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<p style="text-align: justify;">The <strong>Universal Plant ChIP-seq kit</strong> offers the convenience of extracting plant chromatin from a wide variety of plants including Arabidopsis, maize, rice, tomato and poplar. This complete kit has been specifically optimized for <strong>plant chromatin extraction</strong> and includes reagents for chromatin preparation, immunoprecipitation, plant-specific control primer pairs, control antibody, and DNA purification.</p>',
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<h3>Successful ChIP-seq experiments for a variety of plants</h3>
<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Arabidopsis</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG1"> <img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A-small.jpg" /> </a></p>
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<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 1.</strong> ChIP-seq was performed on Arabidopsis thaliana (Col-0) seedlings using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng (green), 500 pg (orange) and 100 pg (red) IP'd DNA and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a public dataset (NCBI GEO Dataset GSM1193621) that we used as an external reference. Enrichments along a wide region of chromosome 5 are uniform regardless of the starting material amount for the preparation of the library.</small></p>
</div>
<div class="small-6 columns">
<h4 class="text-center">Poplar</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG2"><img src="https://www.diagenode.com/img/landing-pages/poplar-small.jpg" /> </a></p>
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<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 3.</strong> ChIP-seq was performed on Populus trichocarpa stem differenciating xylem using the <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with the <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the input and is considered as the background enrichment. The profile in red represents enrichments along a wide region of scaffold 18. Using the same scale, the peaks of the immunoprecipitated samples are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Tomato</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG3"> <img src="https://www.diagenode.com/img/landing-pages/tomtato-small.jpg" /> </a></p>
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<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/tomtato.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 2.</strong> ChIP-seq was performed on Solanum lycopersicum cv. Micro-Tom young leaves using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 750 pg of immunoprecipitated DNA using the Universal Plant ChIP-seq kit (red) and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a dataset obtained from Nguyen et al. 2014 that we used as an external reference. Enrichments are higher and consistent with the reference data along a wide region of chromosome 1.</small></p>
</div>
<div class="small-6 columns">
<h4 class="text-center">Maize</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG4"> <img src="https://www.diagenode.com/img/landing-pages/maize-small.jpg" /> </a></p>
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<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/maize.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 4.</strong> ChIP-seq was performed on Zea mays cv. B73 inner stem using our <a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">Premium H3K27me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the Input and is considered as the background enrichment. The enrichment in red represents enrichments along a wide region of chromosome 3. Using the same scale, the peaks of the immunoprecipitated sample are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<p><strong> </strong></p>
<table style="width: 856px;">
<tbody>
<tr>
<td style="width: 224px;">
<h4><strong>Plant Species</strong></h4>
</td>
<td style="width: 341px;">
<h4><strong>Validated antibodies</strong></h4>
</td>
<td style="width: 357px;">
<h4><strong>Validated primer pairs</strong></h4>
</td>
</tr>
<tr>
<td style="width: 224px;"><strong>Arabidopsis (<em>Arabidopsis thaliana</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-actin-atg-primer-pair-50-ul">Arabidopsis Actin ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-monoclonal-antibody-classic-50-ug-50-ul">H3K4me3 monoclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-atg-primer-pair-50-ul">Arabidopsis FLC-ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-intron1-primer-pair-50-ul">Arabidopsis FLC-intron1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me3-polyclonal-antibody-classic-sample-size-10-ug">H3K9me3 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9-14ac-polyclonal-antibody-classic-sample-size-10-mg">H3K9/14ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27ac-polyclonal-antibody-premium-sample-size-10-ug">H3K27ac polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Maize (<em>Zea mays</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/maize-B73-inner-stem-ZmB1-UTR-primer-pair-50ul">Maize B73 inner stem ZmB1-UTR primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/Maize-B73-inner-stem-ZmCopia-primer-pair-50ul">Maize B73 inner stem ZmCopia primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Tomato (<em>Solanum lycopersicum</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr2-reg8-primer-pair-50ul">Tomato leaves SlChr2-reg8 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr4-NC1-primer-pair-50ul">Tomato leaves SlChr4-NC1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Rice (<em>Oriza sativa</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsChr4-reg9-primer-pair-50ul">Rice seedlings OsChr4-reg9 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsMADS6-primer-pair-50ul">Rice seedlings OsMADS6 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Poplar (<em>Populus trichocarpa, Populus tremula x alba</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrCopia-orth-primer-pair-50ul">Poplar xylem PtrCopia-orth primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9ac-polyclonal-antibody-classic-sample-size-10-ug">H3K9ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrMYBTF1-primer-pair-50ul">Poplar xylem PtrMYBTF1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
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<h4 class="text-center">Arabidopsis</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG1"> <img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A-small.jpg" /> </a></p>
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<p><small><strong>Figure 1.</strong> ChIP-seq was performed on Arabidopsis thaliana (Col-0) seedlings using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng (green), 500 pg (orange) and 100 pg (red) IP'd DNA and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a public dataset (NCBI GEO Dataset GSM1193621) that we used as an external reference. Enrichments along a wide region of chromosome 5 are uniform regardless of the starting material amount for the preparation of the library.</small></p>
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<h4 class="text-center">Poplar</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG2"><img src="https://www.diagenode.com/img/landing-pages/poplar-small.jpg" /> </a></p>
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<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/poplar.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 3.</strong> ChIP-seq was performed on Populus trichocarpa stem differenciating xylem using the <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with the <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the input and is considered as the background enrichment. The profile in red represents enrichments along a wide region of scaffold 18. Using the same scale, the peaks of the immunoprecipitated samples are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Tomato</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG3"> <img src="https://www.diagenode.com/img/landing-pages/tomtato-small.jpg" /> </a></p>
<div id="IMG3" class="reveal-modal" data-reveal="" aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/tomtato.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 2.</strong> ChIP-seq was performed on Solanum lycopersicum cv. Micro-Tom young leaves using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 750 pg of immunoprecipitated DNA using the Universal Plant ChIP-seq kit (red) and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a dataset obtained from Nguyen et al. 2014 that we used as an external reference. Enrichments are higher and consistent with the reference data along a wide region of chromosome 1.</small></p>
</div>
<div class="small-6 columns">
<h4 class="text-center">Maize</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG4"> <img src="https://www.diagenode.com/img/landing-pages/maize-small.jpg" /> </a></p>
<div id="IMG4" class="reveal-modal" data-reveal="" aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/maize.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 4.</strong> ChIP-seq was performed on Zea mays cv. B73 inner stem using our <a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">Premium H3K27me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the Input and is considered as the background enrichment. The enrichment in red represents enrichments along a wide region of chromosome 3. Using the same scale, the peaks of the immunoprecipitated sample are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<p><strong> </strong></p>
<table style="width: 856px;">
<tbody>
<tr>
<td style="width: 224px;">
<h4><strong>Plant Species</strong></h4>
</td>
<td style="width: 341px;">
<h4><strong>Validated antibodies</strong></h4>
</td>
<td style="width: 357px;">
<h4><strong>Validated primer pairs</strong></h4>
</td>
</tr>
<tr>
<td style="width: 224px;"><strong>Arabidopsis (<em>Arabidopsis thaliana</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-actin-atg-primer-pair-50-ul">Arabidopsis Actin ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-monoclonal-antibody-classic-50-ug-50-ul">H3K4me3 monoclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-atg-primer-pair-50-ul">Arabidopsis FLC-ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-intron1-primer-pair-50-ul">Arabidopsis FLC-intron1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me3-polyclonal-antibody-classic-sample-size-10-ug">H3K9me3 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9-14ac-polyclonal-antibody-classic-sample-size-10-mg">H3K9/14ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27ac-polyclonal-antibody-premium-sample-size-10-ug">H3K27ac polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Maize (<em>Zea mays</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/maize-B73-inner-stem-ZmB1-UTR-primer-pair-50ul">Maize B73 inner stem ZmB1-UTR primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/Maize-B73-inner-stem-ZmCopia-primer-pair-50ul">Maize B73 inner stem ZmCopia primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Tomato (<em>Solanum lycopersicum</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr2-reg8-primer-pair-50ul">Tomato leaves SlChr2-reg8 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr4-NC1-primer-pair-50ul">Tomato leaves SlChr4-NC1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Rice (<em>Oriza sativa</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsChr4-reg9-primer-pair-50ul">Rice seedlings OsChr4-reg9 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsMADS6-primer-pair-50ul">Rice seedlings OsMADS6 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Poplar (<em>Populus trichocarpa, Populus tremula x alba</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrCopia-orth-primer-pair-50ul">Poplar xylem PtrCopia-orth primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9ac-polyclonal-antibody-classic-sample-size-10-ug">H3K9ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrMYBTF1-primer-pair-50ul">Poplar xylem PtrMYBTF1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
</tbody>
</table>
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<p style="text-align: justify;"><span>Previous name of the kit: Chromatin Shearing Optimization Kit (Universal Plant ChIP-seq kit)<br /></span></p>
<p style="text-align: justify;"><span>The first critical step of a successful ChIP experiment is the best preparation of sheared chromatin. This <strong>Chromatin EasyShear Kit</strong> is designed to be used in conjunction with the <strong>Universal Plant ChIP-seq kit</strong> and contains the right level of <strong>detergent</strong> for extraction of highest quality plant chromatin for ChIP. In addition, the signature</span><span> crosslinking containers of this kit provide a simple and reliable method for fixation. The content of this kit is enough to perform 12 chromatin extractions.<br /></span></p>
<p style="text-align: justify;"><span>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</span></p>
<p style="text-align: justify;"><span>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></span></p>',
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<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig1.png" alt="H3K27me3 Antibody ChIP Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2.png" alt="H3K27me3 Antibody for ChIP" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 1 million cells. The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation. A titration consisting of 0.5, 1, 2 and 5 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control.</small></p>
<p><small><strong>Figure 1A.</strong> Quantitative PCR was performed with primers specific for the promoter of the active GAPDH and EIF4A2 genes, used as negative controls, and for the inactive TSH2B and MYT1 genes, used as positive controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
<p><small><strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K27me1, H3K27me2, H3K27me3, H3K4me3, H3K9me3 and H3K36me3 modifications and the unmodified H3K27 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K27me3 modification.</small></p>
</div>
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<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2a.png" alt="H3K27me3 Antibody ChIP-seq Grade" /></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
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<div class="extra-spaced"></div>
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<div class="row">
<div class="small-12 columns">
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2b.png" alt="H3K27me3 Antibody for ChIP-seq" /></p>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2c.png" alt="H3K27me3 Antibody for ChIP-seq assay" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2d.png" alt="H3K27me3 Antibody validated in ChIP-seq" /></p>
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</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP was performed on sheared chromatin from 1 million HeLa cells using 1 µg of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2 shows the enrichment in genomic regions of chromosome 6 and 20, surrounding the TSH2B and MYT1 positive control genes (fig 2A and 2B, respectively), and in two genomic regions of chromosome 1 and X (figure 2C and D).</small></p>
</div>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3A.png" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3B.png" /></p>
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<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27me3 (cat. No. C15410195) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions on chromosome and 13 and 20 (figure 3A and B, respectively).</small></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-ELISA-Fig4.png" alt="H3K27me3 Antibody ELISA Validation " /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K27me3 (Cat. No. C15410195). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:3,000.</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-DB-Fig5a.png" alt="H3K27me3 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) with peptides containing other modifications of histone H3 and H4 and the unmodified H3K27 sequence. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:5,000. Figure 5 shows a high specificity of the antibody for the modification of interest. Please note that the antibody also recognizes the modification if S28 is phosphorylated.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-WB-Fig6.png" alt="H3K27me3 Antibody validated in Western Blot" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27me3</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27me3 (cat. No. C15410195) diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-IF-Fig7.png" alt="H3K27me3 Antibody validated for Immunofluorescence" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27me3</strong><br />Human HeLa cells were stained with the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K27me3 antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.</small></p>
</div>
</div>',
'label2' => 'Target Description',
'info2' => '<p><small>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 alter chromatin structure to facilitate transcriptional activation, 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 regulated by histone methyl transferases and histone demethylases. Methylation of histone H3K27 is associated with inactive genomic regions.</small></p>',
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'format' => '50 μg',
'catalog_number' => 'C15410195',
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'sf_code' => 'C15410195-D001-000581',
'type' => 'FRE',
'search_order' => '03-Antibody',
'price_EUR' => '480',
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'meta_title' => 'H3K27me3 Antibody - ChIP-seq Grade (C15410195) | Diagenode',
'meta_keywords' => '',
'meta_description' => 'H3K27me3 (Histone H3 trimethylated at lysine 27) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, CUT&Tag, ELISA, DB, WB and IF. Specificity confirmed by Peptide array assay. Batch-specific data available on the website. Sample size available.',
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'name' => 'Auto Universal Plant ChIP-seq kit',
