crotonylation. The most well characterized PTMs are <strong>methylation,</strong> <strong>acetylation and phosphorylation</strong>. Histone methylation occurs mainly on lysine (K) residues, which can be mono-, di- or tri-methylated, and on arginines (R), which can be mono-methylated and symmetrically or asymmetrically di-methylated. Histone acetylation occurs on lysines and histone phosphorylation mainly on serines (S), threonines (T) and tyrosines (Y).</p>
<p>The PTMs of the different residues are involved in numerous processes such as DNA repair, DNA replication and chromosome condensation. They influence the chromatin organization and can be positively or negatively associated with gene expression. Trimethylation of H3K4, H3K36 and H3K79, and lysine acetylation generally result in an open chromatin configuration (figure below) and are therefore associated with <strong>euchromatin</strong> and gene activation. Trimethylation of H3K9, K3K27 and H4K20, on the other hand, is enriched in <strong>heterochromatin </strong>and associated with gene silencing. The combination of different histone modifications is called the "<strong>histone code</strong>”, analogous to the genetic code.</p>
<p><img src="https://www.diagenode.com/img/categories/antibodies/histone-marks-illustration.png" /></p>
<p>Diagenode is proud to offer a large range of antibodies against histones and histone modifications. Our antibodies are highly specific and have been validated in many applications, including <strong>ChIP</strong> and <strong>ChIP-seq</strong>.</p>
<p>Diagenode’s collection includes antibodies recognizing:</p>
<ul>
<li><strong>Histone H1 variants</strong></li>
<li><strong>Histone H2A, H2A variants and histone H2A</strong> <strong>modifications</strong> (serine phosphorylation, lysine acetylation, lysine ubiquitinylation)</li>
<li><strong>Histone H2B and H2B</strong> <strong>modifications </strong>(serine phosphorylation, lysine acetylation)</li>
<li><strong>Histone H3 and H3 modifications </strong>(lysine methylation (mono-, di- and tri-methylated), lysine acetylation, serine phosphorylation, threonine phosphorylation, arginine methylation (mono-methylated, symmetrically and asymmetrically di-methylated))</li>
<li><strong>Histone H4 and H4 modifications (</strong>lysine methylation (mono-, di- and tri-methylated), lysine acetylation, arginine methylation (mono-methylated and symmetrically di-methylated), serine phosphorylation )</li>
</ul>
<p><span style="font-weight: 400;"><strong>HDAC's HAT's, HMT's and other</strong> <strong>enzymes</strong> which modify histones can be found in the category <a href="../categories/chromatin-modifying-proteins-histone-transferase">Histone modifying enzymes</a><br /></span></p>
<p><span style="font-weight: 400;"> Diagenode’s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> Expert technical support</span></li>
<li><span style="font-weight: 400;"> Sample sizes available</span></li>
<li><span style="font-weight: 400;"> 100% satisfaction guarantee</span></li>
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'meta_description' => 'Polyclonal and Monoclonal Antibodies against Histones and their modifications validated for many applications, including Chromatin Immunoprecipitation (ChIP) and ChIP-Sequencing (ChIP-seq)',
'meta_title' => 'Histone and Modified Histone Antibodies | Diagenode',
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'description' => '<h1><strong>Validated epigenetics antibodies</strong> – care for a sample?<br /> </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> - 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> with rigorous QC and validation</li>
<li><strong>Classified</strong> based on level of validation for flexibility of application</li>
</ul>
<p>Existing sample sizes are listed below. We will soon expand our collection. 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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'description' => '<div class="row">
<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
<p></p>
</div>
</div>
<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
<div class="row">
<div class="small-12 medium-6 large-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" alt="" width="400" height="315" /> </div>
<div class="small-12 medium-6 large-6 columns">
<p></p>
<p></p>
<p></p>
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<p></p>
<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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'meta_description' => 'Diagenode Offers Extensively Validated ChIP-Grade Antibodies, Confirmed for their Specificity, and high level of Performance in Chromatin Immunoprecipitation ChIP',
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'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
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'description' => '<p>More than in any other immuoprecipitation assays, quality antibodies are critical tools in many epigenetics experiments. Since 10 years, Diagenode has developed the most stringent quality production available on the market for antibodies exclusively focused on epigenetic uses. All our antibodies have been qualified to work in epigenetic applications.</p>',
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'name' => 'H3K9 dimethylation safeguards cancer cells against activation of theinterferon pathway.',
'authors' => 'Hansen A. M. et al.',
'description' => '<p>Activation of interferon genes constitutes an important anticancer pathway able to restrict proliferation of cancer cells. Here, we demonstrate that the H3K9me3 histone methyltransferase (HMT) suppressor of variegation 3-9 homolog 1 (SUV39H1) is required for the proliferation of acute myeloid leukemia (AML) and find that its loss leads to activation of the interferon pathway. Mechanistically, we show that this occurs via destabilization of a complex composed of SUV39H1 and the two H3K9me2 HMTs, G9A and GLP. Indeed, loss of H3K9me2 correlated with the activation of key interferon pathway genes, and interference with the activities of G9A/GLP largely phenocopied loss of SUV39H1. Last, we demonstrate that inhibition of G9A/GLP synergized with DNA demethylating agents and that SUV39H1 constitutes a potential biomarker for the response to hypomethylation treatment. Collectively, we uncovered a clinically relevant role for H3K9me2 in safeguarding cancer cells against activation of the interferon pathway.</p>',
'date' => '2022-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35302840',
'doi' => '10.1126/sciadv.abf8627',
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'name' => 'SUV39 SET domains mediate crosstalk of heterochromatic histone marks.',
'authors' => 'Stirpe, Alessandro and Guidotti, Nora and Northall, Sarah Jand Kilic, Sinan and Hainard, Alexandre and Vadas, Oscar andFierz, Beat and Schalch, Thomas',
'description' => '<p>The SUV39 class of methyltransferase enzymes deposits histone H3 lysine 9 di- and trimethylation (H3K9me2/3), the hallmark of constitutive heterochromatin. How these enzymes are regulated to mark specific genomic regions as heterochromatic is poorly understood. Clr4 is the sole H3K9me2/3 methyltransferase in the fission yeast and recent evidence suggests that ubiquitination of lysine 14 on histone H3 (H3K14ub) plays a key role in H3K9 methylation. However, the molecular mechanism of this regulation and its role in heterochromatin formation remain to be determined. Our structure-function approach shows that the H3K14ub substrate binds specifically and tightly to the catalytic domain of Clr4, and thereby stimulates the enzyme by over 250-fold. Mutations that disrupt this mechanism lead to a loss of H3K9me2/3 and abolish heterochromatin silencing similar to deletion. Comparison with mammalian SET domain proteins suggests that the Clr4 SET domain harbors a conserved sensor for H3K14ub, which mediates licensing of heterochromatin formation.</p>',
'date' => '2021-09-01',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/34524082/',
'doi' => '10.7554/eLife.62682',
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'name' => 'A conserved RNA degradation complex required for spreading and epigenetic inheritance of heterochromatin.',
'authors' => 'Shipkovenska G, Durango A, Kalocsay M, Gygi SP, Moazed D',
'description' => '<p>Heterochromatic domains containing histone H3 lysine 9 methylation (H3K9me) can be epigenetically inherited independently of underlying DNA sequence. To gain insight into the mechanisms that mediate epigenetic inheritance, we used a inducible heterochromatin formation system to perform a genetic screen for mutations that abolish heterochromatin inheritance without affecting its establishment. We identified mutations in several pathways, including the conserved and essential Rix1-associated complex (henceforth the rixosome), which contains RNA endonuclease and polynucleotide kinase activities with known roles in ribosomal RNA processing. We show that the rixosome is required for spreading and epigenetic inheritance of heterochromatin in fission yeast. Viable rixosome mutations that disrupt its association with Swi6/HP1 fail to localize to heterochromatin, lead to accumulation of heterochromatic RNAs, and block spreading of H3K9me and silencing into actively transcribed regions. These findings reveal a new pathway for degradation of heterochromatic RNAs with essential roles in heterochromatin spreading and inheritance.</p>',
'date' => '2020-06-03',
'pmid' => 'http://www.pubmed.gov/32491985',
'doi' => '10.7554/eLife.54341',
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'name' => 'Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion.',
'authors' => 'Kurihara M, Kato K, Sanbo C, Shigenobu S, Ohkawa Y, Fuchigami T, Miyanari Y',
'description' => '<p>The promyelocytic leukemia (PML) body is a phase-separated nuclear structure physically associated with chromatin, implying its crucial roles in genome functions. However, its role in transcriptional regulation is largely unknown. We developed APEX-mediated chromatin labeling and purification (ALaP) to identify the genomic regions proximal to PML bodies. We found that PML bodies associate with active regulatory regions across the genome and with ∼300 kb of the short arm of the Y chromosome (YS300) in mouse embryonic stem cells. The PML body association with YS300 is essential for the transcriptional activity of the neighboring Y-linked clustered genes. Mechanistically, PML bodies provide specific nuclear spaces that the de novo DNA methyltransferase DNMT3A cannot access, resulting in the steady maintenance of a hypo-methylated state at Y-linked gene promoters. Our study underscores a new mechanism for gene regulation in the 3D nuclear space and provides insights into the functional properties of nuclear structures for genome function.</p>',
'date' => '2020-04-28',
'pmid' => 'http://www.pubmed.gov/32353257',
'doi' => '10.1016/j.molcel.2020.04.004',
'modified' => '2020-08-17 10:28:27',