'description' => '<p style="text-align: justify;">The <strong>Auto Universal Plant ChIP-seq</strong> kit offers the convenience of extracting plant chromatin from a wide variety of plants including Arabidopsis, maize, rice, tomato and poplar and has been validated for the <strong>IP-Star® automated system</strong>. This complete kit has been specifically optimized for <strong>plant chromatin extraction</strong> and includes reagents for chromatin preparation, immunoprecipitation, plant-specific control primer pairs, control antibody, and DNA purification.</p>',
'label1' => 'Characteristics',
'info1' => '<p></p>
<ul>
<li><strong>Universal compatiblity</strong> with a wide variety of plant species</li>
<li>Optimized and <strong>complete kit</strong> for start-to-finish plant ChIP</li>
<li>Validated for the high throughput <strong>IP-Star® Automated System</strong></li>
</ul>
<h3>Successful ChIP-seq experiments for a variety of plants</h3>
<div class="row">
<div class="small-6 columns"><center>Arabidopsis</center><center><img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A.png" /></center>
<p><small><strong>Figure 1.</strong> ChIP-seq was performed on Arabidopsis thaliana (Col-0) seedlings using our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng (green), 500 pg (orange) and 100 pg (red) IP'd DNA and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a public dataset (NCBI GEO Dataset GSM1193621) that we used as an external reference. Enrichments along a wide region of chromosome 5 are uniform regardless of the starting material amount for the preparation of the library.</small></p>
</div>
<div class="small-6 columns"><center>Poplar</center><center><img src="https://www.diagenode.com/img/landing-pages/poplar.jpg" /></center>
<p><small><strong>Figure 3.</strong> ChIP-seq was performed on Populus trichocarpa stem differenciating xylem using the Premium H3K4me3 ChIP-seq grade antibody. Libraries were prepared with the <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the input and is considered as the background enrichment. The profile in red represents enrichments along a wide region of scaffold 18. Using the same scale, the peaks of the immunoprecipitated samples are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><center>Tomato</center><center><img src="https://www.diagenode.com/img/landing-pages/tomtato.jpg" /></center>
<p><small><strong>Figure 2.</strong> ChIP-seq was performed on Solanum lycopersicum cv. Micro-Tom young leaves using our Premium H3K4me3 ChIP-seq grade antibody. Librairies were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Librairy Preparation™ kit</a> from 750 pg of immunoprecipitated DNA using the Universal Plant ChIP-seq kit (red) and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a dataset obtained from Nguyen et al. 2014 that we used as an external reference. Enrichments are higher and consistent with the reference data along a wide region of chromosome 1.</small></p>
</div>
<div class="small-6 columns"><center>Maize</center><center><img src="https://www.diagenode.com/img/landing-pages/maize.jpg" /></center>
<p><small><strong>Figure 4.</strong> ChIP-seq was performed on Zea mays cv. B73 inner stem using our Premium H3K27me3 ChIP-seq grade antibody. Librairies were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Librairy Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the Input and is considered as the background enrichment. The enrichment in red represents enrichments along a wide region of chromosome 3. Using the same scale, the peaks of the immunoprecipitated sample are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<table style="width: 856px;">
<tbody>
<tr>
<td style="width: 224px;">
<h4><strong>Plant Species</strong></h4>
</td>
<td style="width: 341px;">
<h4><strong>Validated antibodies</strong></h4>
</td>
<td style="width: 357px;">
<h4><strong>Validated primer pairs</strong></h4>
</td>
</tr>
<tr>
<td style="width: 224px;"><strong>Arabidopsis (<em>Arabidopsis thaliana</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-actin-atg-primer-pair-50-ul">Arabidopsis Actin ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-monoclonal-antibody-classic-50-ug-50-ul">H3K4me3 monoclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-atg-primer-pair-50-ul">Arabidopsis FLC-ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-intron1-primer-pair-50-ul">Arabidopsis FLC-intron1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me3-polyclonal-antibody-classic-sample-size-10-ug">H3K9me3 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9-14ac-polyclonal-antibody-classic-sample-size-10-mg">H3K9/14ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27ac-polyclonal-antibody-premium-sample-size-10-ug">H3K27ac polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Maize (<em>Zea mays</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/maize-B73-inner-stem-ZmB1-UTR-primer-pair-50ul">Maize B73 inner stem ZmB1-UTR primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/Maize-B73-inner-stem-ZmCopia-primer-pair-50ul">Maize B73 inner stem ZmCopia primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Tomato (<em>Solanum lycopersicum</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr2-reg8-primer-pair-50ul">Tomato leaves SlChr2-reg8 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr4-NC1-primer-pair-50ul">Tomato leaves SlChr4-NC1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Rice (<em>Oriza sativa</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsChr4-reg9-primer-pair-50ul">Rice seedlings OsChr4-reg9 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsMADS6-primer-pair-50ul">Rice seedlings OsMADS6 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Poplar (<em>Populus trichocarpa, Populus tremula x alba</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrCopia-orth-primer-pair-50ul">Poplar xylem PtrCopia-orth primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9ac-polyclonal-antibody-classic-sample-size-10-ug">H3K9ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrMYBTF1-primer-pair-50ul">Poplar xylem PtrMYBTF1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
</tbody>
</table>',
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'slug' => 'auto-universal-plant-chip-seq-kit-x24-24-rxns',
'meta_title' => 'Auto Universal Plant ChIP-seq kit | Diagenode',
'meta_keywords' => 'plant epigenetics, plant ChIP, plant ChIP-seq, Arabidopsis, maize, rice, tomato, poplar, automated system, automation, IP-Star',
'meta_description' => 'Plant chromatin extraction from Arabidopsis,maize,rice,tomato,poplar.Complete ChIP kit including plant-specific primer pairs,antibody.Compatible with Automation',
'modified' => '2017-08-19 10:28:51',
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'id' => '2686',
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'name' => 'IPure kit v2',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/ipure_kit_v2_manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>Diagenode’s<span> </span><b>IPure</b><b><span> </span>kit<span> </span></b>is the only DNA purification kit using magnetic beads, that is specifically optimized for extracting DNA from<span> </span><b>ChIP</b><b>,<span> </span></b><b>MeDIP</b><span> </span>and<span> </span><b>CUT&Tag</b>. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. This simple and straightforward protocol delivers pure DNA ready for any downstream application (e.g. next generation sequencing). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples.</p>
<center>
<h4>High DNA recovery after purification of ChIP samples using IPure technology</h4>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-chromatin-function.png" width="500" /></center>
<p></p>
<p><small>ChIP assays were performed using different amounts of U2OS cells and the H3K9me3 antibody (Cat. No.<span> </span><span>C15410056</span>; 2 g/IP). <span>The purified DNA was eluted in 50 µl of water and quantified with a Nanodrop.</span></small></p>
<p></p>
<p><strong>Benefits of the IPure kit:</strong></p>
<ul>
<li style="text-align: left;">Provides pure DNA for any downstream application (e. g. Next generation sequencing)</li>
<li style="text-align: left;">Non-toxic</li>
<li style="text-align: left;">Fast & easy to use</li>
<li style="text-align: left;">Optimized for DNA purification after ChIP, MeDIP and CUT&Tag</li>
<li style="text-align: left;">Compatible with automation</li>
<li style="text-align: left;">Validated on the IP-Star Compact</li>
</ul>
</center>',
'label1' => 'Examples of results',
'info1' => '<h2>IPure after ChIP</h2>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-A.png" alt="ChIP-seq figure A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-B.png" alt="ChIP-seq figure B" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-C.png" alt="ChIP-seq figure C" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><small><strong>Figure 1.</strong> Chromatin Immunoprecipitation has been performed using chromatin from HeLa cells, the iDeal ChIP-seq kit for Transcription Factors (containing the IPure module for DNA purification) and the Diagenode ChIP-seq-grade HDAC1 (A), LSD1 (B) and p53 antibody (C). 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. This figure shows the peak distribution in regions of chromosome 3 (A), chromosome 12 (B) and chromosome 6 (C) respectively.</small></p>
<p></p>
<h2>IPure after CUT&Tag</h2>
<p>Successful CUT&Tag results showing a low background with high region-specific enrichment has been generated using 50.000 of K562 cells, 1 µg of H3K4me3 or H3K27me3 antibody (Diagenode, C15410003 or C15410069, respectively) and proteinA-Tn5 (1:250) (Diagenode, C01070001). 1 µg of IgG (C15410206) was used as negative control. Samples were purified using the IPure kit v2 or phenol-chloroform purification. The below figures present the comparison of two purification methods.</p>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-fig2.png" style="display: block; margin-left: auto; margin-right: auto;" width="400" /></center><center>
<p style="text-align: center;"><small><strong>Figure 2.</strong> Heatmap 3kb upstream and downstream of the TSS for H3K4me3</small></p>
</center>
<p></p>
<p><img src="https://www.diagenode.com/img/product/kits/ipure-fig3.png" style="display: block; margin-left: auto; margin-right: auto;" width="600" /></p>
<p></p>
<center><small><strong>Figure 3.</strong> Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using Diagenode’s pA-Tn5 transposase (Cat. No. C01070002), H3K27me3 antibody (Cat. No. C15410069) and IPure kit v2 vs phenol chloroform purification (PC).</small></center>
<p></p>
<p></p>
<h2>IPure after MeDIP</h2>
<center><img src="https://www.diagenode.com/img/product/kits/magmedip-seq-figure_multi3.jpg" alt="medip sequencing coverage" width="600" /></center><center></center><center>
<p></p>
<small><strong>Figure 4.</strong> Consistent coverage and methylation detection from different starting amounts of DNA with the Diagenode MagMeDIP-seq Package (including the Ipure kit for DNA purification). Samples containing decreasing starting amounts of DNA (from the top down: 1000 ng (red), 250 ng (blue), 100 ng (green)) originating from human blood were prepared, revealing a consistent coverage profile for the three different starting amounts, which enables reproducible methylation detection. The CpG islands (CGIs) (marked by yellow boxes in the bottom track) are predominantly unmethylated in the human genome, and as expected, we see a depletion of reads at and around CGIs.</small></center>
<script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script>',
'label2' => 'iPure Workflow',
'info2' => '<h2 style="text-align: center;">Kit Method Overview & Time table</h2>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-ipure-cuttag.png" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<h3><strong>Workflow description</strong></h3>
<h5><strong>IPure after ChIP</strong></h5>
<p><strong>Step 1:</strong> Chromatin is decrosslinked and eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added.<br /> <strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet.<br /> <strong>Step 3:</strong> Proteins and remaining buffer are washed away.<br /> <strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after MeDIP</strong></h5>
<p><strong>Step 1:</strong> DNA is eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Remaining buffer are washed away.<br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after CUT&Tag</strong></h5>
<p><strong>Step 1:</strong> pA-Tn5 is inactivated and DNA released from the cells. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Proteins and remaining buffer are washed away. <br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).</p>
<p></p>
<p></p>
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<div class="large-12 columns">Chromatin Immunoprecipitation (ChIP) coupled with high-throughput massively parallel sequencing as a detection method (ChIP-seq) has become one of the primary methods for epigenomics researchers, namely to investigate protein-DNA interaction on a genome-wide scale. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</div>
<div class="large-12 columns"></div>
<h5 class="large-12 columns"><strong></strong></h5>
<h5 class="large-12 columns"><strong>The ChIP-seq workflow</strong></h5>
<div class="small-12 medium-12 large-12 columns text-center"><br /><img src="https://www.diagenode.com/img/chip-seq-diagram.png" /></div>
<div class="large-12 columns"><br />
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<li class="large-12 columns"><strong>Chromatin preparation: </strong>Crosslink chromatin-bound proteins (histones or transcription factors) to DNA followed by cell lysis.</li>
<li class="large-12 columns"><strong>Chromatin shearing:</strong> Fragment chromatin by sonication to desired fragment size (100-500 bp)</li>
<li class="large-12 columns"><strong>Chromatin IP</strong>: Capture protein-DNA complexes with <strong><a href="../categories/chip-seq-grade-antibodies">specific ChIP-seq grade antibodies</a></strong> against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: Reverse cross-links, elute, and purify </li>
<li class="large-12 columns"><strong>NGS Library Preparation</strong>: Ligate adapters and amplify IP'd material</li>
<li class="large-12 columns"><strong>Bioinformatic analysis</strong>: Perform r<span style="font-weight: 400;">ead filtering and trimming</span>, r<span style="font-weight: 400;">ead specific alignment, enrichment specific peak calling, QC metrics, multi-sample cross-comparison etc. </span></li>
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<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns"><a href="../pages/which-kit-to-choose"><img alt="" src="https://www.diagenode.com/img/banners/banner-decide.png" /></a></div>
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<p class="text-justify">Chromatin Immunoprecipitation (ChIP) coupled with quantitative PCR can be used to investigate protein-DNA interaction at known genomic binding sites. if sites are not known, qPCR primers can also be designed against potential regulatory regions such as promoters. ChIP-qPCR is advantageous in studies that focus on specific genes and potential regulatory regions across differing experimental conditions as the cost of performing real-time PCR is minimal. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</p>
<p class="text-justify"><strong>The ChIP-qPCR workflow</strong></p>
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<div class="small-12 medium-12 large-12 columns text-center"><br /> <img src="https://www.diagenode.com/img/chip-qpcr-diagram.png" /></div>
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<li class="large-12 columns"><strong>Chromatin preparation: </strong>cell fixation (cross-linking) of chromatin-bound proteins such as histones or transcription factors to DNA followed by cell lysis.</li>
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<li class="large-12 columns"><strong>Chromatin IP</strong>: protein-DNA complexe capture using<strong> <a href="https://www.diagenode.com/en/categories/chip-grade-antibodies">specific ChIP-grade antibodies</a></strong> against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: chromatin reverse cross-linking and elution followed by purification<strong> </strong></li>
<li class="large-12 columns"><strong>qPCR and analysis</strong>: using previously designed primers to amplify IP'd material at specific loci</li>
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<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns"><a href="https://www.diagenode.com/pages/which-kit-to-choose"><img src="https://www.diagenode.com/img/banners/banner-decide.png" alt="" /></a></div>
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'name' => 'Temporal modification of H3K9/14ac and H3K4me3 histone marksmediates mechano-responsive gene expression during the accommodationprocess in poplar',
'authors' => 'Ghosh R. et al.',
'description' => '<p>Plants can attenuate their molecular response to repetitive mechanical stimulation as a function of their mechanical history. For instance, a single bending of stem is sufficient to attenuate the gene expression in poplar plants to the subsequent mechanical stimulation, and the state of desensitization can last for several days. The role of histone modifications in memory gene expression and modulating plant response to abiotic or biotic signals is well known. However, such information is still lacking to explain the attenuated expression pattern of mechano-responsive genes in plants under repetitive stimulation. Using poplar as a model plant in this study, we first measured the global level of H3K9/14ac and H3K4me3 marks in the bent stem. The result shows that a single mild bending of the stem for 6 seconds is sufficient to alter the global level of the H3K9/14ac mark in poplar, highlighting the fact that plants are extremely sensitive to mechanical signals. Next, we analyzed the temporal dynamics of these two active histone marks at attenuated (PtaZFP2, PtaXET6, and PtaACA13) and non-attenuated (PtaHRD) mechano-responsive loci during the desensitization and resensitization phases. Enrichment of H3K9/14ac and H3K4me3 in the regulatory region of attenuated genes correlates well with their transient expression pattern after the first bending. Moreover, the levels of H3K4me3 correlate well with their expression pattern after the second bending at desensitization (3 days after the first bending) as well as resensitization (5 days after the first bending) phases. On the other hand, H3K9/14ac status correlates only with their attenuated expression pattern at the desensitization phase. The expression efficiency of the attenuated genes was restored after the second bending in the histone deacetylase inhibitor-treated plants. While both histone modifications contribute to the expression of attenuated genes, mechanostimulated expression of the non-attenuated PtaHRD gene seems to be H3K4me3 dependent.</p>',
'date' => '2023-02-01',
'pmid' => 'https://doi.org/10.1101%2F2023.02.12.526104',
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'name' => 'Winter warming post floral initiation delays flowering via bud dormancyactivation and affects yield in a winter annual crop.',
'authors' => 'Lu Xiang et al.',
'description' => '<p>Winter annual life history is conferred by the requirement for vernalization to promote the floral transition and control the timing of flowering. Here we show using winter oilseed rape that flowering time is controlled by inflorescence bud dormancy in addition to vernalization. Winter warming treatments given to plants in the laboratory and field increase flower bud abscisic acid levels and delay flowering in spring. We show that the promotive effect of chilling reproductive tissues on flowering time is associated with the activity of two FLC genes specifically silenced in response to winter temperatures in developing inflorescences, coupled with activation of a BRANCHED1-dependent bud dormancy transcriptional module. We show that adequate winter chilling is required for normal inflorescence development and high yields in addition to the control of flowering time. Because warming during winter flower development is associated with yield losses at the landscape scale, our work suggests that bud dormancy activation may be important for effects of climate change on winter arable crop yields.</p>',
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'pmid' => 'https://doi.org/10.1073%2Fpnas',
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'name' => 'AUXIN RESPONSE FACTOR 16 (StARF16) regulates defense gene StNPR1 upon infection with necrotrophic pathogen in potato.',
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'description' => '<p><span>We demonstrate a new regulatory mechanism in the jasmonic acid (JA) and salicylic acid (SA) mediated crosstalk in potato defense response, wherein, miR160 target StARF16 (a gene involved in growth and development) binds to the promoter of StNPR1 (a defense gene) and negatively regulates its expression to suppress the SA pathway. Overall, our study establishes the importance of StARF16 in regulation of StNPR1 during JA mediated defense response upon necrotrophic pathogen interaction. Plants employ antagonistic crosstalk between salicylic acid (SA) and jasmonic acid (JA) to effectively defend them from pathogens. During biotrophic pathogen attack, SA pathway activates and suppresses the JA pathway via NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1). However, upon necrotrophic pathogen attack, how JA-mediated defense response suppresses the SA pathway, is still not well-understood. Recently StARF10 (AUXIN RESPONSE FACTOR), a miR160 target, has been shown to regulate SA and binds to the promoter of StGH3.6 (GRETCHEN HAGEN3), a gene proposed to maintain the balance between the free SA and auxin in plants. In the current study, we investigated the role of StARF16 (a miR160 target) in the regulation of the defense gene StNPR1 in potato upon activation of the JA pathway. We observed that a negative correlation exists between StNPR1 and StARF16 upon infection with the pathogen. The results were further confirmed through the exogenous application of SA and JA. Using yeast one-hybrid assay, we demonstrated that StARF16 binds to the StNPR1 promoter through putative ARF binding sites. Additionally, through protoplast transfection and chromatin immunoprecipitation experiments, we showed that StARF16 could bind to the StNPR1 promoter and regulate its expression. Co-transfection assays using promoter deletion constructs established that ARF binding sites are present in the 2.6 kb sequence upstream to the StNPR1 gene and play a key role in its regulation during infection. In summary, we demonstrate the importance of StARF16 in the regulation of StNPR1, and thus SA pathway, during JA-mediated defense response upon necrotrophic pathogen interaction.</span></p>',
'date' => '2022-04-05',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/35380408/',
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'name' => 'GIF1 controls ear inflorescence architecture and floral development byregulating key genes in hormone biosynthesis and meristem determinacy inmaize.',
'authors' => 'Li Manfei et al. ',
'description' => '<p>BACKGROUND: Inflorescence architecture and floral development in flowering plants are determined by genetic control of meristem identity, determinacy, and maintenance. The ear inflorescence meristem in maize (Zea mays) initiates short branch meristems called spikelet pair meristems, thus unlike the tassel inflorescence, the ears lack long branches. Maize growth-regulating factor (GRF)-interacting factor1 (GIF1) regulates branching and size of meristems in the tassel inflorescence by binding to Unbranched3. However, the regulatory pathway of gif1 in ear meristems is relatively unknown. RESULT: In this study, we found that loss-of-function gif1 mutants had highly branched ears, and these extra branches repeatedly produce more branches and florets with unfused carpels and an indeterminate floral apex. In addition, GIF1 interacted in vivo with nine GRFs, subunits of the SWI/SNF chromatin-remodeling complex, and hormone biosynthesis-related proteins. Furthermore, key meristem-determinacy gene RAMOSA2 (RA2) and CLAVATA signaling-related gene CLV3/ENDOSPERM SURROUNDING REGION (ESR) 4a (CLE4a) were directly bound and regulated by GIF1 in the ear inflorescence. CONCLUSIONS: Our findings suggest that GIF1 working together with GRFs recruits SWI/SNF chromatin-remodeling ATPases to influence DNA accessibility in the regions that contain genes involved in hormone biosynthesis, meristem identity and determinacy, thus driving the fate of axillary meristems and floral organ primordia in the ear-inflorescence of maize.</p>',
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'name' => 'Chromosomal variations of species revealed by FISH with rDNAs andcentromeric histone H3 variant associated DNAs',
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'description' => '<p>Lycoris species have various chromosome numbers and karyotypes, but all have a constant total number of chromosome major arms. In addition to three fundamental types, including metacentric (M-), telocentric (T-), and acrocentric (A-) chromosomes, chromosomes in various morphology and size were also observed in natural populations. Both fusion and fission translocation have been considered as main mechanisms leading to the diverse karyotypes among Lycoris species, which suggests the centromere organization playing a role in such arrangements. We detected several chromosomal structure changes in Lycoris including centric fusion, inversion, gene amplification, and segment deletion by using fluorescence in situ hybridization (FISH) probing with rDNAs. An antibody against centromere specific histone H3 (CENH3) of L. aurea (2n = 14, 8M+6T) was raised and used to obtain CENH3-associated DNA sequences of L. aurea by chromatin immunoprecipitation (ChIP) cloning method. Immunostaining with anti-CENH3 antibody could label the centromeres of M-, T-, and A-type chromosomes. Immunostaining also revealed two centromeres on one T-type chromosome and a centromere on individual mini-chromosome. Among 10,000 ChIP clones, 500 clones which showed abundant in L. aurea genome by dot-blotting analysis were FISH mapped on chromosomes to examine their cytological distribution. Five of these 500 clones could generate intense FISH signals at centromeric region on M-type but not T-type chromosomes. FISH signals of these five clones rarely appeared on A-type chromosomes. The five ChIP clones showed similarity in DNA sequences and could generate similar but not identical distribution patterns of FISH signals on individual chromosomes. Furthermore, the distinct distribution patterns of FISH signals on each chromosome generated by these five ChIP clones allow to identify individual chromosome, which is considered difficult by conventional staining approaches. Our results suggest a different organization of centromeres of the three chromosome types in Lycoris species.</p>',
'date' => '2021-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34591908',
'doi' => '10.1371/journal.pone.0258028',
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'name' => 'Expression of in the Stem Cell Domain Is Required for ItsFunction in the Control of Floral Meristem Activity in Arabidopsis',
'authors' => 'Kwaśniewska K. et al. ',
'description' => '<p>In the model plant Arabidopsis thaliana, the zinc-finger transcription factor KNUCKLES (KNU) plays an important role in the termination of floral meristem activity, a process that is crucial for preventing the overgrowth of flowers. The KNU gene is activated in floral meristems by the floral organ identity factor AGAMOUS (AG), and it has been shown that both AG and KNU act in floral meristem control by directly repressing the stem cell regulator WUSCHEL (WUS), which leads to a loss of stem cell activity. When we re-examined the expression pattern of KNU in floral meristems, we found that KNU is expressed throughout the center of floral meristems, which includes, but is considerably broader than the WUS expression domain. We therefore hypothesized that KNU may have additional functions in the control of floral meristem activity. To test this, we employed a gene perturbation approach and knocked down KNU activity at different times and in different domains of the floral meristem. In these experiments we found that early expression in the stem cell domain, which is characterized by the expression of the key meristem regulatory gene CLAVATA3 (CLV3), is crucial for the establishment of KNU expression. The results of additional genetic and molecular analyses suggest that KNU represses floral meristem activity to a large extent by acting on CLV3. Thus, KNU might need to suppress the expression of several meristem regulators to terminate floral meristem activity efficiently.</p>',
'date' => '2021-07-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34367223',
'doi' => '10.3389/fpls.2021.704351',
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'authors' => 'Xia, Qiang-Ming and Miao, Lu-Ke and Xie, Kai-Dong and Yin, Zhao-Ping and
Wu, Xiao-Meng and Chen, Chun-Li and Grosser, Jude W and Guo, Wen-Wu',
'description' => 'KEY MESSAGE: The physical locations of citrus centromere are revealed
by combining genetic and immunological assays for the first time and nine
citrus centromere-specific markers for cytogenetics are mined. Centromere
localization is challenging, because highly redundant repetitive sequences
in centromeric regions make sequence assembly difficult. Although several
citrus genomes have been released, the centromeric regions and their
characteristics remain to be elucidated. Here, we mapped citrus centromeres
through half-tetrad analysis (HTA) that included the genotyping of 54
tetraploid hybrids derived from 2n megagametophytes of Nadorcott tangor
with 212 single nucleotide polymorphism (SNP) markers. The sizes of
centromeric regions, which estimated based on the heterozygosity
restitution rate pattern along the chromosomes, ranged from 1.12 to
18.19 Mb. We also profiled the binding sequences with the
centromere-specific histone variant CenH3 by chromatin immunoprecipitation
sequencing (ChIP-seq). Based on the positions of the top ten
CenH3-enriched contigs, the sizes of centromeric regions were estimated to
range from 0.01 to 7.60 Mb and were either adjacent to or included in the
centromeric regions identified by HTA. We used DNA probes from two
repeats selected from the centromeric regions and seven CenH3-binding
centromeric repeats to verify centromeric locations by fluorescence in situ
hybridization (FISH). Centromere localization in citrus will contribute
to the mining of centromeric/pericentromeric markers, thus to facilitate
the rapid identification of mechanisms underlying 2n gamete formation and
serve the polyploidy breeding.',
'date' => '2020-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32897396',
'doi' => '10.1007/s00299-020-02587-z',
'modified' => '2021-02-18 10:21:53',
'created' => '2021-02-18 10:21:53',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'id' => '4052',
'name' => 'StE(z)2, a Polycomb group methyltransferase and deposition of H3K27me3 andH3K4me3 regulate the expression of tuberization genes in potato.',
'authors' => 'Kumar, Amit and Kondhare, Kirtikumar R and Malankar, Nilam N and Banerjee,Anjan K',
'description' => '<p>Polycomb Repressive Complex (PRC) group proteins regulate various developmental processes in plants by repressing the target genes via H3K27 trimethylation, whereas their function is antagonized by Trithorax group proteins-mediated H3K4 trimethylation. Tuberization in potato is widely studied, but the role of histone modifications in this process is unknown. Recently, we showed that overexpression of StMSI1 (a PRC2 member) alters the expression of tuberization genes in potato. As MSI1 lacks histone-modification activity, we hypothesized that this altered expression could be caused by another PRC2 member, StE(z)2 (a potential H3K27 methyltransferase in potato). Here, we demonstrate that short-day photoperiod influences StE(z)2 expression in leaf and stolon. Moreover, StE(z)2 overexpression alters plant architecture and reduces tuber yield, whereas its knockdown enhanced the yield. ChIP-sequencing using short-day induced stolons revealed that several tuberization and phytohormone-related genes, such as StBEL5/11/29, StSWEET11B, StGA2OX1 and StPIN1 carry H3K4me3 or H3K27me3 marks and/or are StE(z)2 targets. Interestingly, we noticed that another important tuberization gene, StSP6A is targeted by StE(z)2 in leaves and had increased deposition of H3K27me3 under non-induced (long-day) conditions compared to SD. Overall, we show that StE(z)2 and deposition of H3K27me3 and/or H3K4me3 marks could regulate the expression of key tuberization genes in potato.</p>',
'date' => '2020-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33048134',
'doi' => '10.1093/jxb/eraa468',
'modified' => '2021-02-19 14:55:34',
'created' => '2021-02-18 10:21:53',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 8 => array(
'id' => '3959',
'name' => 'The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2).',
'authors' => 'Velanis CN, Perera P, Thomson B, de Leau E, Liang SC, Hartwig B, Förderer A, Thornton H, Arede P, Chen J, Webb KM, Gümüs S, De Jaeger G, Page CA, Hancock CN, Spanos C, Rappsilber J, Voigt P, Turck F, Wellmer F, Goodrich J',
'description' => '<p>A large fraction of plant genomes is composed of transposable elements (TE), which provide a potential source of novel genes through "domestication"-the process whereby the proteins encoded by TE diverge in sequence, lose their ability to catalyse transposition and instead acquire novel functions for their hosts. In Arabidopsis, ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) arose by domestication of the nuclease component of Harbinger class TE and acquired a new function as a component of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a histone H3K27me3 methyltransferase involved in regulation of host genes and in some cases TE. It was not clear how ALP1 associated with PRC2, nor what the functional consequence was. Here, we identify ALP2 genetically as a suppressor of Polycomb-group (PcG) mutant phenotypes and show that it arose from the second, DNA binding component of Harbinger transposases. Molecular analysis of PcG compromised backgrounds reveals that ALP genes oppose silencing and H3K27me3 deposition at key PcG target genes. Proteomic analysis reveals that ALP1 and ALP2 are components of a variant PRC2 complex that contains the four core components but lacks plant-specific accessory components such as the H3K27me3 reader LIKE HETEROCHROMATION PROTEIN 1 (LHP1). We show that the N-terminus of ALP2 interacts directly with ALP1, whereas the C-terminus of ALP2 interacts with MULTICOPY SUPPRESSOR OF IRA1 (MSI1), a core component of PRC2. Proteomic analysis reveals that in alp2 mutant backgrounds ALP1 protein no longer associates with PRC2, consistent with a role for ALP2 in recruitment of ALP1. We suggest that the propensity of Harbinger TE to insert in gene-rich regions of the genome, together with the modular two component nature of their transposases, has predisposed them for domestication and incorporation into chromatin modifying complexes.</p>',
'date' => '2020-05-01',
'pmid' => 'http://www.pubmed.gov/32463832',
'doi' => '10.1371/journal.pgen.1008681',
'modified' => '2020-08-12 09:51:53',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'id' => '3880',
'name' => 'REDOX RESPONSIVE TRANSCRIPTION FACTOR1 (RRFT1) is involved in extracellular ATP regulated Arabidopsis thaliana seedling growth.',
'authors' => 'Zhu R, Dong X, Xue Y, Xu J, Zhang A, Feng M, Zhao Q, Xia S, Yin Y, He S, Li Y, Liu T, Kang E, Shang Z',
'description' => '<p>Extracellular ATP (eATP) is an apoplastic signaling molecule that plays essential roles in the growth and development of plants. Arabidopsis seedlings have been reported to respond to eATP, however, the downstream signaling components are still not well understood. Here, we report that an ethylene responsive factor, Redox Responsive Transcription Factor 1 (RRTF1), is involved in eATP-regulated Arabidopsis thaliana seedling growth. Exogenous ATP inhibited green seedling root growth and induced hypocotyl bending of etiolated seedlings. RRTF1 loss-of-function mutant (rrtf1) seedlings showed decreased responses to eATP, while its complementation or overexpression led to recovered or increased eATP responsiveness. RRTF1 was expressed rapidly after eATP stimulation and then migrated into the nuclei of root tip cells. eATP-induced auxin accumulation in root tip or hypocotyl cells was impaired in rrtf1. Chromatin immunoprecipitation (ChIP) and high-throughput sequencing results indicated that eATP induced some genes related to cell growth and development in wild type but not in rrtf1 cells. These results suggest that RRTF1 may be involved in eATP signaling by regulating functional gene expression and cell metabolism in Arabidopsis seedlings.</p>',