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'name' => 'Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin.',
'authors' => 'Dong W, Oya E, Zahedi Y, Prasad P, Svensson JP, Lennartsson A, Ekwall K, Durand-Dubief M',
'description' => '<p>Heterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.</p>',
'date' => '2020-04-08',
'pmid' => 'http://www.pubmed.gov/32269268',
'doi' => '10.1038/s41598-020-63209-y',
'modified' => '2020-08-17 10:48:09',
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'id' => '3825',
'name' => 'Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance.',
'authors' => 'Iglesias N, Paulo JA, Tatarakis A, Wang X, Edwards AL, Bhanu NV, Garcia BA, Haas W, Gygi SP, Moazed D',
'description' => '<p>Spatially and functionally distinct domains of heterochromatin and euchromatin play important roles in the maintenance of chromosome stability and regulation of gene expression, but a comprehensive knowledge of their composition is lacking. Here, we develop a strategy for the isolation of native Schizosaccharomyces pombe heterochromatin and euchromatin fragments and analyze their composition by using quantitative mass spectrometry. The shared and euchromatin-specific proteomes contain proteins involved in DNA and chromatin metabolism and in transcription, respectively. The heterochromatin-specific proteome includes all proteins with known roles in heterochromatin formation and, in addition, is enriched for subsets of nucleoporins and inner nuclear membrane (INM) proteins, which associate with different chromatin domains. While the INM proteins are required for the integrity of the nucleolus, containing ribosomal DNA repeats, the nucleoporins are required for aggregation of heterochromatic foci and epigenetic inheritance. The results provide a comprehensive picture of heterochromatin-associated proteins and suggest a role for specific nucleoporins in heterochromatin function.</p>',
'date' => '2019-11-07',
'pmid' => 'http://www.pubmed.gov/31784357',
'doi' => '10.1016/j.molcel.2019.10.018',
'modified' => '2020-02-25 13:37:25',
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'name' => 'Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer.',
'authors' => 'Du Q, Bert SA, Armstrong NJ, Caldon CE, Song JZ, Nair SS, Gould CM, Luu PL, Peters T, Khoury A, Qu W, Zotenko E, Stirzaker C, Clark SJ',
'description' => '<p>DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.</p>',
'date' => '2019-01-24',
'pmid' => 'http://www.pubmed.gov/30679435',
'doi' => '10.1038/s41467-019-08302-1',
'modified' => '2019-07-01 11:26:49',
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'id' => '3623',
'name' => 'Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability.',
'authors' => 'Iglesias N, Currie MA, Jih G, Paulo JA, Siuti N, Kalocsay M, Gygi SP, Moazed D',
'description' => '<p>Histone H3 lysine 9 methylation (H3K9me) mediates heterochromatic gene silencing and is important for genome stability and the regulation of gene expression. The establishment and epigenetic maintenance of heterochromatin involve the recruitment of H3K9 methyltransferases to specific sites on DNA, followed by the recognition of pre-existing H3K9me by the methyltransferase and methylation of proximal histone H3. This positive feedback loop must be tightly regulated to prevent deleterious epigenetic gene silencing. Extrinsic anti-silencing mechanisms involving histone demethylation or boundary elements help to limit the spread of inappropriate H3K9me. However, how H3K9 methyltransferase activity is locally restricted or prevented from initiating random H3K9me-which would lead to aberrant gene silencing and epigenetic instability-is not fully understood. Here we reveal an autoinhibited conformation in the conserved H3K9 methyltransferase Clr4 (also known as Suv39h) of the fission yeast Schizosaccharomyces pombe that has a critical role in preventing aberrant heterochromatin formation. Biochemical and X-ray crystallographic data show that an internal loop in Clr4 inhibits the catalytic activity of this enzyme by blocking the histone H3K9 substrate-binding pocket, and that automethylation of specific lysines in this loop promotes a conformational switch that enhances the H3K9me activity of Clr4. Mutations that are predicted to disrupt this regulation lead to aberrant H3K9me, loss of heterochromatin domains and inhibition of growth, demonstrating the importance of the intrinsic inhibition and auto-activation of Clr4 in regulating the deposition of H3K9me and in preventing epigenetic instability. Conservation of the Clr4 autoregulatory loop in other H3K9 methyltransferases and the automethylation of a corresponding lysine in the human SUV39H2 homologue suggest that the mechanism described here is broadly conserved.</p>',
'date' => '2018-08-01',
'pmid' => 'http://www.pubmed.gov/30051891',
'doi' => '10.1038/s41586-018-0398-2',
'modified' => '2019-05-16 11:19:37',
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(int) 8 => array(
'id' => '3626',
'name' => 'Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation.',
'authors' => 'Yu R, Wang X, Moazed D',
'description' => '<p>Histone post-translational modifications (PTMs) are associated with epigenetic states that form the basis for cell-type-specific gene expression. Once established, histone PTMs can be maintained by positive feedback involving enzymes that recognize a pre-existing histone modification and catalyse the same modification on newly deposited histones. Recent studies suggest that in wild-type cells, histone PTM-based positive feedback is too weak to mediate epigenetic inheritance in the absence of other inputs. RNA interference (RNAi)-mediated histone H3 lysine 9 methylation (H3K9me) and heterochromatin formation define a potential epigenetic inheritance mechanism in which positive feedback involving short interfering RNA (siRNA) amplification can be directly coupled to histone PTM positive feedback. However, it is not known whether the coupling of these two feedback loops can maintain epigenetic silencing independently of DNA sequence and in the absence of enabling mutations that disrupt genome-wide chromatin structure or transcription. Here, using the fission yeast Schizosaccharomyces pombe, we show that siRNA-induced H3K9me and silencing of a euchromatic gene can be epigenetically inherited in cis during multiple mitotic and meiotic cell divisions in wild-type cells. This inheritance involves the spreading of secondary siRNAs and H3K9me3 to the targeted gene and surrounding areas, and requires both RNAi and H3K9me, suggesting that the siRNA and H3K9me positive-feedback loops act synergistically to maintain silencing. By contrast, when maintained solely by histone PTM positive feedback, silencing is erased by H3K9 demethylation promoted by Epe1, or by interallelic interactions that occur after mating to cells containing an expressed allele even in the absence of Epe1. These findings demonstrate that the RNAi machinery can mediate transgenerational epigenetic inheritance independently of DNA sequence or enabling mutations, and reveal a role for the coupling of the siRNA and H3K9me positive-feedback loops in the protection of epigenetic alleles from erasure.</p>',
'date' => '2018-06-20',
'pmid' => 'http://www.pubmed.gov/29925950',
'doi' => '10.1038/s41586-018-0239-3',
'modified' => '2019-05-16 11:13:23',
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'id' => '3230',
'name' => 'Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription',
'authors' => 'Jih G. et al.',
'description' => '<p>Heterochromatic DNA domains have important roles in the regulation of gene expression and maintenance of genome stability by silencing repetitive DNA elements and transposons. From fission yeast to mammals, heterochromatin assembly at DNA repeats involves the activity of small noncoding RNAs (sRNAs) associated with the RNA interference (RNAi) pathway. Typically, sRNAs, originating from long noncoding RNAs, guide Argonaute-containing effector complexes to complementary nascent RNAs to initiate histone H3 lysine 9 di- and trimethylation (H3K9me2 and H3K9me3, respectively) and the formation of heterochromatin. H3K9me is in turn required for the recruitment of RNAi to chromatin to promote the amplification of sRNA. Yet, how heterochromatin formation, which silences transcription, can proceed by a co-transcriptional mechanism that also promotes sRNA generation remains paradoxical. Here, using Clr4, the fission yeast Schizosaccharomyces pombe homologue of mammalian SUV39H H3K9 methyltransferases, we design active-site mutations that block H3K9me3, but allow H3K9me2 catalysis. We show that H3K9me2 defines a functionally distinct heterochromatin state that is sufficient for RNAi-dependent co-transcriptional gene silencing at pericentromeric DNA repeats. Unlike H3K9me3 domains, which are transcriptionally silent, H3K9me2 domains are transcriptionally active, contain modifications associated with euchromatic transcription, and couple RNAi-mediated transcript degradation to the establishment of H3K9me domains. The two H3K9me states recruit reader proteins with different efficiencies, explaining their different downstream silencing functions. Furthermore, the transition from H3K9me2 to H3K9me3 is required for RNAi-independent epigenetic inheritance of H3K9me domains. Our findings demonstrate that H3K9me2 and H3K9me3 define functionally distinct chromatin states and uncover a mechanism for the formation of transcriptionally permissive heterochromatin that is compatible with its broadly conserved role in sRNA-mediated genome defence.</p>',
'date' => '2017-07-27',
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP.png" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="288" height="254" /></p>
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
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<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
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<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
<ul>
<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
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<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