'date' => '2020-02-12',
'pmid' => 'http://www.pubmed.gov/32049334',
'doi' => '10.1093/pcp/pcaa014/5734653',
'modified' => '2020-03-20 17:32:29',
'created' => '2020-03-13 13:45:54',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 10 => array(
'id' => '3872',
'name' => 'An inferred fitness consequence map of the rice genome.',
'authors' => 'Joly-Lopez Z, Platts AE, Gulko B, Choi JY, Groen SC, Zhong X, Siepel A, Purugganan MD',
'description' => '<p>The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa). We inferred fitCons scores (ρ) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae. We found ρ to be multimodal, with ~9% of the rice genome falling into classes where more than half of the bases would probably have a fitness consequence if mutated. Around 2% of the rice genome showed evidence of weak negative selection, frequently at candidate regulatory sites, including a novel set of 1,000 potentially active enhancer elements. This fitCons map provides perspective on the evolutionary forces associated with genome diversity, aids in genome annotation and can guide crop breeding programs.</p>',
'date' => '2020-02-02',
'pmid' => 'http://www.pubmed.gov/32042156',
'doi' => '10.1038/s41477-019-0589-3',
'modified' => '2020-03-20 17:43:24',
'created' => '2020-03-13 13:45:54',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 11 => array(
'id' => '3191',
'name' => 'Transcription Factor Interplay between LEAFY and APETALA1/CAULIFLOWER during Floral Initiation',
'authors' => 'Goslin K. et al.',
'description' => '<p>The transcription factors LEAFY (LFY) and APETALA1 (AP1), together with the AP1 paralog CAULIFLOWER (CAL), control the onset of flower development in a partially redundant manner. This redundancy is thought to be mediated, at least in part, through the regulation of a shared set of target genes. However, whether these genes are independently or cooperatively regulated by LFY and AP1/CAL is currently unknown. To better understand the regulatory relationship between LFY and AP1/CAL and to obtain deeper insights into the control of floral initiation, we monitored the activity of LFY in the absence of AP1/CAL function. We found that the regulation of several known LFY target genes is unaffected by AP1/CAL perturbation, while others appear to require AP1/CAL activity. Furthermore, we obtained evidence that LFY and AP1/CAL control the expression of some genes in an antagonistic manner. Notably, these include key regulators of floral initiation such as <i>TERMINAL FLOWER1</i> (<i>TFL1</i>), which had been previously reported to be directly repressed by both LFY and AP1. We show here that <i>TFL1</i> expression is suppressed by AP1 but promoted by LFY. We further demonstrate that LFY has an inhibitory effect on flower formation in the absence of AP1/CAL activity. We propose that LFY and AP1/CAL act as part of an incoherent feed-forward loop, a network motif where two interconnected pathways or transcription factors act in opposite directions on a target gene, to control the establishment of a stable developmental program for the formation of flowers.</p>',
'date' => '2017-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28385730',
'doi' => '',
'modified' => '2017-06-19 10:57:08',
'created' => '2017-06-19 10:57:08',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 12 => array(
'id' => '3358',
'name' => 'Characterization of the Polycomb-Group Mark H3K27me3 in Unicellular Algae',
'authors' => 'Mikulski P. et al.',
'description' => '<p>Polycomb Group (PcG) proteins mediate chromatin repression in plants and animals by catalyzing H3K27 methylation and H2AK118/119 mono-ubiquitination through the activity of the Polycomb repressive complex 2 (PRC2) and PRC1, respectively. PcG proteins were extensively studied in higher plants, but their function and target genes in unicellular branches of the green lineage remain largely unknown. To shed light on PcG function and <i>modus operandi</i> in a broad evolutionary context, we demonstrate phylogenetic relationship of core PRC1 and PRC2 proteins and H3K27me3 biochemical presence in several unicellular algae of different phylogenetic subclades. We focus then on one of the species, the model red alga <i>Cyanidioschizon merolae</i>, and show that H3K27me3 occupies both, genes and repetitive elements, and mediates the strength of repression depending on the differential occupancy over gene bodies. Furthermore, we report that H3K27me3 in <i>C. merolae</i> is enriched in telomeric and subtelomeric regions of the chromosomes and has unique preferential binding toward intein-containing genes involved in protein splicing. Thus, our study gives important insight for Polycomb-mediated repression in lower eukaryotes, uncovering a previously unknown link between H3K27me3 targets and protein splicing.</p>',
'date' => '2017-04-26',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28491069',
'doi' => '',
'modified' => '2018-04-05 13:09:46',
'created' => '2018-04-05 13:09:46',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 13 => array(
'id' => '3099',
'name' => 'Nitric oxide modulates histone acetylation at stress genes by inhibition of histone deacetylases',
'authors' => 'Mengel A. et al.',
'description' => '<p>Histone acetylation, which is an important mechanism to regulate gene expression, is controlled by the opposing action of histone acetyltransferases (HATs) and histone deacetylases (HDACs). In animals, several HDACs are subjected to regulation by nitric oxide (NO), in plants however, it is unknown whether NO affects histone acetylation. We found that treatment with the physiological NO-donor S-nitroso-glutathione (GSNO) increased the abundance of several histone acetylation marks in Arabidopsis, which was strongly diminished in the presence of the NO scavenger 2-4-carboxyphenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO). This increase was likely triggered by NO-dependent inhibition of HDAC activity since GSNO and S-nitroso-N-acetyl-DL-penicillamine (SNAP) significantly and reversibly reduced total HDAC activity in vitro (in nuclear extracts) and in vivo (in protoplasts). Next, genome-wide H3K9/14ac profiles in Arabidopsis seedlings were generated by ChIP-sequencing and changes induced by GSNO, GSNO/cPTIO or trichostatin A (HDAC inhibitor) were quantified thereby identifying genes which display putative NO-regulated histone acetylation. Functional classification of these genes revealed that many of them are involved in the plant defense response and the abiotic stress response. Furthermore, salicylic acid (SA), which is the major plant defense hormone against biotrophic pathogens, inhibited HDAC activity and increased histone acetylation by inducing endogenous NO production. These data suggest, that NO affects histone acetylation by targeting and inhibiting HDAC complexes, resulting in the hyperacetylation of specific genes. This mechanism might operate in the plant stress response by facilitating stress-induced transcription of genes.</p>',
'date' => '2016-12-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27980017',
'doi' => '',
'modified' => '2017-06-20 10:24:53',
'created' => '2017-01-03 14:41:10',
'ProductsPublication' => array(
[maximum depth reached]
)
)
),
'Testimonial' => array(),
'Area' => array(
(int) 0 => array(
'id' => '5',
'parent_id' => null,
'name' => 'Plant',
'description' => '<div class="extra-spaced">
<p><img src="https://www.diagenode.com/img/areas/plant.jpg" /></p>
</div>
<div class="extra-spaced">
<h2>Epigenetic Regulation in Plants</h2>
<p>Plants utilize a number of gene regulation mechanisms to ensure proper development, function, growth, and survival under different environmental conditions. Plants depend on changes in gene expression to respond to environmental stimuli, in which the full repertoire of histone modifications, DNA methylation, and small ncRNAs play an important role in epigenetic regulation.</p>
<p>Studying the epigenetics of model plants such as Arabidopsis thaliana have allowed researchers to understand pathways that maintain chromatin modifications as well as the mapping of modifications such as DNA methylation on a genome-wide scale. Small RNAs have also been implicated in playing a role in the distribution of chromatin modifications, and RNA may also play a role in the complex epigenetic interactions that occur between homologous sequences (Moazed et al, 2009). In the future, by understanding epigenetic control, researchers can uncover the research necessary to improve plant growth, yields, and transformation efficiency especially in the face of climate change and other environmental factors.</p>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-3 large-3 columns">
<p><img src="https://www.diagenode.com/img/areas/chromatin-and-transcription-factors.jpg" /></p>
</div>
<div class="small-12 medium-9 large-9 columns">
<h3 style="font-weight: 100; margin-top: 0;">Chromatin</h3>
<p>Chromatin consists of nucleosomes formed by a complex of histone proteins and DNA, which allows the packaging of DNA into the nucleus. The less condensed euchromatin represents transcriptionally active regions, while heterochromatin is usually inactive (Vaillant and Paszkowski, 2007). Chromatin state is known to be influenced by both DNA methylation and histone modifications which in turn impact gene expression and the structure of chromosomes. In a recent study, the role of chromatin modifications during plant reproduction elucidated 3-dimensional chromosome reorganization mediated by histones and DNA methylation (Dukowic-Schulze et al. 2017). In addition, gibberellins have been shown in increasing the level of histone acetylation, which affects regions of chromatin involved in maize seed germination (Zheng et al. 2017). Another study reports a novel function of a tomato histone deacetylase gene in the regulation of fruit ripening (Guo et al. 2017).</p>
</div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-3 large-3 columns">
<p><img src="https://www.diagenode.com/img/areas/cherry-tomato-common-grape-vine-ripening-fruit-vegetable-cherry-tomatoes.jpg" /></p>
</div>
<div class="small-12 medium-9 large-9 columns">
<p>In addition, multigene families encode transcription factors, with members found throughout the genome or clustered on the same chromosome. Numerous DNA binding proteins that interact with plant promoters have been identified -- some are similar to well-characterized transcription factors in animals or yeast, while others are unique to plants. For example, diverse members of the subfamily X of the plant-specific ethylene response factor (ERF) transcription factors coordinate stress signaling with wound repair activation. Tissue repair is also enhanced through a protein complex of ERF and GRAS TFs (Heyman et. al,.2018). A compilation of known plant transcription factors can be found in the plant transcription factor database at http://plntfdb.bio.uni-potsdam.de/v3.0/.</p>
</div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-3 large-3 columns">
<p><img src="https://www.diagenode.com/img/areas/rna-strand.jpg" /></p>
</div>
<div class="small-12 medium-9 large-9 columns">
<h3 style="font-weight: 100; margin-top: 0;">RNA</h3>
<p>Recent research shows that a number of classes of small RNAs are key epigenetic regulators. In many cases, small RNAs have been implicated in DNA methylation and chromatin modification (Meyer, 2015). In addition, the role of small RNAs has been implicated in plant stress tolerance (Kumar et al., 2017). López-Galiano et al also provided insight into a coordinated function of a miRNA gene and histone modifications in regulating the expression of a WRKY transcription factor in response to stress.</p>
<p>RNA interference (RNAi) is another epigenetic mechanism that leads to small RNA generation, which mediates gene silencing at the post-transcriptional level. RNAi technology has immense potential for plant disease resistance.</p>
</div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-3 large-3 columns">
<p><img src="https://www.diagenode.com/img/areas/dna-methylation.jpg" /></p>
</div>
<div class="small-12 medium-9 large-9 columns">
<h3 style="font-weight: 100; margin-top: 0;">DNA methylation</h3>
<p>Plants, unlike animals, have three sites that can be methylated G, CHG (H can be A, C, T), and CHH (Law and Jacobsen, 2010). DNA methylation has attracted particular interest. In Arabidopsis, one-third of methylated genes occur in transcribed regions, and 5% of genes are methylated in promoter regions, suggesting that many of these are epigenetically regulated. (Zhang et al., 2006).</p>
<p>There are thousands of differentially methylated regions (DMRs) that influence phenotype by influencing gene expression. The analysis of epigenetic recombinant inbred line (epiRIL) plants from Arabidopsis points to the evidence of the influence of DMRs. An epiRIL results from crossing two genetically identical plants with differing DNA methylation levels (with one parent as a homozygous mutant for an essential DNA methylation maintenance gene). The offspring of these plants have similar genomes that vary only in methylation levels. Many traits have been studied using epiRILs -- flowering time, plant height, and response to abiotic stress, some of which have now been mapped to DMRs (Zhang et al. 2018)</p>
<p>Regulation by DNA methylation has been shown to be important in many aspects of plant development and response such as vernalization, hybrid vigor, and self-incompatibility (Itabashi et al. 2017). For example, vernalization treatments have shown reduced DNA methylation and subsequent initiation of flowering (Burn et al., 1993). Stress can also influence DNA methylation in plants as a response to environmental stimuli. (Steward et al., 2002; Song et al., 2012). A high degree of DNA methylation has also suggested the role in the improvement of plant fitness under different environmental conditions (Saéz-Laguna et al., 2014). In addition, methylation can affect normal fruit and hypomethylation predicts homeotic transformation and loss of fruit yield (Ong-Abdullah et al., 2015)</p>
</div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-3 large-3 columns">
<p><img src="https://www.diagenode.com/img/areas/plant-development.jpg" class="left" style="padding-right: 15px;" /></p>
</div>
<div class="small-12 medium-9 large-9 columns">
<p>DNA demethylation has also been implied in various aspects of plant development including pollen tube formation, embryogenesis, fruit ripening, stomatal development, and nodule formation ( Li et al. 2017). Demethylation of rice genomic DNA caused an altered pattern of gene expression, inducing dwarf plants (Sano et al., 1990).</p>
<p>Epigenetic modifications contribute to the stability and survival of the plants and their ability to adapt in different environmental conditions.</p>
</div>
</div>
<h3>Diagenode products for your epigenomics research in plants</h3>
<div class="row extra-spaced">
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #099f92; height: 275px;">
<h3 class="text-center"><a href="https://www.diagenode.com/en/categories/chromatin-function">Chromatin analysis</a></h3>
<center><a href="https://www.diagenode.com/en/categories/chromatin-function"><img src="https://www.diagenode.com/img/cancer/chromatin-icon.png" /></a></center>
<p class="text-left">Understand the role of chromatin in plant function and development</p>
</div>
<ul>
<li><a href="https://www.diagenode.com/en/categories/chromatin-function">Learn about our chromatin analysis products</a></li>
<li><a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns"> Learn about the Universal Plant ChIP Kit</a></li>
</ul>
</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #30415c; height: 275px;">
<h3 class="text-center"><a href="https://www.diagenode.com/en/categories/dna-methylation" style="color: #30415c;">DNA methylation</a></h3>
<center><a href="https://www.diagenode.com/en/categories/dna-methylation"><img src="https://www.diagenode.com/img/cancer/dna-icon.png" /></a></center>
<p class="text-left">DNA methylation and demethylation and the effects on plant response and function</p>
</div>
<ul>
<li><a href="https://www.diagenode.com/en/categories/dna-methylation">Discover DNA methylation analysis solutions at any resolution</a></li>
</ul>
</div>
<div class="small-12 medium-4 large-4 columns text-left">
<div class="panel" style="border-color: #474546; height: 275px;">
<h3 class="text-center"><span class="darkgrey">Non-coding RNAs</span></h3>
<center><img src="https://www.diagenode.com/img/cancer/non-coding-icon.png" /></center>
<p class="text-left">Discover noncoding RNAs in the regulation of gene expression in plants</p>
</div>
<ul>
<li><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">Library prep for RNA-seq studies for ncRNAs</a></li>
</ul>
</div>
</div>
<h3>References</h3>
<p><small> Burn, J. et al (1993). DNA methylation, vernalization, and the initiation of flowering. Proc. Natl. Acad. Sci. U.S.A. 90, 287–291. doi: 10.1006/scdb.1996.0055 </small></p>
<p><small> Dukowic-Schulze S, Liu C, Chen C (2017) Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2222-0</small></p>
<p><small> Guo J et al (2017) A histone deacetylase gene, SlHDA3, acts as a negative regulator of fruit ripening and carotenoid accumulation. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2211-3</small></p>
<p><small> Heyman J, et.al (2018) Journal of Cell Science Emerging role of the plant ERF transcription factors in coordinating wound defense responses and repair doi: 10.1242/jcs.208215</small></p>
<p><small> Itabashi E, Osabe K, Fujimoto R, Kakizaki T (2017) Epigenetic regulation of agronomical traits in Brassicaceae. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2223-z</small></p>
<p><small> Kumar V et al (2017) Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2210-4</small></p>
<p><small> Law, J. A., and Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220. doi: 10.1038/nrg2719</small></p>
<p><small> Meyer, P. (2015). Epigenetic variation and environmental change. J. Exp. Bot. 66, 3541–3548. doi: 10.1093/jxb/eru502</small></p>
<p><small> Moazed, D. (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature. doi: 10.1038/nature07756</small></p>
<p><small> Ong-Abdullah et al. (2015). Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525, 533–537. doi: 10.1038/nature15365</small></p>
<p><small> Saéz-Laguna et al. (2014). Epigenetic variability in the genetically uniform forest tree species. PLoS One 9:e103145. doi: 10.1371/journal.pone.0103145</small></p>
<p><small> Sano, H. et al. (1990). A single treatment of rice seedlings with 5-azacytidine induces heritable dwarfism and undermethylation of genomic DNA. Mol. Gen. Genet. 220, 441–447. doi: 10.1007/BF00391751</small></p>
<p><small> Song, J et al (2012). Vernalization – A cold-induced epigenetic switch. J. Cell Sci. 125, 3723–3731. doi: 10.1242/jcs.084764</small></p>
<p><small> Steward, N et al. (2002). Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J. Biol. Chem. 277, 37741–37746. doi: 10.1074/jbc.M204050200</small></p>
<p><small> Vaillant, I., and Paszkowski, J. (2007). Role of histone and DNA methylation in gene regulation. Curr. Opin. Plant Biol. 10, 528–533. doi: 10.1016/j.pbi.2007.06.008</small></p>
<p><small> Zhang, et al. (2006). Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189–1201. doi: 10.1016/j.cell.2006.08.003</small></p>
<p><small> Zhang et al. 2018 Understanding the evolutionary potential of epigenetic variation: a comparison of heritable phenotypic variation in epiRILs, RILs, and natural ecotypes of Arabidopsis thaliana. Heredity 121, 257–265 (2018) doi:10.1038/s41437-018-0095-9</small></p>
<p><small> Zheng X et al (2017) Histone acetylation is involved in GA-mediated 45S rDNA decondensation in maize aleurone layers. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2207-z</small></p>
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'name' => 'IPure kit v2',
'description' => '<p><a href="https://www.diagenode.com/files/products/kits/ipure_kit_v2_manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>Diagenode’s<span> </span><b>IPure</b><b><span> </span>kit<span> </span></b>is the only DNA purification kit using magnetic beads, that is specifically optimized for extracting DNA from<span> </span><b>ChIP</b><b>,<span> </span></b><b>MeDIP</b><span> </span>and<span> </span><b>CUT&Tag</b>. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. This simple and straightforward protocol delivers pure DNA ready for any downstream application (e.g. next generation sequencing). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples.</p>
<center>
<h4>High DNA recovery after purification of ChIP samples using IPure technology</h4>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-chromatin-function.png" width="500" /></center>
<p></p>
<p><small>ChIP assays were performed using different amounts of U2OS cells and the H3K9me3 antibody (Cat. No.<span> </span><span>C15410056</span>; 2 g/IP). <span>The purified DNA was eluted in 50 µl of water and quantified with a Nanodrop.</span></small></p>
<p></p>
<p><strong>Benefits of the IPure kit:</strong></p>
<ul>
<li style="text-align: left;">Provides pure DNA for any downstream application (e. g. Next generation sequencing)</li>
<li style="text-align: left;">Non-toxic</li>
<li style="text-align: left;">Fast & easy to use</li>
<li style="text-align: left;">Optimized for DNA purification after ChIP, MeDIP and CUT&Tag</li>
<li style="text-align: left;">Compatible with automation</li>
<li style="text-align: left;">Validated on the IP-Star Compact</li>
</ul>
</center>',
'label1' => 'Examples of results',
'info1' => '<h2>IPure after ChIP</h2>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-A.png" alt="ChIP-seq figure A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-B.png" alt="ChIP-seq figure B" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-C.png" alt="ChIP-seq figure C" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><small><strong>Figure 1.</strong> Chromatin Immunoprecipitation has been performed using chromatin from HeLa cells, the iDeal ChIP-seq kit for Transcription Factors (containing the IPure module for DNA purification) and the Diagenode ChIP-seq-grade HDAC1 (A), LSD1 (B) and p53 antibody (C). 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. This figure shows the peak distribution in regions of chromosome 3 (A), chromosome 12 (B) and chromosome 6 (C) respectively.</small></p>
<p></p>
<h2>IPure after CUT&Tag</h2>
<p>Successful CUT&Tag results showing a low background with high region-specific enrichment has been generated using 50.000 of K562 cells, 1 µg of H3K4me3 or H3K27me3 antibody (Diagenode, C15410003 or C15410069, respectively) and proteinA-Tn5 (1:250) (Diagenode, C01070001). 1 µg of IgG (C15410206) was used as negative control. Samples were purified using the IPure kit v2 or phenol-chloroform purification. The below figures present the comparison of two purification methods.</p>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-fig2.png" style="display: block; margin-left: auto; margin-right: auto;" width="400" /></center><center>
<p style="text-align: center;"><small><strong>Figure 2.</strong> Heatmap 3kb upstream and downstream of the TSS for H3K4me3</small></p>
</center>
<p></p>
<p><img src="https://www.diagenode.com/img/product/kits/ipure-fig3.png" style="display: block; margin-left: auto; margin-right: auto;" width="600" /></p>
<p></p>
<center><small><strong>Figure 3.</strong> Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using Diagenode’s pA-Tn5 transposase (Cat. No. C01070002), H3K27me3 antibody (Cat. No. C15410069) and IPure kit v2 vs phenol chloroform purification (PC).</small></center>
<p></p>
<p></p>
<h2>IPure after MeDIP</h2>
<center><img src="https://www.diagenode.com/img/product/kits/magmedip-seq-figure_multi3.jpg" alt="medip sequencing coverage" width="600" /></center><center></center><center>
<p></p>
<small><strong>Figure 4.</strong> Consistent coverage and methylation detection from different starting amounts of DNA with the Diagenode MagMeDIP-seq Package (including the Ipure kit for DNA purification). Samples containing decreasing starting amounts of DNA (from the top down: 1000 ng (red), 250 ng (blue), 100 ng (green)) originating from human blood were prepared, revealing a consistent coverage profile for the three different starting amounts, which enables reproducible methylation detection. The CpG islands (CGIs) (marked by yellow boxes in the bottom track) are predominantly unmethylated in the human genome, and as expected, we see a depletion of reads at and around CGIs.</small></center>
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'label2' => 'iPure Workflow',
'info2' => '<h2 style="text-align: center;">Kit Method Overview & Time table</h2>
<p><img src="https://www.diagenode.com/img/product/kits/workflow-ipure-cuttag.png" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<h3><strong>Workflow description</strong></h3>
<h5><strong>IPure after ChIP</strong></h5>
<p><strong>Step 1:</strong> Chromatin is decrosslinked and eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added.<br /> <strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet.<br /> <strong>Step 3:</strong> Proteins and remaining buffer are washed away.<br /> <strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after MeDIP</strong></h5>
<p><strong>Step 1:</strong> DNA is eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Remaining buffer are washed away.<br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after CUT&Tag</strong></h5>
<p><strong>Step 1:</strong> pA-Tn5 is inactivated and DNA released from the cells. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Proteins and remaining buffer are washed away. <br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).</p>
<p></p>
<p></p>
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<p style="text-align: justify;">The <strong>Universal Plant ChIP-seq kit</strong> offers the convenience of extracting plant chromatin from a wide variety of plants including Arabidopsis, maize, rice, tomato and poplar. This complete kit has been specifically optimized for <strong>plant chromatin extraction</strong> and includes reagents for chromatin preparation, immunoprecipitation, plant-specific control primer pairs, control antibody, and DNA purification.</p>',
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<h4 class="text-center">Arabidopsis</h4>
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<p><small><strong>Figure 1.</strong> ChIP-seq was performed on Arabidopsis thaliana (Col-0) seedlings using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng (green), 500 pg (orange) and 100 pg (red) IP'd DNA and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a public dataset (NCBI GEO Dataset GSM1193621) that we used as an external reference. Enrichments along a wide region of chromosome 5 are uniform regardless of the starting material amount for the preparation of the library.</small></p>
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<h4 class="text-center">Poplar</h4>
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<p><small><strong>Figure 3.</strong> ChIP-seq was performed on Populus trichocarpa stem differenciating xylem using the <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with the <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the input and is considered as the background enrichment. The profile in red represents enrichments along a wide region of scaffold 18. Using the same scale, the peaks of the immunoprecipitated samples are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
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<h4 class="text-center">Tomato</h4>
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<p><small><strong>Figure 2.</strong> ChIP-seq was performed on Solanum lycopersicum cv. Micro-Tom young leaves using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 750 pg of immunoprecipitated DNA using the Universal Plant ChIP-seq kit (red) and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a dataset obtained from Nguyen et al. 2014 that we used as an external reference. Enrichments are higher and consistent with the reference data along a wide region of chromosome 1.</small></p>
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<div class="small-6 columns">
<h4 class="text-center">Maize</h4>
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<p><small><strong>Figure 4.</strong> ChIP-seq was performed on Zea mays cv. B73 inner stem using our <a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">Premium H3K27me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the Input and is considered as the background enrichment. The enrichment in red represents enrichments along a wide region of chromosome 3. Using the same scale, the peaks of the immunoprecipitated sample are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
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<td style="width: 341px;">
<h4><strong>Validated antibodies</strong></h4>
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<td style="width: 224px;"><strong>Arabidopsis (<em>Arabidopsis thaliana</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-actin-atg-primer-pair-50-ul">Arabidopsis Actin ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-monoclonal-antibody-classic-50-ug-50-ul">H3K4me3 monoclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-atg-primer-pair-50-ul">Arabidopsis FLC-ATG primer pair</a></td>
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<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-intron1-primer-pair-50-ul">Arabidopsis FLC-intron1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me3-polyclonal-antibody-classic-sample-size-10-ug">H3K9me3 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9-14ac-polyclonal-antibody-classic-sample-size-10-mg">H3K9/14ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27ac-polyclonal-antibody-premium-sample-size-10-ug">H3K27ac polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Maize (<em>Zea mays</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/maize-B73-inner-stem-ZmB1-UTR-primer-pair-50ul">Maize B73 inner stem ZmB1-UTR primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/Maize-B73-inner-stem-ZmCopia-primer-pair-50ul">Maize B73 inner stem ZmCopia primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Tomato (<em>Solanum lycopersicum</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr2-reg8-primer-pair-50ul">Tomato leaves SlChr2-reg8 primer pair</a></td>
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<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr4-NC1-primer-pair-50ul">Tomato leaves SlChr4-NC1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
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<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
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<tr>
<td style="width: 224px;"><strong>Rice (<em>Oriza sativa</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsChr4-reg9-primer-pair-50ul">Rice seedlings OsChr4-reg9 primer pair</a></td>
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<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
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</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
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<td style="width: 224px;"><strong>Poplar (<em>Populus trichocarpa, Populus tremula x alba</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrCopia-orth-primer-pair-50ul">Poplar xylem PtrCopia-orth primer pair</a></td>
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<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9ac-polyclonal-antibody-classic-sample-size-10-ug">H3K9ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrMYBTF1-primer-pair-50ul">Poplar xylem PtrMYBTF1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
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<p style="text-align: justify;">The <strong>Universal Plant ChIP-seq kit</strong> offers the convenience of extracting plant chromatin from a wide variety of plants including Arabidopsis, maize, rice, tomato and poplar. This complete kit has been specifically optimized for <strong>plant chromatin extraction</strong> and includes reagents for chromatin preparation, immunoprecipitation, plant-specific control primer pairs, control antibody, and DNA purification.</p>',
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<h3>Successful ChIP-seq experiments for a variety of plants</h3>
<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Arabidopsis</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG1"> <img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A-small.jpg" /> </a></p>
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<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A.png" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 1.</strong> ChIP-seq was performed on Arabidopsis thaliana (Col-0) seedlings using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng (green), 500 pg (orange) and 100 pg (red) IP'd DNA and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a public dataset (NCBI GEO Dataset GSM1193621) that we used as an external reference. Enrichments along a wide region of chromosome 5 are uniform regardless of the starting material amount for the preparation of the library.</small></p>
</div>
<div class="small-6 columns">
<h4 class="text-center">Poplar</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG2"><img src="https://www.diagenode.com/img/landing-pages/poplar-small.jpg" /> </a></p>
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<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/poplar.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 3.</strong> ChIP-seq was performed on Populus trichocarpa stem differenciating xylem using the <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with the <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the input and is considered as the background enrichment. The profile in red represents enrichments along a wide region of scaffold 18. Using the same scale, the peaks of the immunoprecipitated samples are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Tomato</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG3"> <img src="https://www.diagenode.com/img/landing-pages/tomtato-small.jpg" /> </a></p>
<div id="IMG3" class="reveal-modal" data-reveal="" aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/tomtato.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 2.</strong> ChIP-seq was performed on Solanum lycopersicum cv. Micro-Tom young leaves using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 750 pg of immunoprecipitated DNA using the Universal Plant ChIP-seq kit (red) and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a dataset obtained from Nguyen et al. 2014 that we used as an external reference. Enrichments are higher and consistent with the reference data along a wide region of chromosome 1.</small></p>
</div>
<div class="small-6 columns">
<h4 class="text-center">Maize</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG4"> <img src="https://www.diagenode.com/img/landing-pages/maize-small.jpg" /> </a></p>
<div id="IMG4" class="reveal-modal" data-reveal="" aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/maize.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 4.</strong> ChIP-seq was performed on Zea mays cv. B73 inner stem using our <a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">Premium H3K27me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the Input and is considered as the background enrichment. The enrichment in red represents enrichments along a wide region of chromosome 3. Using the same scale, the peaks of the immunoprecipitated sample are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<p><strong> </strong></p>
<table style="width: 856px;">
<tbody>
<tr>
<td style="width: 224px;">
<h4><strong>Plant Species</strong></h4>
</td>
<td style="width: 341px;">
<h4><strong>Validated antibodies</strong></h4>
</td>
<td style="width: 357px;">
<h4><strong>Validated primer pairs</strong></h4>
</td>
</tr>
<tr>