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'description' => '<p>Heterochromatic DNA domains have important roles in the regulation of gene expression and maintenance of genome stability by silencing repetitive DNA elements and transposons. From fission yeast to mammals, heterochromatin assembly at DNA repeats involves the activity of small noncoding RNAs (sRNAs) associated with the RNA interference (RNAi) pathway. Typically, sRNAs, originating from long noncoding RNAs, guide Argonaute-containing effector complexes to complementary nascent RNAs to initiate histone H3 lysine 9 di- and trimethylation (H3K9me2 and H3K9me3, respectively) and the formation of heterochromatin. H3K9me is in turn required for the recruitment of RNAi to chromatin to promote the amplification of sRNA. Yet, how heterochromatin formation, which silences transcription, can proceed by a co-transcriptional mechanism that also promotes sRNA generation remains paradoxical. Here, using Clr4, the fission yeast Schizosaccharomyces pombe homologue of mammalian SUV39H H3K9 methyltransferases, we design active-site mutations that block H3K9me3, but allow H3K9me2 catalysis. We show that H3K9me2 defines a functionally distinct heterochromatin state that is sufficient for RNAi-dependent co-transcriptional gene silencing at pericentromeric DNA repeats. Unlike H3K9me3 domains, which are transcriptionally silent, H3K9me2 domains are transcriptionally active, contain modifications associated with euchromatic transcription, and couple RNAi-mediated transcript degradation to the establishment of H3K9me domains. The two H3K9me states recruit reader proteins with different efficiencies, explaining their different downstream silencing functions. Furthermore, the transition from H3K9me2 to H3K9me3 is required for RNAi-independent epigenetic inheritance of H3K9me domains. Our findings demonstrate that H3K9me2 and H3K9me3 define functionally distinct chromatin states and uncover a mechanism for the formation of transcriptionally permissive heterochromatin that is compatible with its broadly conserved role in sRNA-mediated genome defence.</p>',
'date' => '2017-07-27',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28682306',
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
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<p><small><strong>Material required</strong></small></p>
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<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
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<p></p>
<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-D.png" alt="H3K9me3 Antibody validated in ChIP-seq" caption="false" width="447" height="66" /></p>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-IF.png" alt="H3K9me3 Antibody validated in Immunofluorescence" caption="false" width="288" height="292" /></p>
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<div class="small-8 columns">
<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
</div>
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<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
<ul>
<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
</ul>
<p></p>
<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
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<p>Diagenode offers huge selection of highly sensitive antibodies validated in IF.</p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15200229-IF.jpg" alt="" height="245" width="256" /></p>
<p><sup><strong>Immunofluorescence using the Diagenode monoclonal antibody directed against CRISPR/Cas9</strong></sup></p>
<p><sup>HeLa cells transfected with a Cas9 expression vector (left) or untransfected cells (right) were fixed in methanol at -20°C, permeabilized with acetone at -20°C and blocked with PBS containing 2% BSA. The cells were stained with the Cas9 C-terminal antibody (Cat. No. C15200229) diluted 1:400, followed by incubation with an anti-mouse secondary antibody coupled to AF488. The bottom images show counter-staining of the nuclei with Hoechst 33342.</sup></p>
<h5><sup>Check our selection of antibodies validated in IF.</sup></h5>',
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<p><span style="font-weight: 400;">Diagenode provides leading solutions for epigenetic research. Because ChIP-seq is a widely-used technique, we validate our antibodies in ChIP and ChIP-seq experiments (in addition to conventional methods like Western blot, Dot blot, ELISA, and immunofluorescence) to provide the highest quality antibody. We standardize our validation and production to guarantee high product quality without technical bias. Diagenode guarantees ChIP-seq grade antibody performance under our suggested conditions.</span></p>
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<div class="small-12 medium-9 large-9 columns">
<p><strong>ChIP-seq profile</strong> of active (H3K4me3 and H3K36me3) and inactive (H3K27me3) marks using Diagenode antibodies.</p>
<img src="https://www.diagenode.com/img/categories/antibodies/chip-seq-grade-antibodies.png" /></div>
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<p><small> ChIP was performed on sheared chromatin from 100,000 K562 cells using iDeal ChIP-seq kit for Histones (cat. No. C01010051) with 1 µg of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 µg of the antibody against H3K36me3 (cat. No. C15410192). The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. The figure shows the signal distribution along the complete sequence of human chromosome 3, a zoomin to a 10 Mb region and a further zoomin to a 1.5 Mb region. </small></p>
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<p>Diagenode’s highly validated antibodies:</p>
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<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
<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>
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'description' => '<p>Histones are the main protein components of chromatin involved in the compaction of DNA into nucleosomes, the basic units of chromatin. A <strong>nucleosome</strong> consists of one pair of each of the core histones (<strong>H2A</strong>, <strong>H2B</strong>, <strong>H3</strong> and <strong>H4</strong>) forming an octameric structure wrapped by 146 base pairs of DNA. The different nucleosomes are linked by the linker histone<strong> H1, </strong>allowing for further condensation of chromatin.</p>
<p>The core histones have a globular structure with large unstructured N-terminal tails protruding from the nucleosome. They can undergo to multiple post-translational modifications (PTM), mainly at the N-terminal tails. These <strong>post-translational modifications </strong>include methylation, acetylation, phosphorylation, ubiquitinylation, citrullination, sumoylation, deamination and crotonylation. The most well characterized PTMs are <strong>methylation,</strong> <strong>acetylation and phosphorylation</strong>. Histone methylation occurs mainly on lysine (K) residues, which can be mono-, di- or tri-methylated, and on arginines (R), which can be mono-methylated and symmetrically or asymmetrically di-methylated. Histone acetylation occurs on lysines and histone phosphorylation mainly on serines (S), threonines (T) and tyrosines (Y).</p>
<p>The PTMs of the different residues are involved in numerous processes such as DNA repair, DNA replication and chromosome condensation. They influence the chromatin organization and can be positively or negatively associated with gene expression. Trimethylation of H3K4, H3K36 and H3K79, and lysine acetylation generally result in an open chromatin configuration (figure below) and are therefore associated with <strong>euchromatin</strong> and gene activation. Trimethylation of H3K9, K3K27 and H4K20, on the other hand, is enriched in <strong>heterochromatin </strong>and associated with gene silencing. The combination of different histone modifications is called the "<strong>histone code</strong>”, analogous to the genetic code.</p>
<p><img src="https://www.diagenode.com/img/categories/antibodies/histone-marks-illustration.png" /></p>
<p>Diagenode is proud to offer a large range of antibodies against histones and histone modifications. Our antibodies are highly specific and have been validated in many applications, including <strong>ChIP</strong> and <strong>ChIP-seq</strong>.</p>
<p>Diagenode’s collection includes antibodies recognizing:</p>
<ul>
<li><strong>Histone H1 variants</strong></li>
<li><strong>Histone H2A, H2A variants and histone H2A</strong> <strong>modifications</strong> (serine phosphorylation, lysine acetylation, lysine ubiquitinylation)</li>
<li><strong>Histone H2B and H2B</strong> <strong>modifications </strong>(serine phosphorylation, lysine acetylation)</li>
<li><strong>Histone H3 and H3 modifications </strong>(lysine methylation (mono-, di- and tri-methylated), lysine acetylation, serine phosphorylation, threonine phosphorylation, arginine methylation (mono-methylated, symmetrically and asymmetrically di-methylated))</li>
<li><strong>Histone H4 and H4 modifications (</strong>lysine methylation (mono-, di- and tri-methylated), lysine acetylation, arginine methylation (mono-methylated and symmetrically di-methylated), serine phosphorylation )</li>
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<p><span style="font-weight: 400;"><strong>HDAC's HAT's, HMT's and other</strong> <strong>enzymes</strong> which modify histones can be found in the category <a href="../categories/chromatin-modifying-proteins-histone-transferase">Histone modifying enzymes</a><br /></span></p>
<p><span style="font-weight: 400;"> Diagenode’s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> Expert technical support</span></li>
<li><span style="font-weight: 400;"> Sample sizes available</span></li>
<li><span style="font-weight: 400;"> 100% satisfaction guarantee</span></li>
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<p>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>
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<li><strong>Focused</strong> - 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> with rigorous QC and validation</li>
<li><strong>Classified</strong> 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. 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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<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
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<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
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<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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'description' => '<p>The SUV39 class of methyltransferase enzymes deposits histone H3 lysine 9 di- and trimethylation (H3K9me2/3), the hallmark of constitutive heterochromatin. How these enzymes are regulated to mark specific genomic regions as heterochromatic is poorly understood. Clr4 is the sole H3K9me2/3 methyltransferase in the fission yeast and recent evidence suggests that ubiquitination of lysine 14 on histone H3 (H3K14ub) plays a key role in H3K9 methylation. However, the molecular mechanism of this regulation and its role in heterochromatin formation remain to be determined. Our structure-function approach shows that the H3K14ub substrate binds specifically and tightly to the catalytic domain of Clr4, and thereby stimulates the enzyme by over 250-fold. Mutations that disrupt this mechanism lead to a loss of H3K9me2/3 and abolish heterochromatin silencing similar to deletion. Comparison with mammalian SET domain proteins suggests that the Clr4 SET domain harbors a conserved sensor for H3K14ub, which mediates licensing of heterochromatin formation.</p>',