<td style="width: 224px;"><strong>Arabidopsis (<em>Arabidopsis thaliana</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-actin-atg-primer-pair-50-ul">Arabidopsis Actin ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-monoclonal-antibody-classic-50-ug-50-ul">H3K4me3 monoclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-atg-primer-pair-50-ul">Arabidopsis FLC-ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-intron1-primer-pair-50-ul">Arabidopsis FLC-intron1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me3-polyclonal-antibody-classic-sample-size-10-ug">H3K9me3 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9-14ac-polyclonal-antibody-classic-sample-size-10-mg">H3K9/14ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27ac-polyclonal-antibody-premium-sample-size-10-ug">H3K27ac polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Maize (<em>Zea mays</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/maize-B73-inner-stem-ZmB1-UTR-primer-pair-50ul">Maize B73 inner stem ZmB1-UTR primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/Maize-B73-inner-stem-ZmCopia-primer-pair-50ul">Maize B73 inner stem ZmCopia primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Tomato (<em>Solanum lycopersicum</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr2-reg8-primer-pair-50ul">Tomato leaves SlChr2-reg8 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr4-NC1-primer-pair-50ul">Tomato leaves SlChr4-NC1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Rice (<em>Oriza sativa</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsChr4-reg9-primer-pair-50ul">Rice seedlings OsChr4-reg9 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsMADS6-primer-pair-50ul">Rice seedlings OsMADS6 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Poplar (<em>Populus trichocarpa, Populus tremula x alba</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrCopia-orth-primer-pair-50ul">Poplar xylem PtrCopia-orth primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9ac-polyclonal-antibody-classic-sample-size-10-ug">H3K9ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrMYBTF1-primer-pair-50ul">Poplar xylem PtrMYBTF1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
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<p style="text-align: justify;"><span>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></span></p>',
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<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig1.png" alt="H3K27me3 Antibody ChIP Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2.png" alt="H3K27me3 Antibody for ChIP" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 1 million cells. The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation. A titration consisting of 0.5, 1, 2 and 5 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control.</small></p>
<p><small><strong>Figure 1A.</strong> Quantitative PCR was performed with primers specific for the promoter of the active GAPDH and EIF4A2 genes, used as negative controls, and for the inactive TSH2B and MYT1 genes, used as positive controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
<p><small><strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K27me1, H3K27me2, H3K27me3, H3K4me3, H3K9me3 and H3K36me3 modifications and the unmodified H3K27 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K27me3 modification.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2a.png" alt="H3K27me3 Antibody ChIP-seq Grade" /></p>
</div>
</div>
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<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2b.png" alt="H3K27me3 Antibody for ChIP-seq" /></p>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2c.png" alt="H3K27me3 Antibody for ChIP-seq assay" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2d.png" alt="H3K27me3 Antibody validated in ChIP-seq" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP was performed on sheared chromatin from 1 million HeLa cells using 1 µg of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2 shows the enrichment in genomic regions of chromosome 6 and 20, surrounding the TSH2B and MYT1 positive control genes (fig 2A and 2B, respectively), and in two genomic regions of chromosome 1 and X (figure 2C and D).</small></p>
</div>
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<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3A.png" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3B.png" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27me3 (cat. No. C15410195) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions on chromosome and 13 and 20 (figure 3A and B, respectively).</small></p>
</div>
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<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-ELISA-Fig4.png" alt="H3K27me3 Antibody ELISA Validation " /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K27me3 (Cat. No. C15410195). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:3,000.</small></p>
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</div>
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<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-DB-Fig5a.png" alt="H3K27me3 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) with peptides containing other modifications of histone H3 and H4 and the unmodified H3K27 sequence. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:5,000. Figure 5 shows a high specificity of the antibody for the modification of interest. Please note that the antibody also recognizes the modification if S28 is phosphorylated.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-WB-Fig6.png" alt="H3K27me3 Antibody validated in Western Blot" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27me3</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27me3 (cat. No. C15410195) diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-IF-Fig7.png" alt="H3K27me3 Antibody validated for Immunofluorescence" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27me3</strong><br />Human HeLa cells were stained with the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K27me3 antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.</small></p>
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'description' => '<p style="text-align: justify;">The <strong>Auto Universal Plant ChIP-seq</strong> kit offers the convenience of extracting plant chromatin from a wide variety of plants including Arabidopsis, maize, rice, tomato and poplar and has been validated for the <strong>IP-Star® automated system</strong>. This complete kit has been specifically optimized for <strong>plant chromatin extraction</strong> and includes reagents for chromatin preparation, immunoprecipitation, plant-specific control primer pairs, control antibody, and DNA purification.</p>',
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<li><strong>Universal compatiblity</strong> with a wide variety of plant species</li>
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<li>Validated for the high throughput <strong>IP-Star® Automated System</strong></li>
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<h3>Successful ChIP-seq experiments for a variety of plants</h3>
<div class="row">
<div class="small-6 columns"><center>Arabidopsis</center><center><img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A.png" /></center>
<p><small><strong>Figure 1.</strong> ChIP-seq was performed on Arabidopsis thaliana (Col-0) seedlings using our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng (green), 500 pg (orange) and 100 pg (red) IP'd DNA and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a public dataset (NCBI GEO Dataset GSM1193621) that we used as an external reference. Enrichments along a wide region of chromosome 5 are uniform regardless of the starting material amount for the preparation of the library.</small></p>
</div>
<div class="small-6 columns"><center>Poplar</center><center><img src="https://www.diagenode.com/img/landing-pages/poplar.jpg" /></center>
<p><small><strong>Figure 3.</strong> ChIP-seq was performed on Populus trichocarpa stem differenciating xylem using the Premium H3K4me3 ChIP-seq grade antibody. Libraries were prepared with the <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the input and is considered as the background enrichment. The profile in red represents enrichments along a wide region of scaffold 18. Using the same scale, the peaks of the immunoprecipitated samples are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><center>Tomato</center><center><img src="https://www.diagenode.com/img/landing-pages/tomtato.jpg" /></center>
<p><small><strong>Figure 2.</strong> ChIP-seq was performed on Solanum lycopersicum cv. Micro-Tom young leaves using our Premium H3K4me3 ChIP-seq grade antibody. Librairies were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Librairy Preparation™ kit</a> from 750 pg of immunoprecipitated DNA using the Universal Plant ChIP-seq kit (red) and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a dataset obtained from Nguyen et al. 2014 that we used as an external reference. Enrichments are higher and consistent with the reference data along a wide region of chromosome 1.</small></p>
</div>
<div class="small-6 columns"><center>Maize</center><center><img src="https://www.diagenode.com/img/landing-pages/maize.jpg" /></center>
<p><small><strong>Figure 4.</strong> ChIP-seq was performed on Zea mays cv. B73 inner stem using our Premium H3K27me3 ChIP-seq grade antibody. Librairies were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Librairy Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the Input and is considered as the background enrichment. The enrichment in red represents enrichments along a wide region of chromosome 3. Using the same scale, the peaks of the immunoprecipitated sample are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<table style="width: 856px;">
<tbody>
<tr>
<td style="width: 224px;">
<h4><strong>Plant Species</strong></h4>
</td>
<td style="width: 341px;">
<h4><strong>Validated antibodies</strong></h4>
</td>
<td style="width: 357px;">
<h4><strong>Validated primer pairs</strong></h4>
</td>
</tr>
<tr>
<td style="width: 224px;"><strong>Arabidopsis (<em>Arabidopsis thaliana</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-actin-atg-primer-pair-50-ul">Arabidopsis Actin ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-monoclonal-antibody-classic-50-ug-50-ul">H3K4me3 monoclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-atg-primer-pair-50-ul">Arabidopsis FLC-ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-intron1-primer-pair-50-ul">Arabidopsis FLC-intron1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me3-polyclonal-antibody-classic-sample-size-10-ug">H3K9me3 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9-14ac-polyclonal-antibody-classic-sample-size-10-mg">H3K9/14ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27ac-polyclonal-antibody-premium-sample-size-10-ug">H3K27ac polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Maize (<em>Zea mays</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/maize-B73-inner-stem-ZmB1-UTR-primer-pair-50ul">Maize B73 inner stem ZmB1-UTR primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/Maize-B73-inner-stem-ZmCopia-primer-pair-50ul">Maize B73 inner stem ZmCopia primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Tomato (<em>Solanum lycopersicum</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr2-reg8-primer-pair-50ul">Tomato leaves SlChr2-reg8 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr4-NC1-primer-pair-50ul">Tomato leaves SlChr4-NC1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Rice (<em>Oriza sativa</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsChr4-reg9-primer-pair-50ul">Rice seedlings OsChr4-reg9 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsMADS6-primer-pair-50ul">Rice seedlings OsMADS6 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Poplar (<em>Populus trichocarpa, Populus tremula x alba</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrCopia-orth-primer-pair-50ul">Poplar xylem PtrCopia-orth primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9ac-polyclonal-antibody-classic-sample-size-10-ug">H3K9ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrMYBTF1-primer-pair-50ul">Poplar xylem PtrMYBTF1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
</tbody>
</table>',
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'description' => '<p><a href="https://www.diagenode.com/files/products/kits/ipure_kit_v2_manual.pdf"><img src="https://www.diagenode.com/img/buttons/bt-manual.png" /></a></p>
<p>Diagenode’s<span> </span><b>IPure</b><b><span> </span>kit<span> </span></b>is the only DNA purification kit using magnetic beads, that is specifically optimized for extracting DNA from<span> </span><b>ChIP</b><b>,<span> </span></b><b>MeDIP</b><span> </span>and<span> </span><b>CUT&Tag</b>. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. This simple and straightforward protocol delivers pure DNA ready for any downstream application (e.g. next generation sequencing). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples.</p>
<center>
<h4>High DNA recovery after purification of ChIP samples using IPure technology</h4>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-chromatin-function.png" width="500" /></center>
<p></p>
<p><small>ChIP assays were performed using different amounts of U2OS cells and the H3K9me3 antibody (Cat. No.<span> </span><span>C15410056</span>; 2 g/IP). <span>The purified DNA was eluted in 50 µl of water and quantified with a Nanodrop.</span></small></p>
<p></p>
<p><strong>Benefits of the IPure kit:</strong></p>
<ul>
<li style="text-align: left;">Provides pure DNA for any downstream application (e. g. Next generation sequencing)</li>
<li style="text-align: left;">Non-toxic</li>
<li style="text-align: left;">Fast & easy to use</li>
<li style="text-align: left;">Optimized for DNA purification after ChIP, MeDIP and CUT&Tag</li>
<li style="text-align: left;">Compatible with automation</li>
<li style="text-align: left;">Validated on the IP-Star Compact</li>
</ul>
</center>',
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'info1' => '<h2>IPure after ChIP</h2>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-A.png" alt="ChIP-seq figure A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-B.png" alt="ChIP-seq figure B" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-C.png" alt="ChIP-seq figure C" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><small><strong>Figure 1.</strong> Chromatin Immunoprecipitation has been performed using chromatin from HeLa cells, the iDeal ChIP-seq kit for Transcription Factors (containing the IPure module for DNA purification) and the Diagenode ChIP-seq-grade HDAC1 (A), LSD1 (B) and p53 antibody (C). 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. This figure shows the peak distribution in regions of chromosome 3 (A), chromosome 12 (B) and chromosome 6 (C) respectively.</small></p>
<p></p>
<h2>IPure after CUT&Tag</h2>
<p>Successful CUT&Tag results showing a low background with high region-specific enrichment has been generated using 50.000 of K562 cells, 1 µg of H3K4me3 or H3K27me3 antibody (Diagenode, C15410003 or C15410069, respectively) and proteinA-Tn5 (1:250) (Diagenode, C01070001). 1 µg of IgG (C15410206) was used as negative control. Samples were purified using the IPure kit v2 or phenol-chloroform purification. The below figures present the comparison of two purification methods.</p>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-fig2.png" style="display: block; margin-left: auto; margin-right: auto;" width="400" /></center><center>
<p style="text-align: center;"><small><strong>Figure 2.</strong> Heatmap 3kb upstream and downstream of the TSS for H3K4me3</small></p>
</center>
<p></p>
<p><img src="https://www.diagenode.com/img/product/kits/ipure-fig3.png" style="display: block; margin-left: auto; margin-right: auto;" width="600" /></p>
<p></p>
<center><small><strong>Figure 3.</strong> Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using Diagenode’s pA-Tn5 transposase (Cat. No. C01070002), H3K27me3 antibody (Cat. No. C15410069) and IPure kit v2 vs phenol chloroform purification (PC).</small></center>
<p></p>
<p></p>
<h2>IPure after MeDIP</h2>
<center><img src="https://www.diagenode.com/img/product/kits/magmedip-seq-figure_multi3.jpg" alt="medip sequencing coverage" width="600" /></center><center></center><center>
<p></p>
<small><strong>Figure 4.</strong> Consistent coverage and methylation detection from different starting amounts of DNA with the Diagenode MagMeDIP-seq Package (including the Ipure kit for DNA purification). Samples containing decreasing starting amounts of DNA (from the top down: 1000 ng (red), 250 ng (blue), 100 ng (green)) originating from human blood were prepared, revealing a consistent coverage profile for the three different starting amounts, which enables reproducible methylation detection. The CpG islands (CGIs) (marked by yellow boxes in the bottom track) are predominantly unmethylated in the human genome, and as expected, we see a depletion of reads at and around CGIs.</small></center>
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-ipure-cuttag.png" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<h3><strong>Workflow description</strong></h3>
<h5><strong>IPure after ChIP</strong></h5>
<p><strong>Step 1:</strong> Chromatin is decrosslinked and eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added.<br /> <strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet.<br /> <strong>Step 3:</strong> Proteins and remaining buffer are washed away.<br /> <strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after MeDIP</strong></h5>
<p><strong>Step 1:</strong> DNA is eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Remaining buffer are washed away.<br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after CUT&Tag</strong></h5>
<p><strong>Step 1:</strong> pA-Tn5 is inactivated and DNA released from the cells. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Proteins and remaining buffer are washed away. <br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).</p>
<p></p>
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<div class="large-12 columns">Chromatin Immunoprecipitation (ChIP) coupled with high-throughput massively parallel sequencing as a detection method (ChIP-seq) has become one of the primary methods for epigenomics researchers, namely to investigate protein-DNA interaction on a genome-wide scale. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</div>