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'name' => 'A conserved RNA degradation complex required for spreading and epigenetic inheritance of heterochromatin.',
'authors' => 'Shipkovenska G, Durango A, Kalocsay M, Gygi SP, Moazed D',
'description' => '<p>Heterochromatic domains containing histone H3 lysine 9 methylation (H3K9me) can be epigenetically inherited independently of underlying DNA sequence. To gain insight into the mechanisms that mediate epigenetic inheritance, we used a inducible heterochromatin formation system to perform a genetic screen for mutations that abolish heterochromatin inheritance without affecting its establishment. We identified mutations in several pathways, including the conserved and essential Rix1-associated complex (henceforth the rixosome), which contains RNA endonuclease and polynucleotide kinase activities with known roles in ribosomal RNA processing. We show that the rixosome is required for spreading and epigenetic inheritance of heterochromatin in fission yeast. Viable rixosome mutations that disrupt its association with Swi6/HP1 fail to localize to heterochromatin, lead to accumulation of heterochromatic RNAs, and block spreading of H3K9me and silencing into actively transcribed regions. These findings reveal a new pathway for degradation of heterochromatic RNAs with essential roles in heterochromatin spreading and inheritance.</p>',
'date' => '2020-06-03',
'pmid' => 'http://www.pubmed.gov/32491985',
'doi' => '10.7554/eLife.54341',
'modified' => '2020-08-12 09:50:01',
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'id' => '3939',
'name' => 'Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion.',
'authors' => 'Kurihara M, Kato K, Sanbo C, Shigenobu S, Ohkawa Y, Fuchigami T, Miyanari Y',
'description' => '<p>The promyelocytic leukemia (PML) body is a phase-separated nuclear structure physically associated with chromatin, implying its crucial roles in genome functions. However, its role in transcriptional regulation is largely unknown. We developed APEX-mediated chromatin labeling and purification (ALaP) to identify the genomic regions proximal to PML bodies. We found that PML bodies associate with active regulatory regions across the genome and with ∼300 kb of the short arm of the Y chromosome (YS300) in mouse embryonic stem cells. The PML body association with YS300 is essential for the transcriptional activity of the neighboring Y-linked clustered genes. Mechanistically, PML bodies provide specific nuclear spaces that the de novo DNA methyltransferase DNMT3A cannot access, resulting in the steady maintenance of a hypo-methylated state at Y-linked gene promoters. Our study underscores a new mechanism for gene regulation in the 3D nuclear space and provides insights into the functional properties of nuclear structures for genome function.</p>',
'date' => '2020-04-28',
'pmid' => 'http://www.pubmed.gov/32353257',
'doi' => '10.1016/j.molcel.2020.04.004',
'modified' => '2020-08-17 10:28:27',
'created' => '2020-08-10 12:12:25',
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(int) 4 => array(
'id' => '3927',
'name' => 'Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin.',
'authors' => 'Dong W, Oya E, Zahedi Y, Prasad P, Svensson JP, Lennartsson A, Ekwall K, Durand-Dubief M',
'description' => '<p>Heterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.</p>',
'date' => '2020-04-08',
'pmid' => 'http://www.pubmed.gov/32269268',
'doi' => '10.1038/s41598-020-63209-y',
'modified' => '2020-08-17 10:48:09',
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(int) 5 => array(
'id' => '3825',
'name' => 'Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance.',
'authors' => 'Iglesias N, Paulo JA, Tatarakis A, Wang X, Edwards AL, Bhanu NV, Garcia BA, Haas W, Gygi SP, Moazed D',
'description' => '<p>Spatially and functionally distinct domains of heterochromatin and euchromatin play important roles in the maintenance of chromosome stability and regulation of gene expression, but a comprehensive knowledge of their composition is lacking. Here, we develop a strategy for the isolation of native Schizosaccharomyces pombe heterochromatin and euchromatin fragments and analyze their composition by using quantitative mass spectrometry. The shared and euchromatin-specific proteomes contain proteins involved in DNA and chromatin metabolism and in transcription, respectively. The heterochromatin-specific proteome includes all proteins with known roles in heterochromatin formation and, in addition, is enriched for subsets of nucleoporins and inner nuclear membrane (INM) proteins, which associate with different chromatin domains. While the INM proteins are required for the integrity of the nucleolus, containing ribosomal DNA repeats, the nucleoporins are required for aggregation of heterochromatic foci and epigenetic inheritance. The results provide a comprehensive picture of heterochromatin-associated proteins and suggest a role for specific nucleoporins in heterochromatin function.</p>',
'date' => '2019-11-07',
'pmid' => 'http://www.pubmed.gov/31784357',
'doi' => '10.1016/j.molcel.2019.10.018',
'modified' => '2020-02-25 13:37:25',
'created' => '2020-02-13 10:02:44',
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(int) 6 => array(
'id' => '3672',
'name' => 'Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer.',
'authors' => 'Du Q, Bert SA, Armstrong NJ, Caldon CE, Song JZ, Nair SS, Gould CM, Luu PL, Peters T, Khoury A, Qu W, Zotenko E, Stirzaker C, Clark SJ',
'description' => '<p>DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.</p>',
'date' => '2019-01-24',
'pmid' => 'http://www.pubmed.gov/30679435',
'doi' => '10.1038/s41467-019-08302-1',
'modified' => '2019-07-01 11:26:49',
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'id' => '3623',
'name' => 'Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability.',
'authors' => 'Iglesias N, Currie MA, Jih G, Paulo JA, Siuti N, Kalocsay M, Gygi SP, Moazed D',
'description' => '<p>Histone H3 lysine 9 methylation (H3K9me) mediates heterochromatic gene silencing and is important for genome stability and the regulation of gene expression. The establishment and epigenetic maintenance of heterochromatin involve the recruitment of H3K9 methyltransferases to specific sites on DNA, followed by the recognition of pre-existing H3K9me by the methyltransferase and methylation of proximal histone H3. This positive feedback loop must be tightly regulated to prevent deleterious epigenetic gene silencing. Extrinsic anti-silencing mechanisms involving histone demethylation or boundary elements help to limit the spread of inappropriate H3K9me. However, how H3K9 methyltransferase activity is locally restricted or prevented from initiating random H3K9me-which would lead to aberrant gene silencing and epigenetic instability-is not fully understood. Here we reveal an autoinhibited conformation in the conserved H3K9 methyltransferase Clr4 (also known as Suv39h) of the fission yeast Schizosaccharomyces pombe that has a critical role in preventing aberrant heterochromatin formation. Biochemical and X-ray crystallographic data show that an internal loop in Clr4 inhibits the catalytic activity of this enzyme by blocking the histone H3K9 substrate-binding pocket, and that automethylation of specific lysines in this loop promotes a conformational switch that enhances the H3K9me activity of Clr4. Mutations that are predicted to disrupt this regulation lead to aberrant H3K9me, loss of heterochromatin domains and inhibition of growth, demonstrating the importance of the intrinsic inhibition and auto-activation of Clr4 in regulating the deposition of H3K9me and in preventing epigenetic instability. Conservation of the Clr4 autoregulatory loop in other H3K9 methyltransferases and the automethylation of a corresponding lysine in the human SUV39H2 homologue suggest that the mechanism described here is broadly conserved.</p>',
'date' => '2018-08-01',
'pmid' => 'http://www.pubmed.gov/30051891',
'doi' => '10.1038/s41586-018-0398-2',
'modified' => '2019-05-16 11:19:37',
'created' => '2019-04-25 11:11:44',
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(int) 8 => array(
'id' => '3626',
'name' => 'Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation.',
'authors' => 'Yu R, Wang X, Moazed D',
'description' => '<p>Histone post-translational modifications (PTMs) are associated with epigenetic states that form the basis for cell-type-specific gene expression. Once established, histone PTMs can be maintained by positive feedback involving enzymes that recognize a pre-existing histone modification and catalyse the same modification on newly deposited histones. Recent studies suggest that in wild-type cells, histone PTM-based positive feedback is too weak to mediate epigenetic inheritance in the absence of other inputs. RNA interference (RNAi)-mediated histone H3 lysine 9 methylation (H3K9me) and heterochromatin formation define a potential epigenetic inheritance mechanism in which positive feedback involving short interfering RNA (siRNA) amplification can be directly coupled to histone PTM positive feedback. However, it is not known whether the coupling of these two feedback loops can maintain epigenetic silencing independently of DNA sequence and in the absence of enabling mutations that disrupt genome-wide chromatin structure or transcription. Here, using the fission yeast Schizosaccharomyces pombe, we show that siRNA-induced H3K9me and silencing of a euchromatic gene can be epigenetically inherited in cis during multiple mitotic and meiotic cell divisions in wild-type cells. This inheritance involves the spreading of secondary siRNAs and H3K9me3 to the targeted gene and surrounding areas, and requires both RNAi and H3K9me, suggesting that the siRNA and H3K9me positive-feedback loops act synergistically to maintain silencing. By contrast, when maintained solely by histone PTM positive feedback, silencing is erased by H3K9 demethylation promoted by Epe1, or by interallelic interactions that occur after mating to cells containing an expressed allele even in the absence of Epe1. These findings demonstrate that the RNAi machinery can mediate transgenerational epigenetic inheritance independently of DNA sequence or enabling mutations, and reveal a role for the coupling of the siRNA and H3K9me positive-feedback loops in the protection of epigenetic alleles from erasure.</p>',
'date' => '2018-06-20',
'pmid' => 'http://www.pubmed.gov/29925950',
'doi' => '10.1038/s41586-018-0239-3',
'modified' => '2019-05-16 11:13:23',
'created' => '2019-04-25 11:11:44',
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'id' => '3230',
'name' => 'Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription',
'authors' => 'Jih G. et al.',
'description' => '<p>Heterochromatic DNA domains have important roles in the regulation of gene expression and maintenance of genome stability by silencing repetitive DNA elements and transposons. From fission yeast to mammals, heterochromatin assembly at DNA repeats involves the activity of small noncoding RNAs (sRNAs) associated with the RNA interference (RNAi) pathway. Typically, sRNAs, originating from long noncoding RNAs, guide Argonaute-containing effector complexes to complementary nascent RNAs to initiate histone H3 lysine 9 di- and trimethylation (H3K9me2 and H3K9me3, respectively) and the formation of heterochromatin. H3K9me is in turn required for the recruitment of RNAi to chromatin to promote the amplification of sRNA. Yet, how heterochromatin formation, which silences transcription, can proceed by a co-transcriptional mechanism that also promotes sRNA generation remains paradoxical. Here, using Clr4, the fission yeast Schizosaccharomyces pombe homologue of mammalian SUV39H H3K9 methyltransferases, we design active-site mutations that block H3K9me3, but allow H3K9me2 catalysis. We show that H3K9me2 defines a functionally distinct heterochromatin state that is sufficient for RNAi-dependent co-transcriptional gene silencing at pericentromeric DNA repeats. Unlike H3K9me3 domains, which are transcriptionally silent, H3K9me2 domains are transcriptionally active, contain modifications associated with euchromatic transcription, and couple RNAi-mediated transcript degradation to the establishment of H3K9me domains. The two H3K9me states recruit reader proteins with different efficiencies, explaining their different downstream silencing functions. Furthermore, the transition from H3K9me2 to H3K9me3 is required for RNAi-independent epigenetic inheritance of H3K9me domains. Our findings demonstrate that H3K9me2 and H3K9me3 define functionally distinct chromatin states and uncover a mechanism for the formation of transcriptionally permissive heterochromatin that is compatible with its broadly conserved role in sRNA-mediated genome defence.</p>',
'date' => '2017-07-27',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28682306',
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'id' => '2434',
'antibody_id' => '361',
'name' => 'H3K9me3 recombinant antibody and negative control',
'description' => '<p><span>Diagenode is pleased to offer the first recombinant antibody against <strong>H3K9me3</strong>. It has has been selected using tailored phage-display libraries, and produced in </span><em>E.coli</em><span> eliminating animals from the antibody-production process. This recombinant antibody shows superior specificity and affinity as well as no lot-to-lot variation.</span></p>',
'label1' => 'Validation Data',
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP.png" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="288" height="254" /></p>
</div>
<div class="small-8 columns">
<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-A.png" alt="H3K9me3 Antibody ChIP-seq Grade" caption="false" width="447" height="189" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-B.png" alt="H3K9me3 Antibody for ChIP-seq" caption="false" width="447" height="60" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-C.png" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="447" height="59" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-D.png" alt="H3K9me3 Antibody validated in ChIP-seq" caption="false" width="447" height="66" /></p>
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<div class="small-6 columns">
<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-IF.png" alt="H3K9me3 Antibody validated in Immunofluorescence" caption="false" width="288" height="292" /></p>
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<div class="small-8 columns">
<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
</div>
</div>
<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
<ul>
<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
</ul>
<p></p>
<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
'label2' => 'Target Description',
'info2' => '<p>Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Trimethylation of histone H3K9 is associated with imprinted regions, satellite repeats and ZNF repeat genes.</p>',
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'description' => '<p><span>Diagenode is pleased to offer the first recombinant antibody against <strong>H3K9me3</strong>. It has has been selected using tailored phage-display libraries, and produced in </span><em>E.coli</em><span> eliminating animals from the antibody-production process. This recombinant antibody shows superior specificity and affinity as well as no lot-to-lot variation.</span></p>',
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP.png" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="288" height="254" /></p>
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-C.png" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="447" height="59" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-D.png" alt="H3K9me3 Antibody validated in ChIP-seq" caption="false" width="447" height="66" /></p>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
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<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
<ul>
<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
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<p></p>
<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-A.png" alt="H3K9me3 Antibody ChIP-seq Grade" caption="false" width="447" height="189" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-B.png" alt="H3K9me3 Antibody for ChIP-seq" caption="false" width="447" height="60" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-C.png" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="447" height="59" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-D.png" alt="H3K9me3 Antibody validated in ChIP-seq" caption="false" width="447" height="66" /></p>
</div>
<div class="small-6 columns">
<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-IF.png" alt="H3K9me3 Antibody validated in Immunofluorescence" caption="false" width="288" height="292" /></p>
</div>
<div class="small-8 columns">
<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
</div>
</div>
<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
<ul>
<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
</ul>
<p></p>
<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
'label2' => 'Target Description',
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'meta_title' => 'H3K9me3 Antibody - ChIP-seq Grade (C15500003) | Diagenode',
'meta_keywords' => 'H3K9me3 recombinant antibody,Chromatin immunoprecipitation sequencing(ChIP-seq)',
'meta_description' => 'H3K9me3 Recombinant Antibody and negative control validated in ChIP-seq, ChIP-qPCR and IF. Batch-specific data available on the website. Sample size available.',
'modified' => '2022-02-09 09:45:49',
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'description' => 'Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”. Histone methylation and demethylation is dynamically regulated by respectively histone methyl transferases and histone demethylases. Trimethylation of histone H3K9 is associated with imprinted regions, satellite repeats and ZNF repeat genes.',
'clonality' => '',
'isotype' => '',
'lot' => '001',
'concentration' => '0.25 µg/µl',
'reactivity' => 'Human, mouse, drosophila, yeast',
'type' => 'Monoclonal, Recombinant',
'purity' => 'affinity purified',
'classification' => '',
'application_table' => '<table>
<thead>
<tr>
<th>Applications</th>
<th>Suggested dilution/amount</th>
<th>References</th>
</tr>
</thead>
<tbody>
<tr>
<td>ChIP/ChIP-seq <sup>*</sup></td>
<td>0.2-1.8 μg per ChIP</td>
<td>Fig 1, 2</td>
</tr>
<tr>
<td>Immunofluorescence</td>
<td>1:500</td>
<td>Fig 3</td>
</tr>
</tbody>
</table>
<p><small><sup>*</sup> Please note that the optimal antibody amount per IP should be determined by the end-user. We recommend testing 0.5-5 μg per IP.</small></p>',
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'storage_buffer' => '',
'precautions' => 'This product is for research use only. Not for use in diagnostic or therapeutic procedures.',
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'name' => 'H3K9me3 recombinant antibody and negative control',
'description' => '<p><span>Diagenode is pleased to offer the first recombinant antibody against <strong>H3K9me3</strong>. It has has been selected using tailored phage-display libraries, and produced in </span><em>E.coli</em><span> eliminating animals from the antibody-production process. This recombinant antibody shows superior specificity and affinity as well as no lot-to-lot variation.</span></p>',
'label1' => 'Validation Data',
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP.png" alt="H3K9me3 Antibody ChIP Grade" caption="false" width="288" height="254" /></p>
</div>
<div class="small-8 columns">
<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-A.png" alt="H3K9me3 Antibody ChIP-seq Grade" caption="false" width="447" height="189" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-B.png" alt="H3K9me3 Antibody for ChIP-seq" caption="false" width="447" height="60" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-C.png" alt="H3K9me3 Antibody for ChIP-seq assay" caption="false" width="447" height="59" /></p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-ChIP-seq-D.png" alt="H3K9me3 Antibody validated in ChIP-seq" caption="false" width="447" height="66" /></p>
</div>
<div class="small-6 columns">
<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
</div>
</div>
<div class="row">
<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15500003-IF.png" alt="H3K9me3 Antibody validated in Immunofluorescence" caption="false" width="288" height="292" /></p>
</div>
<div class="small-8 columns">
<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
</div>
</div>
<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
<ul>
<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
</ul>
<p></p>
<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
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<p>Diagenode offers huge selection of highly sensitive antibodies validated in IF.</p>
<p><img src="https://www.diagenode.com/img/product/antibodies/C15200229-IF.jpg" alt="" height="245" width="256" /></p>
<p><sup><strong>Immunofluorescence using the Diagenode monoclonal antibody directed against CRISPR/Cas9</strong></sup></p>
<p><sup>HeLa cells transfected with a Cas9 expression vector (left) or untransfected cells (right) were fixed in methanol at -20°C, permeabilized with acetone at -20°C and blocked with PBS containing 2% BSA. The cells were stained with the Cas9 C-terminal antibody (Cat. No. C15200229) diluted 1:400, followed by incubation with an anti-mouse secondary antibody coupled to AF488. The bottom images show counter-staining of the nuclei with Hoechst 33342.</sup></p>
<h5><sup>Check our selection of antibodies validated in IF.</sup></h5>',