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<h5 class="large-12 columns"><strong></strong></h5>
<h5 class="large-12 columns"><strong>The ChIP-seq workflow</strong></h5>
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<li class="large-12 columns"><strong>Chromatin IP</strong>: Capture protein-DNA complexes with <strong><a href="../categories/chip-seq-grade-antibodies">specific ChIP-seq grade antibodies</a></strong> against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: Reverse cross-links, elute, and purify </li>
<li class="large-12 columns"><strong>NGS Library Preparation</strong>: Ligate adapters and amplify IP'd material</li>
<li class="large-12 columns"><strong>Bioinformatic analysis</strong>: Perform r<span style="font-weight: 400;">ead filtering and trimming</span>, r<span style="font-weight: 400;">ead specific alignment, enrichment specific peak calling, QC metrics, multi-sample cross-comparison etc. </span></li>
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<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns"><a href="../pages/which-kit-to-choose"><img alt="" src="https://www.diagenode.com/img/banners/banner-decide.png" /></a></div>
<div class="small-6 medium-6 large-6 columns"><a href="../pages/chip-kit-customizer-1"><img alt="" src="https://www.diagenode.com/img/banners/banner-customizer.png" /></a></div>
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<p class="text-justify">Chromatin Immunoprecipitation (ChIP) coupled with quantitative PCR can be used to investigate protein-DNA interaction at known genomic binding sites. if sites are not known, qPCR primers can also be designed against potential regulatory regions such as promoters. ChIP-qPCR is advantageous in studies that focus on specific genes and potential regulatory regions across differing experimental conditions as the cost of performing real-time PCR is minimal. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</p>
<p class="text-justify"><strong>The ChIP-qPCR workflow</strong></p>
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<div class="small-12 medium-12 large-12 columns text-center"><br /> <img src="https://www.diagenode.com/img/chip-qpcr-diagram.png" /></div>
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<li class="large-12 columns"><strong>Chromatin IP</strong>: protein-DNA complexe capture using<strong> <a href="https://www.diagenode.com/en/categories/chip-grade-antibodies">specific ChIP-grade antibodies</a></strong> against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: chromatin reverse cross-linking and elution followed by purification<strong> </strong></li>
<li class="large-12 columns"><strong>qPCR and analysis</strong>: using previously designed primers to amplify IP'd material at specific loci</li>
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<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns"><a href="https://www.diagenode.com/pages/which-kit-to-choose"><img src="https://www.diagenode.com/img/banners/banner-decide.png" alt="" /></a></div>
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'authors' => 'Ghosh R. et al.',
'description' => '<p>Plants can attenuate their molecular response to repetitive mechanical stimulation as a function of their mechanical history. For instance, a single bending of stem is sufficient to attenuate the gene expression in poplar plants to the subsequent mechanical stimulation, and the state of desensitization can last for several days. The role of histone modifications in memory gene expression and modulating plant response to abiotic or biotic signals is well known. However, such information is still lacking to explain the attenuated expression pattern of mechano-responsive genes in plants under repetitive stimulation. Using poplar as a model plant in this study, we first measured the global level of H3K9/14ac and H3K4me3 marks in the bent stem. The result shows that a single mild bending of the stem for 6 seconds is sufficient to alter the global level of the H3K9/14ac mark in poplar, highlighting the fact that plants are extremely sensitive to mechanical signals. Next, we analyzed the temporal dynamics of these two active histone marks at attenuated (PtaZFP2, PtaXET6, and PtaACA13) and non-attenuated (PtaHRD) mechano-responsive loci during the desensitization and resensitization phases. Enrichment of H3K9/14ac and H3K4me3 in the regulatory region of attenuated genes correlates well with their transient expression pattern after the first bending. Moreover, the levels of H3K4me3 correlate well with their expression pattern after the second bending at desensitization (3 days after the first bending) as well as resensitization (5 days after the first bending) phases. On the other hand, H3K9/14ac status correlates only with their attenuated expression pattern at the desensitization phase. The expression efficiency of the attenuated genes was restored after the second bending in the histone deacetylase inhibitor-treated plants. While both histone modifications contribute to the expression of attenuated genes, mechanostimulated expression of the non-attenuated PtaHRD gene seems to be H3K4me3 dependent.</p>',
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'description' => '<p><span>We demonstrate a new regulatory mechanism in the jasmonic acid (JA) and salicylic acid (SA) mediated crosstalk in potato defense response, wherein, miR160 target StARF16 (a gene involved in growth and development) binds to the promoter of StNPR1 (a defense gene) and negatively regulates its expression to suppress the SA pathway. Overall, our study establishes the importance of StARF16 in regulation of StNPR1 during JA mediated defense response upon necrotrophic pathogen interaction. Plants employ antagonistic crosstalk between salicylic acid (SA) and jasmonic acid (JA) to effectively defend them from pathogens. During biotrophic pathogen attack, SA pathway activates and suppresses the JA pathway via NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1). However, upon necrotrophic pathogen attack, how JA-mediated defense response suppresses the SA pathway, is still not well-understood. Recently StARF10 (AUXIN RESPONSE FACTOR), a miR160 target, has been shown to regulate SA and binds to the promoter of StGH3.6 (GRETCHEN HAGEN3), a gene proposed to maintain the balance between the free SA and auxin in plants. In the current study, we investigated the role of StARF16 (a miR160 target) in the regulation of the defense gene StNPR1 in potato upon activation of the JA pathway. We observed that a negative correlation exists between StNPR1 and StARF16 upon infection with the pathogen. The results were further confirmed through the exogenous application of SA and JA. Using yeast one-hybrid assay, we demonstrated that StARF16 binds to the StNPR1 promoter through putative ARF binding sites. Additionally, through protoplast transfection and chromatin immunoprecipitation experiments, we showed that StARF16 could bind to the StNPR1 promoter and regulate its expression. Co-transfection assays using promoter deletion constructs established that ARF binding sites are present in the 2.6 kb sequence upstream to the StNPR1 gene and play a key role in its regulation during infection. In summary, we demonstrate the importance of StARF16 in the regulation of StNPR1, and thus SA pathway, during JA-mediated defense response upon necrotrophic pathogen interaction.</span></p>',
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(int) 3 => array(
'id' => '4564',
'name' => 'GIF1 controls ear inflorescence architecture and floral development byregulating key genes in hormone biosynthesis and meristem determinacy inmaize.',
'authors' => 'Li Manfei et al. ',
'description' => '<p>BACKGROUND: Inflorescence architecture and floral development in flowering plants are determined by genetic control of meristem identity, determinacy, and maintenance. The ear inflorescence meristem in maize (Zea mays) initiates short branch meristems called spikelet pair meristems, thus unlike the tassel inflorescence, the ears lack long branches. Maize growth-regulating factor (GRF)-interacting factor1 (GIF1) regulates branching and size of meristems in the tassel inflorescence by binding to Unbranched3. However, the regulatory pathway of gif1 in ear meristems is relatively unknown. RESULT: In this study, we found that loss-of-function gif1 mutants had highly branched ears, and these extra branches repeatedly produce more branches and florets with unfused carpels and an indeterminate floral apex. In addition, GIF1 interacted in vivo with nine GRFs, subunits of the SWI/SNF chromatin-remodeling complex, and hormone biosynthesis-related proteins. Furthermore, key meristem-determinacy gene RAMOSA2 (RA2) and CLAVATA signaling-related gene CLV3/ENDOSPERM SURROUNDING REGION (ESR) 4a (CLE4a) were directly bound and regulated by GIF1 in the ear inflorescence. CONCLUSIONS: Our findings suggest that GIF1 working together with GRFs recruits SWI/SNF chromatin-remodeling ATPases to influence DNA accessibility in the regions that contain genes involved in hormone biosynthesis, meristem identity and determinacy, thus driving the fate of axillary meristems and floral organ primordia in the ear-inflorescence of maize.</p>',
'date' => '2022-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35303806',
'doi' => '10.1186/s12870-022-03517-9',
'modified' => '2022-11-24 09:10:14',
'created' => '2022-11-24 08:49:52',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'id' => '4250',
'name' => 'Chromosomal variations of species revealed by FISH with rDNAs andcentromeric histone H3 variant associated DNAs',
'authors' => 'Liu Mao-Sen et al.',
'description' => '<p>Lycoris species have various chromosome numbers and karyotypes, but all have a constant total number of chromosome major arms. In addition to three fundamental types, including metacentric (M-), telocentric (T-), and acrocentric (A-) chromosomes, chromosomes in various morphology and size were also observed in natural populations. Both fusion and fission translocation have been considered as main mechanisms leading to the diverse karyotypes among Lycoris species, which suggests the centromere organization playing a role in such arrangements. We detected several chromosomal structure changes in Lycoris including centric fusion, inversion, gene amplification, and segment deletion by using fluorescence in situ hybridization (FISH) probing with rDNAs. An antibody against centromere specific histone H3 (CENH3) of L. aurea (2n = 14, 8M+6T) was raised and used to obtain CENH3-associated DNA sequences of L. aurea by chromatin immunoprecipitation (ChIP) cloning method. Immunostaining with anti-CENH3 antibody could label the centromeres of M-, T-, and A-type chromosomes. Immunostaining also revealed two centromeres on one T-type chromosome and a centromere on individual mini-chromosome. Among 10,000 ChIP clones, 500 clones which showed abundant in L. aurea genome by dot-blotting analysis were FISH mapped on chromosomes to examine their cytological distribution. Five of these 500 clones could generate intense FISH signals at centromeric region on M-type but not T-type chromosomes. FISH signals of these five clones rarely appeared on A-type chromosomes. The five ChIP clones showed similarity in DNA sequences and could generate similar but not identical distribution patterns of FISH signals on individual chromosomes. Furthermore, the distinct distribution patterns of FISH signals on each chromosome generated by these five ChIP clones allow to identify individual chromosome, which is considered difficult by conventional staining approaches. Our results suggest a different organization of centromeres of the three chromosome types in Lycoris species.</p>',
'date' => '2021-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34591908',
'doi' => '10.1371/journal.pone.0258028',
'modified' => '2022-05-20 09:36:20',
'created' => '2022-05-19 10:41:50',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '4346',
'name' => 'Expression of in the Stem Cell Domain Is Required for ItsFunction in the Control of Floral Meristem Activity in Arabidopsis',
'authors' => 'Kwaśniewska K. et al. ',
'description' => '<p>In the model plant Arabidopsis thaliana, the zinc-finger transcription factor KNUCKLES (KNU) plays an important role in the termination of floral meristem activity, a process that is crucial for preventing the overgrowth of flowers. The KNU gene is activated in floral meristems by the floral organ identity factor AGAMOUS (AG), and it has been shown that both AG and KNU act in floral meristem control by directly repressing the stem cell regulator WUSCHEL (WUS), which leads to a loss of stem cell activity. When we re-examined the expression pattern of KNU in floral meristems, we found that KNU is expressed throughout the center of floral meristems, which includes, but is considerably broader than the WUS expression domain. We therefore hypothesized that KNU may have additional functions in the control of floral meristem activity. To test this, we employed a gene perturbation approach and knocked down KNU activity at different times and in different domains of the floral meristem. In these experiments we found that early expression in the stem cell domain, which is characterized by the expression of the key meristem regulatory gene CLAVATA3 (CLV3), is crucial for the establishment of KNU expression. The results of additional genetic and molecular analyses suggest that KNU represses floral meristem activity to a large extent by acting on CLV3. Thus, KNU might need to suppress the expression of several meristem regulators to terminate floral meristem activity efficiently.</p>',
'date' => '2021-07-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34367223',
'doi' => '10.3389/fpls.2021.704351',
'modified' => '2022-08-03 16:54:07',
'created' => '2022-05-19 10:41:50',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'id' => '4080',
'name' => 'Localization and characterization of Citrus centromeres by combining
half-tetrad analysis and CenH3-associated sequence profiling.',
'authors' => 'Xia, Qiang-Ming and Miao, Lu-Ke and Xie, Kai-Dong and Yin, Zhao-Ping and
Wu, Xiao-Meng and Chen, Chun-Li and Grosser, Jude W and Guo, Wen-Wu',
'description' => 'KEY MESSAGE: The physical locations of citrus centromere are revealed
by combining genetic and immunological assays for the first time and nine
citrus centromere-specific markers for cytogenetics are mined. Centromere
localization is challenging, because highly redundant repetitive sequences
in centromeric regions make sequence assembly difficult. Although several
citrus genomes have been released, the centromeric regions and their
characteristics remain to be elucidated. Here, we mapped citrus centromeres
through half-tetrad analysis (HTA) that included the genotyping of 54
tetraploid hybrids derived from 2n megagametophytes of Nadorcott tangor
with 212 single nucleotide polymorphism (SNP) markers. The sizes of
centromeric regions, which estimated based on the heterozygosity
restitution rate pattern along the chromosomes, ranged from 1.12 to
18.19 Mb. We also profiled the binding sequences with the
centromere-specific histone variant CenH3 by chromatin immunoprecipitation
sequencing (ChIP-seq). Based on the positions of the top ten
CenH3-enriched contigs, the sizes of centromeric regions were estimated to
range from 0.01 to 7.60 Mb and were either adjacent to or included in the
centromeric regions identified by HTA. We used DNA probes from two
repeats selected from the centromeric regions and seven CenH3-binding
centromeric repeats to verify centromeric locations by fluorescence in situ
hybridization (FISH). Centromere localization in citrus will contribute
to the mining of centromeric/pericentromeric markers, thus to facilitate
the rapid identification of mechanisms underlying 2n gamete formation and
serve the polyploidy breeding.',
'date' => '2020-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32897396',
'doi' => '10.1007/s00299-020-02587-z',
'modified' => '2021-02-18 10:21:53',
'created' => '2021-02-18 10:21:53',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'id' => '4052',
'name' => 'StE(z)2, a Polycomb group methyltransferase and deposition of H3K27me3 andH3K4me3 regulate the expression of tuberization genes in potato.',
'authors' => 'Kumar, Amit and Kondhare, Kirtikumar R and Malankar, Nilam N and Banerjee,Anjan K',
'description' => '<p>Polycomb Repressive Complex (PRC) group proteins regulate various developmental processes in plants by repressing the target genes via H3K27 trimethylation, whereas their function is antagonized by Trithorax group proteins-mediated H3K4 trimethylation. Tuberization in potato is widely studied, but the role of histone modifications in this process is unknown. Recently, we showed that overexpression of StMSI1 (a PRC2 member) alters the expression of tuberization genes in potato. As MSI1 lacks histone-modification activity, we hypothesized that this altered expression could be caused by another PRC2 member, StE(z)2 (a potential H3K27 methyltransferase in potato). Here, we demonstrate that short-day photoperiod influences StE(z)2 expression in leaf and stolon. Moreover, StE(z)2 overexpression alters plant architecture and reduces tuber yield, whereas its knockdown enhanced the yield. ChIP-sequencing using short-day induced stolons revealed that several tuberization and phytohormone-related genes, such as StBEL5/11/29, StSWEET11B, StGA2OX1 and StPIN1 carry H3K4me3 or H3K27me3 marks and/or are StE(z)2 targets. Interestingly, we noticed that another important tuberization gene, StSP6A is targeted by StE(z)2 in leaves and had increased deposition of H3K27me3 under non-induced (long-day) conditions compared to SD. Overall, we show that StE(z)2 and deposition of H3K27me3 and/or H3K4me3 marks could regulate the expression of key tuberization genes in potato.</p>',
'date' => '2020-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33048134',
'doi' => '10.1093/jxb/eraa468',
'modified' => '2021-02-19 14:55:34',
'created' => '2021-02-18 10:21:53',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 8 => array(
'id' => '3959',
'name' => 'The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2).',
'authors' => 'Velanis CN, Perera P, Thomson B, de Leau E, Liang SC, Hartwig B, Förderer A, Thornton H, Arede P, Chen J, Webb KM, Gümüs S, De Jaeger G, Page CA, Hancock CN, Spanos C, Rappsilber J, Voigt P, Turck F, Wellmer F, Goodrich J',