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<p><span style="font-weight: 400;">Diagenode provides leading solutions for epigenetic research. Because ChIP-seq is a widely-used technique, we validate our antibodies in ChIP and ChIP-seq experiments (in addition to conventional methods like Western blot, Dot blot, ELISA, and immunofluorescence) to provide the highest quality antibody. We standardize our validation and production to guarantee high product quality without technical bias. Diagenode guarantees ChIP-seq grade antibody performance under our suggested conditions.</span></p>
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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 µg of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 µg of the antibody against H3K36me3 (cat. No. C15410192). The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. The figure shows the signal distribution along the complete sequence of human chromosome 3, a zoomin to a 10 Mb region and a further zoomin to a 1.5 Mb region. </small></p>
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<p>Diagenode’s highly validated antibodies:</p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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'description' => '<p>Histones are the main protein components of chromatin involved in the compaction of DNA into nucleosomes, the basic units of chromatin. A <strong>nucleosome</strong> consists of one pair of each of the core histones (<strong>H2A</strong>, <strong>H2B</strong>, <strong>H3</strong> and <strong>H4</strong>) forming an octameric structure wrapped by 146 base pairs of DNA. The different nucleosomes are linked by the linker histone<strong> H1, </strong>allowing for further condensation of chromatin.</p>
<p>The core histones have a globular structure with large unstructured N-terminal tails protruding from the nucleosome. They can undergo to multiple post-translational modifications (PTM), mainly at the N-terminal tails. These <strong>post-translational modifications </strong>include methylation, acetylation, phosphorylation, ubiquitinylation, citrullination, sumoylation, deamination and crotonylation. The most well characterized PTMs are <strong>methylation,</strong> <strong>acetylation and phosphorylation</strong>. Histone methylation occurs mainly on lysine (K) residues, which can be mono-, di- or tri-methylated, and on arginines (R), which can be mono-methylated and symmetrically or asymmetrically di-methylated. Histone acetylation occurs on lysines and histone phosphorylation mainly on serines (S), threonines (T) and tyrosines (Y).</p>
<p>The PTMs of the different residues are involved in numerous processes such as DNA repair, DNA replication and chromosome condensation. They influence the chromatin organization and can be positively or negatively associated with gene expression. Trimethylation of H3K4, H3K36 and H3K79, and lysine acetylation generally result in an open chromatin configuration (figure below) and are therefore associated with <strong>euchromatin</strong> and gene activation. Trimethylation of H3K9, K3K27 and H4K20, on the other hand, is enriched in <strong>heterochromatin </strong>and associated with gene silencing. The combination of different histone modifications is called the "<strong>histone code</strong>”, analogous to the genetic code.</p>
<p><img src="https://www.diagenode.com/img/categories/antibodies/histone-marks-illustration.png" /></p>
<p>Diagenode is proud to offer a large range of antibodies against histones and histone modifications. Our antibodies are highly specific and have been validated in many applications, including <strong>ChIP</strong> and <strong>ChIP-seq</strong>.</p>
<p>Diagenode’s collection includes antibodies recognizing:</p>
<ul>
<li><strong>Histone H1 variants</strong></li>
<li><strong>Histone H2A, H2A variants and histone H2A</strong> <strong>modifications</strong> (serine phosphorylation, lysine acetylation, lysine ubiquitinylation)</li>
<li><strong>Histone H2B and H2B</strong> <strong>modifications </strong>(serine phosphorylation, lysine acetylation)</li>
<li><strong>Histone H3 and H3 modifications </strong>(lysine methylation (mono-, di- and tri-methylated), lysine acetylation, serine phosphorylation, threonine phosphorylation, arginine methylation (mono-methylated, symmetrically and asymmetrically di-methylated))</li>
<li><strong>Histone H4 and H4 modifications (</strong>lysine methylation (mono-, di- and tri-methylated), lysine acetylation, arginine methylation (mono-methylated and symmetrically di-methylated), serine phosphorylation )</li>
</ul>
<p><span style="font-weight: 400;"><strong>HDAC's HAT's, HMT's and other</strong> <strong>enzymes</strong> which modify histones can be found in the category <a href="../categories/chromatin-modifying-proteins-histone-transferase">Histone modifying enzymes</a><br /></span></p>
<p><span style="font-weight: 400;"> Diagenode’s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> Expert technical support</span></li>
<li><span style="font-weight: 400;"> Sample sizes available</span></li>
<li><span style="font-weight: 400;"> 100% satisfaction guarantee</span></li>
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'meta_description' => 'Polyclonal and Monoclonal Antibodies against Histones and their modifications validated for many applications, including Chromatin Immunoprecipitation (ChIP) and ChIP-Sequencing (ChIP-seq)',
'meta_title' => 'Histone and Modified Histone Antibodies | Diagenode',
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'description' => '<h1><strong>Validated epigenetics antibodies</strong> – care for a sample?<br /> </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> - 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> with rigorous QC and validation</li>
<li><strong>Classified</strong> based on level of validation for flexibility of application</li>
</ul>
<p>Existing sample sizes are listed below. We will soon expand our collection. 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' => 'ChIP-grade antibodies',
'description' => '<div class="row">
<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
<p></p>
</div>
</div>
<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
<div class="row">
<div class="small-12 medium-6 large-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" alt="" width="400" height="315" /> </div>
<div class="small-12 medium-6 large-6 columns">
<p></p>
<p></p>
<p></p>
</div>
</div>
<p></p>
<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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'meta_description' => 'Diagenode Offers Extensively Validated ChIP-Grade Antibodies, Confirmed for their Specificity, and high level of Performance in Chromatin Immunoprecipitation ChIP',
'meta_title' => 'Chromatin immunoprecipitation ChIP-grade antibodies | Diagenode',
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'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
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'description' => '<p>More than in any other immuoprecipitation assays, quality antibodies are critical tools in many epigenetics experiments. Since 10 years, Diagenode has developed the most stringent quality production available on the market for antibodies exclusively focused on epigenetic uses. All our antibodies have been qualified to work in epigenetic applications.</p>',
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'name' => 'H3K9 dimethylation safeguards cancer cells against activation of theinterferon pathway.',
'authors' => 'Hansen A. M. et al.',
'description' => '<p>Activation of interferon genes constitutes an important anticancer pathway able to restrict proliferation of cancer cells. Here, we demonstrate that the H3K9me3 histone methyltransferase (HMT) suppressor of variegation 3-9 homolog 1 (SUV39H1) is required for the proliferation of acute myeloid leukemia (AML) and find that its loss leads to activation of the interferon pathway. Mechanistically, we show that this occurs via destabilization of a complex composed of SUV39H1 and the two H3K9me2 HMTs, G9A and GLP. Indeed, loss of H3K9me2 correlated with the activation of key interferon pathway genes, and interference with the activities of G9A/GLP largely phenocopied loss of SUV39H1. Last, we demonstrate that inhibition of G9A/GLP synergized with DNA demethylating agents and that SUV39H1 constitutes a potential biomarker for the response to hypomethylation treatment. Collectively, we uncovered a clinically relevant role for H3K9me2 in safeguarding cancer cells against activation of the interferon pathway.</p>',
'date' => '2022-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35302840',
'doi' => '10.1126/sciadv.abf8627',
'modified' => '2022-08-04 16:13:55',
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'id' => '4246',
'name' => 'SUV39 SET domains mediate crosstalk of heterochromatic histone marks.',
'authors' => 'Stirpe, Alessandro and Guidotti, Nora and Northall, Sarah Jand Kilic, Sinan and Hainard, Alexandre and Vadas, Oscar andFierz, Beat and Schalch, Thomas',
'description' => '<p>The SUV39 class of methyltransferase enzymes deposits histone H3 lysine 9 di- and trimethylation (H3K9me2/3), the hallmark of constitutive heterochromatin. How these enzymes are regulated to mark specific genomic regions as heterochromatic is poorly understood. Clr4 is the sole H3K9me2/3 methyltransferase in the fission yeast and recent evidence suggests that ubiquitination of lysine 14 on histone H3 (H3K14ub) plays a key role in H3K9 methylation. However, the molecular mechanism of this regulation and its role in heterochromatin formation remain to be determined. Our structure-function approach shows that the H3K14ub substrate binds specifically and tightly to the catalytic domain of Clr4, and thereby stimulates the enzyme by over 250-fold. Mutations that disrupt this mechanism lead to a loss of H3K9me2/3 and abolish heterochromatin silencing similar to deletion. Comparison with mammalian SET domain proteins suggests that the Clr4 SET domain harbors a conserved sensor for H3K14ub, which mediates licensing of heterochromatin formation.</p>',
'date' => '2021-09-01',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/34524082/',
'doi' => '10.7554/eLife.62682',
'modified' => '2022-05-20 09:25:15',
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'id' => '3960',
'name' => 'A conserved RNA degradation complex required for spreading and epigenetic inheritance of heterochromatin.',
'authors' => 'Shipkovenska G, Durango A, Kalocsay M, Gygi SP, Moazed D',
'description' => '<p>Heterochromatic domains containing histone H3 lysine 9 methylation (H3K9me) can be epigenetically inherited independently of underlying DNA sequence. To gain insight into the mechanisms that mediate epigenetic inheritance, we used a inducible heterochromatin formation system to perform a genetic screen for mutations that abolish heterochromatin inheritance without affecting its establishment. We identified mutations in several pathways, including the conserved and essential Rix1-associated complex (henceforth the rixosome), which contains RNA endonuclease and polynucleotide kinase activities with known roles in ribosomal RNA processing. We show that the rixosome is required for spreading and epigenetic inheritance of heterochromatin in fission yeast. Viable rixosome mutations that disrupt its association with Swi6/HP1 fail to localize to heterochromatin, lead to accumulation of heterochromatic RNAs, and block spreading of H3K9me and silencing into actively transcribed regions. These findings reveal a new pathway for degradation of heterochromatic RNAs with essential roles in heterochromatin spreading and inheritance.</p>',
'date' => '2020-06-03',
'pmid' => 'http://www.pubmed.gov/32491985',
'doi' => '10.7554/eLife.54341',
'modified' => '2020-08-12 09:50:01',
'created' => '2020-08-10 12:12:25',
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'id' => '3939',
'name' => 'Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion.',
'authors' => 'Kurihara M, Kato K, Sanbo C, Shigenobu S, Ohkawa Y, Fuchigami T, Miyanari Y',
'description' => '<p>The promyelocytic leukemia (PML) body is a phase-separated nuclear structure physically associated with chromatin, implying its crucial roles in genome functions. However, its role in transcriptional regulation is largely unknown. We developed APEX-mediated chromatin labeling and purification (ALaP) to identify the genomic regions proximal to PML bodies. We found that PML bodies associate with active regulatory regions across the genome and with ∼300 kb of the short arm of the Y chromosome (YS300) in mouse embryonic stem cells. The PML body association with YS300 is essential for the transcriptional activity of the neighboring Y-linked clustered genes. Mechanistically, PML bodies provide specific nuclear spaces that the de novo DNA methyltransferase DNMT3A cannot access, resulting in the steady maintenance of a hypo-methylated state at Y-linked gene promoters. Our study underscores a new mechanism for gene regulation in the 3D nuclear space and provides insights into the functional properties of nuclear structures for genome function.</p>',
'date' => '2020-04-28',
'pmid' => 'http://www.pubmed.gov/32353257',
'doi' => '10.1016/j.molcel.2020.04.004',
'modified' => '2020-08-17 10:28:27',
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'id' => '3927',
'name' => 'Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin.',
'authors' => 'Dong W, Oya E, Zahedi Y, Prasad P, Svensson JP, Lennartsson A, Ekwall K, Durand-Dubief M',
'description' => '<p>Heterochromatin regulation is critical for genomic stability. Different H3K9 methylation states have been discovered, with distinct roles in heterochromatin formation and silencing. However, how the transition from H3K9me2 to H3K9me3 is controlled is still unclear. Here, we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining global nucleosome organisation in fission yeast. We identified several key factors involved in heterochromatin silencing that interact genetically with Abo1: histone deacetylase Clr3, H3K9 methyltransferase Clr4, and HP1 homolog Swi6. Cells lacking Abo1 cultivated at 30 °C exhibit an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin has increased H3K9me2 but decreased H3K9me3 levels compared to wild-type. In contrast, facultative heterochromatin regions exhibit reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both the centromeres and subtelomeres, but not in a subset of heterochromatin islands in our condition. Thus, our work uncovers a role of Abo1 in stabilising directly or indirectly Clr4 recruitment to allow the H3K9me2 to H3K9me3 transition in heterochromatin.</p>',
'date' => '2020-04-08',
'pmid' => 'http://www.pubmed.gov/32269268',
'doi' => '10.1038/s41598-020-63209-y',
'modified' => '2020-08-17 10:48:09',
'created' => '2020-08-10 12:12:25',
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(int) 5 => array(
'id' => '3825',
'name' => 'Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance.',
'authors' => 'Iglesias N, Paulo JA, Tatarakis A, Wang X, Edwards AL, Bhanu NV, Garcia BA, Haas W, Gygi SP, Moazed D',
'description' => '<p>Spatially and functionally distinct domains of heterochromatin and euchromatin play important roles in the maintenance of chromosome stability and regulation of gene expression, but a comprehensive knowledge of their composition is lacking. Here, we develop a strategy for the isolation of native Schizosaccharomyces pombe heterochromatin and euchromatin fragments and analyze their composition by using quantitative mass spectrometry. The shared and euchromatin-specific proteomes contain proteins involved in DNA and chromatin metabolism and in transcription, respectively. The heterochromatin-specific proteome includes all proteins with known roles in heterochromatin formation and, in addition, is enriched for subsets of nucleoporins and inner nuclear membrane (INM) proteins, which associate with different chromatin domains. While the INM proteins are required for the integrity of the nucleolus, containing ribosomal DNA repeats, the nucleoporins are required for aggregation of heterochromatic foci and epigenetic inheritance. The results provide a comprehensive picture of heterochromatin-associated proteins and suggest a role for specific nucleoporins in heterochromatin function.</p>',
'date' => '2019-11-07',
'pmid' => 'http://www.pubmed.gov/31784357',
'doi' => '10.1016/j.molcel.2019.10.018',
'modified' => '2020-02-25 13:37:25',
'created' => '2020-02-13 10:02:44',
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(int) 6 => array(
'id' => '3672',
'name' => 'Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer.',
'authors' => 'Du Q, Bert SA, Armstrong NJ, Caldon CE, Song JZ, Nair SS, Gould CM, Luu PL, Peters T, Khoury A, Qu W, Zotenko E, Stirzaker C, Clark SJ',
'description' => '<p>DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.</p>',
'date' => '2019-01-24',
'pmid' => 'http://www.pubmed.gov/30679435',
'doi' => '10.1038/s41467-019-08302-1',
'modified' => '2019-07-01 11:26:49',
'created' => '2019-06-21 14:55:31',
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(int) 7 => array(
'id' => '3623',
'name' => 'Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability.',
'authors' => 'Iglesias N, Currie MA, Jih G, Paulo JA, Siuti N, Kalocsay M, Gygi SP, Moazed D',
'description' => '<p>Histone H3 lysine 9 methylation (H3K9me) mediates heterochromatic gene silencing and is important for genome stability and the regulation of gene expression. The establishment and epigenetic maintenance of heterochromatin involve the recruitment of H3K9 methyltransferases to specific sites on DNA, followed by the recognition of pre-existing H3K9me by the methyltransferase and methylation of proximal histone H3. This positive feedback loop must be tightly regulated to prevent deleterious epigenetic gene silencing. Extrinsic anti-silencing mechanisms involving histone demethylation or boundary elements help to limit the spread of inappropriate H3K9me. However, how H3K9 methyltransferase activity is locally restricted or prevented from initiating random H3K9me-which would lead to aberrant gene silencing and epigenetic instability-is not fully understood. Here we reveal an autoinhibited conformation in the conserved H3K9 methyltransferase Clr4 (also known as Suv39h) of the fission yeast Schizosaccharomyces pombe that has a critical role in preventing aberrant heterochromatin formation. Biochemical and X-ray crystallographic data show that an internal loop in Clr4 inhibits the catalytic activity of this enzyme by blocking the histone H3K9 substrate-binding pocket, and that automethylation of specific lysines in this loop promotes a conformational switch that enhances the H3K9me activity of Clr4. Mutations that are predicted to disrupt this regulation lead to aberrant H3K9me, loss of heterochromatin domains and inhibition of growth, demonstrating the importance of the intrinsic inhibition and auto-activation of Clr4 in regulating the deposition of H3K9me and in preventing epigenetic instability. Conservation of the Clr4 autoregulatory loop in other H3K9 methyltransferases and the automethylation of a corresponding lysine in the human SUV39H2 homologue suggest that the mechanism described here is broadly conserved.</p>',
'date' => '2018-08-01',
'pmid' => 'http://www.pubmed.gov/30051891',
'doi' => '10.1038/s41586-018-0398-2',
'modified' => '2019-05-16 11:19:37',
'created' => '2019-04-25 11:11:44',
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(int) 8 => array(
'id' => '3626',
'name' => 'Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation.',
'authors' => 'Yu R, Wang X, Moazed D',
'description' => '<p>Histone post-translational modifications (PTMs) are associated with epigenetic states that form the basis for cell-type-specific gene expression. Once established, histone PTMs can be maintained by positive feedback involving enzymes that recognize a pre-existing histone modification and catalyse the same modification on newly deposited histones. Recent studies suggest that in wild-type cells, histone PTM-based positive feedback is too weak to mediate epigenetic inheritance in the absence of other inputs. RNA interference (RNAi)-mediated histone H3 lysine 9 methylation (H3K9me) and heterochromatin formation define a potential epigenetic inheritance mechanism in which positive feedback involving short interfering RNA (siRNA) amplification can be directly coupled to histone PTM positive feedback. However, it is not known whether the coupling of these two feedback loops can maintain epigenetic silencing independently of DNA sequence and in the absence of enabling mutations that disrupt genome-wide chromatin structure or transcription. Here, using the fission yeast Schizosaccharomyces pombe, we show that siRNA-induced H3K9me and silencing of a euchromatic gene can be epigenetically inherited in cis during multiple mitotic and meiotic cell divisions in wild-type cells. This inheritance involves the spreading of secondary siRNAs and H3K9me3 to the targeted gene and surrounding areas, and requires both RNAi and H3K9me, suggesting that the siRNA and H3K9me positive-feedback loops act synergistically to maintain silencing. By contrast, when maintained solely by histone PTM positive feedback, silencing is erased by H3K9 demethylation promoted by Epe1, or by interallelic interactions that occur after mating to cells containing an expressed allele even in the absence of Epe1. These findings demonstrate that the RNAi machinery can mediate transgenerational epigenetic inheritance independently of DNA sequence or enabling mutations, and reveal a role for the coupling of the siRNA and H3K9me positive-feedback loops in the protection of epigenetic alleles from erasure.</p>',
'date' => '2018-06-20',
'pmid' => 'http://www.pubmed.gov/29925950',
'doi' => '10.1038/s41586-018-0239-3',
'modified' => '2019-05-16 11:13:23',
'created' => '2019-04-25 11:11:44',
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(int) 9 => array(
'id' => '3230',
'name' => 'Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription',
'authors' => 'Jih G. et al.',
'description' => '<p>Heterochromatic DNA domains have important roles in the regulation of gene expression and maintenance of genome stability by silencing repetitive DNA elements and transposons. From fission yeast to mammals, heterochromatin assembly at DNA repeats involves the activity of small noncoding RNAs (sRNAs) associated with the RNA interference (RNAi) pathway. Typically, sRNAs, originating from long noncoding RNAs, guide Argonaute-containing effector complexes to complementary nascent RNAs to initiate histone H3 lysine 9 di- and trimethylation (H3K9me2 and H3K9me3, respectively) and the formation of heterochromatin. H3K9me is in turn required for the recruitment of RNAi to chromatin to promote the amplification of sRNA. Yet, how heterochromatin formation, which silences transcription, can proceed by a co-transcriptional mechanism that also promotes sRNA generation remains paradoxical. Here, using Clr4, the fission yeast Schizosaccharomyces pombe homologue of mammalian SUV39H H3K9 methyltransferases, we design active-site mutations that block H3K9me3, but allow H3K9me2 catalysis. We show that H3K9me2 defines a functionally distinct heterochromatin state that is sufficient for RNAi-dependent co-transcriptional gene silencing at pericentromeric DNA repeats. Unlike H3K9me3 domains, which are transcriptionally silent, H3K9me2 domains are transcriptionally active, contain modifications associated with euchromatic transcription, and couple RNAi-mediated transcript degradation to the establishment of H3K9me domains. The two H3K9me states recruit reader proteins with different efficiencies, explaining their different downstream silencing functions. Furthermore, the transition from H3K9me2 to H3K9me3 is required for RNAi-independent epigenetic inheritance of H3K9me domains. Our findings demonstrate that H3K9me2 and H3K9me3 define functionally distinct chromatin states and uncover a mechanism for the formation of transcriptionally permissive heterochromatin that is compatible with its broadly conserved role in sRNA-mediated genome defence.</p>',
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
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<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
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<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
</ul>
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP assays were performed using human HeLa cells, the Diagenode recombinant antibody against H3K9me3 and optimized PCR primer sets for qPCR. ChIP was performed on sheared chromatin from 100,000 and 5,000 cells with the “True MicroChIP kit (cat. No. C01010130). See page 4: Protocol for binding the recombinant H3K9me3 antibody to streptavidin- coated beads (Hattori T. et al., 2013). Different amounts of the antibody were analysed. A negative control recombinant antibody 1 or 5 μg/IP) was used as negative IP control. QPCR was performed with primers for the heterochromatin marker Sat2 and for the ZNF510 gene, used as positive controls, and for the promoters of the active EIF4A2 and GAPDH genes, used as negative controls. Figure 1 shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis). </small></p>
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<p><small><strong> Figure 2. ChIP-seq results obtained with the Diagenode recombinant antibody directed against H3K9me3</strong><br /> ChIP was performed with 1.3 μg of the Diagenode antibody against H3K9me3 on sheared chromatin from 4 million K562 cells. The IP’d DNA was analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The sequenced reads were aligned to human genome version 19 using the ELAND algorithm. Figure 2A shows the signal distribution along the long arm of chromosome 19 and a zoomin to an enriched region containing several ZNF repeat genes. Figure 2B shows the enrichment at ZNF510 and Figure 2 C and D show the enrichment at the MEG3 and KCNQ1 imprinted genes. </small></p>
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<p><small><strong> Figure 3. Immunofluorescence using the Diagenode recombinant antibody directed against H3K9me3</strong><br /> NIH 3T3 cells were stained with the Diagenode antibody against H3K9me3, left or with the negative control recombinant antibody, right. The bottom panel shows counterstaining of the cells with DAPI. (Hattori T. et al., 2013). </small></p>
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<p><small>Protocol for binding the recombinant H3K9me3 antibody to streptavidin-coated beads (Hattori T. et al., 2013). The recombinant H3K9me3 antibody (Cat. No. C15500003) has been validated in ChIP with the True MicroChIP kit (Cat. No. C01010130). However, since this antibody is a biotinylated Fab fragment, the protocol was slightly adapted. The protein A/G coated magnetic beads included in the True MicroChIP kit were replaced by streptavidin-coated beads to capture the recombinant antibody. The protocol below is intended for binding of the antibody to streptavidin beads for one ChIP experiment. Scale up accordingly for larger numbers of ChIP experiments.</small></p>
<p><small><strong>Material required</strong></small></p>
<ul>
<li><small>Dynabeads M280 Streptavidin (Invitrogen)<br /> Alternatively Streptavidin MagneSphere paramagnetic beads (Promega) can be used</small></li>
<li><small>TBS containing 0.5% BSA (called TBS/BSA in the protocol)</small></li>
<li><small>Biotin. Prepare a solution of 5 μM biotin in TBS containing 0.5 % BSA</small></li>
<li><small>Diamag 1.5 magnetic rack (Cat No. kch-816-015)</small></li>
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<p><small><strong>NOTE:</strong> Please proceed with <strong>STEP 1</strong> - Cell collection and DNA-protein crosslinking as well as <strong>STEP 2</strong> - Cell lysis and chromatin shearing, as explained in the True MicroChIP kit protocol. In <strong>STEP 3</strong> – Magnetic Immunoprecipitation and washes, proceed up to <strong>point 22</strong> for <strong>Detailed protocol</strong> or <strong>point 1</strong>3 for<strong> Short protocol</strong> (ie proceed up to chromatin dilution after the shearing and use this diluted chromatin at the end of the recombinant antibody binding protocol below).The protocol below is optimized for working with 100 000 cells. When using less cells, you should decrease the amount of antibody and beads to use.</small></p>',
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'id' => '4452',
'product_id' => '2823',
'application_id' => '43'
)
)
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(int) 0 => 'chip-qpcr-antibodies'
)
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'id' => '43',
'position' => '10',
'parent_id' => '40',
'name' => 'ChIP-qPCR (ab)',
'description' => '',
'in_footer' => false,
'in_menu' => false,
'online' => true,
'tabular' => true,
'slug' => 'chip-qpcr-antibodies',
'meta_keywords' => 'Chromatin Immunoprecipitation Sequencing,ChIP-Seq,ChIP-seq grade antibodies,DNA purification,qPCR,Shearing of chromatin',
'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',
'modified' => '2016-01-20 11:30:24',
'created' => '2015-10-20 11:45:36',
'locale' => 'eng'
)
$description = ''
$name = 'ChIP-qPCR (ab)'
$document = array(
'id' => '295',
'name' => 'Datasheet H3K9me3 C15500003',
'description' => 'Datasheet description',
'image_id' => null,
'type' => 'Datasheet',
'url' => 'files/products/antibodies/Datasheet_H3K9me3_C15500003.pdf',
'slug' => 'datasheet-h3k9me3-c15500003',
'meta_keywords' => null,
'meta_description' => null,
'modified' => '2015-07-07 11:47:43',
'created' => '2015-07-07 11:47:43',
'ProductsDocument' => array(
'id' => '2170',
'product_id' => '2823',
'document_id' => '295'
)
)
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'id' => '516',
'name' => 'H3K9me3 recombinant antibody and negative control SDS ES es',
'language' => 'es',
'url' => 'files/SDS/H3K9me3/SDS-C15500003-H3K9me3_recombinant_antibody_and_negative_control-ES-es-GHS_2_0.pdf',
'countries' => 'ES',
'modified' => '2020-07-01 12:38:39',
'created' => '2020-07-01 12:38:39',
'ProductsSafetySheet' => array(
'id' => '991',
'product_id' => '2823',
'safety_sheet_id' => '516'
)
)
$publication = array(
'id' => '3230',
'name' => 'Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription',
'authors' => 'Jih G. et al.',
'description' => '<p>Heterochromatic DNA domains have important roles in the regulation of gene expression and maintenance of genome stability by silencing repetitive DNA elements and transposons. From fission yeast to mammals, heterochromatin assembly at DNA repeats involves the activity of small noncoding RNAs (sRNAs) associated with the RNA interference (RNAi) pathway. Typically, sRNAs, originating from long noncoding RNAs, guide Argonaute-containing effector complexes to complementary nascent RNAs to initiate histone H3 lysine 9 di- and trimethylation (H3K9me2 and H3K9me3, respectively) and the formation of heterochromatin. H3K9me is in turn required for the recruitment of RNAi to chromatin to promote the amplification of sRNA. Yet, how heterochromatin formation, which silences transcription, can proceed by a co-transcriptional mechanism that also promotes sRNA generation remains paradoxical. Here, using Clr4, the fission yeast Schizosaccharomyces pombe homologue of mammalian SUV39H H3K9 methyltransferases, we design active-site mutations that block H3K9me3, but allow H3K9me2 catalysis. We show that H3K9me2 defines a functionally distinct heterochromatin state that is sufficient for RNAi-dependent co-transcriptional gene silencing at pericentromeric DNA repeats. Unlike H3K9me3 domains, which are transcriptionally silent, H3K9me2 domains are transcriptionally active, contain modifications associated with euchromatic transcription, and couple RNAi-mediated transcript degradation to the establishment of H3K9me domains. The two H3K9me states recruit reader proteins with different efficiencies, explaining their different downstream silencing functions. Furthermore, the transition from H3K9me2 to H3K9me3 is required for RNAi-independent epigenetic inheritance of H3K9me domains. Our findings demonstrate that H3K9me2 and H3K9me3 define functionally distinct chromatin states and uncover a mechanism for the formation of transcriptionally permissive heterochromatin that is compatible with its broadly conserved role in sRNA-mediated genome defence.</p>',
'date' => '2017-07-27',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28682306',
'doi' => '',
'modified' => '2017-08-24 09:36:48',
'created' => '2017-08-24 09:36:48',
'ProductsPublication' => array(
'id' => '2236',
'product_id' => '2823',
'publication_id' => '3230'
)
)
$externalLink = ' <a href="https://www.ncbi.nlm.nih.gov/pubmed/28682306" target="_blank"><i class="fa fa-external-link"></i></a>'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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