'description' => '<p>A large fraction of plant genomes is composed of transposable elements (TE), which provide a potential source of novel genes through "domestication"-the process whereby the proteins encoded by TE diverge in sequence, lose their ability to catalyse transposition and instead acquire novel functions for their hosts. In Arabidopsis, ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) arose by domestication of the nuclease component of Harbinger class TE and acquired a new function as a component of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a histone H3K27me3 methyltransferase involved in regulation of host genes and in some cases TE. It was not clear how ALP1 associated with PRC2, nor what the functional consequence was. Here, we identify ALP2 genetically as a suppressor of Polycomb-group (PcG) mutant phenotypes and show that it arose from the second, DNA binding component of Harbinger transposases. Molecular analysis of PcG compromised backgrounds reveals that ALP genes oppose silencing and H3K27me3 deposition at key PcG target genes. Proteomic analysis reveals that ALP1 and ALP2 are components of a variant PRC2 complex that contains the four core components but lacks plant-specific accessory components such as the H3K27me3 reader LIKE HETEROCHROMATION PROTEIN 1 (LHP1). We show that the N-terminus of ALP2 interacts directly with ALP1, whereas the C-terminus of ALP2 interacts with MULTICOPY SUPPRESSOR OF IRA1 (MSI1), a core component of PRC2. Proteomic analysis reveals that in alp2 mutant backgrounds ALP1 protein no longer associates with PRC2, consistent with a role for ALP2 in recruitment of ALP1. We suggest that the propensity of Harbinger TE to insert in gene-rich regions of the genome, together with the modular two component nature of their transposases, has predisposed them for domestication and incorporation into chromatin modifying complexes.</p>',
'date' => '2020-05-01',
'pmid' => 'http://www.pubmed.gov/32463832',
'doi' => '10.1371/journal.pgen.1008681',
'modified' => '2020-08-12 09:51:53',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'id' => '3880',
'name' => 'REDOX RESPONSIVE TRANSCRIPTION FACTOR1 (RRFT1) is involved in extracellular ATP regulated Arabidopsis thaliana seedling growth.',
'authors' => 'Zhu R, Dong X, Xue Y, Xu J, Zhang A, Feng M, Zhao Q, Xia S, Yin Y, He S, Li Y, Liu T, Kang E, Shang Z',
'description' => '<p>Extracellular ATP (eATP) is an apoplastic signaling molecule that plays essential roles in the growth and development of plants. Arabidopsis seedlings have been reported to respond to eATP, however, the downstream signaling components are still not well understood. Here, we report that an ethylene responsive factor, Redox Responsive Transcription Factor 1 (RRTF1), is involved in eATP-regulated Arabidopsis thaliana seedling growth. Exogenous ATP inhibited green seedling root growth and induced hypocotyl bending of etiolated seedlings. RRTF1 loss-of-function mutant (rrtf1) seedlings showed decreased responses to eATP, while its complementation or overexpression led to recovered or increased eATP responsiveness. RRTF1 was expressed rapidly after eATP stimulation and then migrated into the nuclei of root tip cells. eATP-induced auxin accumulation in root tip or hypocotyl cells was impaired in rrtf1. Chromatin immunoprecipitation (ChIP) and high-throughput sequencing results indicated that eATP induced some genes related to cell growth and development in wild type but not in rrtf1 cells. These results suggest that RRTF1 may be involved in eATP signaling by regulating functional gene expression and cell metabolism in Arabidopsis seedlings.</p>',
'date' => '2020-02-12',
'pmid' => 'http://www.pubmed.gov/32049334',
'doi' => '10.1093/pcp/pcaa014/5734653',
'modified' => '2020-03-20 17:32:29',
'created' => '2020-03-13 13:45:54',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 10 => array(
'id' => '3872',
'name' => 'An inferred fitness consequence map of the rice genome.',
'authors' => 'Joly-Lopez Z, Platts AE, Gulko B, Choi JY, Groen SC, Zhong X, Siepel A, Purugganan MD',
'description' => '<p>The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa). We inferred fitCons scores (ρ) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae. We found ρ to be multimodal, with ~9% of the rice genome falling into classes where more than half of the bases would probably have a fitness consequence if mutated. Around 2% of the rice genome showed evidence of weak negative selection, frequently at candidate regulatory sites, including a novel set of 1,000 potentially active enhancer elements. This fitCons map provides perspective on the evolutionary forces associated with genome diversity, aids in genome annotation and can guide crop breeding programs.</p>',
'date' => '2020-02-02',
'pmid' => 'http://www.pubmed.gov/32042156',
'doi' => '10.1038/s41477-019-0589-3',
'modified' => '2020-03-20 17:43:24',
'created' => '2020-03-13 13:45:54',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 11 => array(
'id' => '3191',
'name' => 'Transcription Factor Interplay between LEAFY and APETALA1/CAULIFLOWER during Floral Initiation',
'authors' => 'Goslin K. et al.',
'description' => '<p>The transcription factors LEAFY (LFY) and APETALA1 (AP1), together with the AP1 paralog CAULIFLOWER (CAL), control the onset of flower development in a partially redundant manner. This redundancy is thought to be mediated, at least in part, through the regulation of a shared set of target genes. However, whether these genes are independently or cooperatively regulated by LFY and AP1/CAL is currently unknown. To better understand the regulatory relationship between LFY and AP1/CAL and to obtain deeper insights into the control of floral initiation, we monitored the activity of LFY in the absence of AP1/CAL function. We found that the regulation of several known LFY target genes is unaffected by AP1/CAL perturbation, while others appear to require AP1/CAL activity. Furthermore, we obtained evidence that LFY and AP1/CAL control the expression of some genes in an antagonistic manner. Notably, these include key regulators of floral initiation such as <i>TERMINAL FLOWER1</i> (<i>TFL1</i>), which had been previously reported to be directly repressed by both LFY and AP1. We show here that <i>TFL1</i> expression is suppressed by AP1 but promoted by LFY. We further demonstrate that LFY has an inhibitory effect on flower formation in the absence of AP1/CAL activity. We propose that LFY and AP1/CAL act as part of an incoherent feed-forward loop, a network motif where two interconnected pathways or transcription factors act in opposite directions on a target gene, to control the establishment of a stable developmental program for the formation of flowers.</p>',
'date' => '2017-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28385730',
'doi' => '',
'modified' => '2017-06-19 10:57:08',
'created' => '2017-06-19 10:57:08',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 12 => array(
'id' => '3358',
'name' => 'Characterization of the Polycomb-Group Mark H3K27me3 in Unicellular Algae',
'authors' => 'Mikulski P. et al.',
'description' => '<p>Polycomb Group (PcG) proteins mediate chromatin repression in plants and animals by catalyzing H3K27 methylation and H2AK118/119 mono-ubiquitination through the activity of the Polycomb repressive complex 2 (PRC2) and PRC1, respectively. PcG proteins were extensively studied in higher plants, but their function and target genes in unicellular branches of the green lineage remain largely unknown. To shed light on PcG function and <i>modus operandi</i> in a broad evolutionary context, we demonstrate phylogenetic relationship of core PRC1 and PRC2 proteins and H3K27me3 biochemical presence in several unicellular algae of different phylogenetic subclades. We focus then on one of the species, the model red alga <i>Cyanidioschizon merolae</i>, and show that H3K27me3 occupies both, genes and repetitive elements, and mediates the strength of repression depending on the differential occupancy over gene bodies. Furthermore, we report that H3K27me3 in <i>C. merolae</i> is enriched in telomeric and subtelomeric regions of the chromosomes and has unique preferential binding toward intein-containing genes involved in protein splicing. Thus, our study gives important insight for Polycomb-mediated repression in lower eukaryotes, uncovering a previously unknown link between H3K27me3 targets and protein splicing.</p>',
'date' => '2017-04-26',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28491069',
'doi' => '',
'modified' => '2018-04-05 13:09:46',
'created' => '2018-04-05 13:09:46',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 13 => array(
'id' => '3099',
'name' => 'Nitric oxide modulates histone acetylation at stress genes by inhibition of histone deacetylases',
'authors' => 'Mengel A. et al.',
'description' => '<p>Histone acetylation, which is an important mechanism to regulate gene expression, is controlled by the opposing action of histone acetyltransferases (HATs) and histone deacetylases (HDACs). In animals, several HDACs are subjected to regulation by nitric oxide (NO), in plants however, it is unknown whether NO affects histone acetylation. We found that treatment with the physiological NO-donor S-nitroso-glutathione (GSNO) increased the abundance of several histone acetylation marks in Arabidopsis, which was strongly diminished in the presence of the NO scavenger 2-4-carboxyphenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO). This increase was likely triggered by NO-dependent inhibition of HDAC activity since GSNO and S-nitroso-N-acetyl-DL-penicillamine (SNAP) significantly and reversibly reduced total HDAC activity in vitro (in nuclear extracts) and in vivo (in protoplasts). Next, genome-wide H3K9/14ac profiles in Arabidopsis seedlings were generated by ChIP-sequencing and changes induced by GSNO, GSNO/cPTIO or trichostatin A (HDAC inhibitor) were quantified thereby identifying genes which display putative NO-regulated histone acetylation. Functional classification of these genes revealed that many of them are involved in the plant defense response and the abiotic stress response. Furthermore, salicylic acid (SA), which is the major plant defense hormone against biotrophic pathogens, inhibited HDAC activity and increased histone acetylation by inducing endogenous NO production. These data suggest, that NO affects histone acetylation by targeting and inhibiting HDAC complexes, resulting in the hyperacetylation of specific genes. This mechanism might operate in the plant stress response by facilitating stress-induced transcription of genes.</p>',
'date' => '2016-12-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27980017',
'doi' => '',
'modified' => '2017-06-20 10:24:53',
'created' => '2017-01-03 14:41:10',
'ProductsPublication' => array(
[maximum depth reached]
)
)
),
'Testimonial' => array(),
'Area' => array(
(int) 0 => array(
'id' => '5',
'parent_id' => null,
'name' => 'Plant',
'description' => '<div class="extra-spaced">
<p><img src="https://www.diagenode.com/img/areas/plant.jpg" /></p>
</div>
<div class="extra-spaced">
<h2>Epigenetic Regulation in Plants</h2>
<p>Plants utilize a number of gene regulation mechanisms to ensure proper development, function, growth, and survival under different environmental conditions. Plants depend on changes in gene expression to respond to environmental stimuli, in which the full repertoire of histone modifications, DNA methylation, and small ncRNAs play an important role in epigenetic regulation.</p>
<p>Studying the epigenetics of model plants such as Arabidopsis thaliana have allowed researchers to understand pathways that maintain chromatin modifications as well as the mapping of modifications such as DNA methylation on a genome-wide scale. Small RNAs have also been implicated in playing a role in the distribution of chromatin modifications, and RNA may also play a role in the complex epigenetic interactions that occur between homologous sequences (Moazed et al, 2009). In the future, by understanding epigenetic control, researchers can uncover the research necessary to improve plant growth, yields, and transformation efficiency especially in the face of climate change and other environmental factors.</p>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-3 large-3 columns">
<p><img src="https://www.diagenode.com/img/areas/chromatin-and-transcription-factors.jpg" /></p>
</div>
<div class="small-12 medium-9 large-9 columns">
<h3 style="font-weight: 100; margin-top: 0;">Chromatin</h3>
<p>Chromatin consists of nucleosomes formed by a complex of histone proteins and DNA, which allows the packaging of DNA into the nucleus. The less condensed euchromatin represents transcriptionally active regions, while heterochromatin is usually inactive (Vaillant and Paszkowski, 2007). Chromatin state is known to be influenced by both DNA methylation and histone modifications which in turn impact gene expression and the structure of chromosomes. In a recent study, the role of chromatin modifications during plant reproduction elucidated 3-dimensional chromosome reorganization mediated by histones and DNA methylation (Dukowic-Schulze et al. 2017). In addition, gibberellins have been shown in increasing the level of histone acetylation, which affects regions of chromatin involved in maize seed germination (Zheng et al. 2017). Another study reports a novel function of a tomato histone deacetylase gene in the regulation of fruit ripening (Guo et al. 2017).</p>
</div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-3 large-3 columns">
<p><img src="https://www.diagenode.com/img/areas/cherry-tomato-common-grape-vine-ripening-fruit-vegetable-cherry-tomatoes.jpg" /></p>
</div>
<div class="small-12 medium-9 large-9 columns">
<p>In addition, multigene families encode transcription factors, with members found throughout the genome or clustered on the same chromosome. Numerous DNA binding proteins that interact with plant promoters have been identified -- some are similar to well-characterized transcription factors in animals or yeast, while others are unique to plants. For example, diverse members of the subfamily X of the plant-specific ethylene response factor (ERF) transcription factors coordinate stress signaling with wound repair activation. Tissue repair is also enhanced through a protein complex of ERF and GRAS TFs (Heyman et. al,.2018). A compilation of known plant transcription factors can be found in the plant transcription factor database at http://plntfdb.bio.uni-potsdam.de/v3.0/.</p>
</div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-3 large-3 columns">
<p><img src="https://www.diagenode.com/img/areas/rna-strand.jpg" /></p>
</div>
<div class="small-12 medium-9 large-9 columns">
<h3 style="font-weight: 100; margin-top: 0;">RNA</h3>
<p>Recent research shows that a number of classes of small RNAs are key epigenetic regulators. In many cases, small RNAs have been implicated in DNA methylation and chromatin modification (Meyer, 2015). In addition, the role of small RNAs has been implicated in plant stress tolerance (Kumar et al., 2017). López-Galiano et al also provided insight into a coordinated function of a miRNA gene and histone modifications in regulating the expression of a WRKY transcription factor in response to stress.</p>
<p>RNA interference (RNAi) is another epigenetic mechanism that leads to small RNA generation, which mediates gene silencing at the post-transcriptional level. RNAi technology has immense potential for plant disease resistance.</p>
</div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-3 large-3 columns">
<p><img src="https://www.diagenode.com/img/areas/dna-methylation.jpg" /></p>
</div>
<div class="small-12 medium-9 large-9 columns">
<h3 style="font-weight: 100; margin-top: 0;">DNA methylation</h3>
<p>Plants, unlike animals, have three sites that can be methylated G, CHG (H can be A, C, T), and CHH (Law and Jacobsen, 2010). DNA methylation has attracted particular interest. In Arabidopsis, one-third of methylated genes occur in transcribed regions, and 5% of genes are methylated in promoter regions, suggesting that many of these are epigenetically regulated. (Zhang et al., 2006).</p>
<p>There are thousands of differentially methylated regions (DMRs) that influence phenotype by influencing gene expression. The analysis of epigenetic recombinant inbred line (epiRIL) plants from Arabidopsis points to the evidence of the influence of DMRs. An epiRIL results from crossing two genetically identical plants with differing DNA methylation levels (with one parent as a homozygous mutant for an essential DNA methylation maintenance gene). The offspring of these plants have similar genomes that vary only in methylation levels. Many traits have been studied using epiRILs -- flowering time, plant height, and response to abiotic stress, some of which have now been mapped to DMRs (Zhang et al. 2018)</p>
<p>Regulation by DNA methylation has been shown to be important in many aspects of plant development and response such as vernalization, hybrid vigor, and self-incompatibility (Itabashi et al. 2017). For example, vernalization treatments have shown reduced DNA methylation and subsequent initiation of flowering (Burn et al., 1993). Stress can also influence DNA methylation in plants as a response to environmental stimuli. (Steward et al., 2002; Song et al., 2012). A high degree of DNA methylation has also suggested the role in the improvement of plant fitness under different environmental conditions (Saéz-Laguna et al., 2014). In addition, methylation can affect normal fruit and hypomethylation predicts homeotic transformation and loss of fruit yield (Ong-Abdullah et al., 2015)</p>
</div>
</div>
<div class="row extra-spaced">
<div class="small-12 medium-3 large-3 columns">
<p><img src="https://www.diagenode.com/img/areas/plant-development.jpg" class="left" style="padding-right: 15px;" /></p>
</div>
<div class="small-12 medium-9 large-9 columns">
<p>DNA demethylation has also been implied in various aspects of plant development including pollen tube formation, embryogenesis, fruit ripening, stomatal development, and nodule formation ( Li et al. 2017). Demethylation of rice genomic DNA caused an altered pattern of gene expression, inducing dwarf plants (Sano et al., 1990).</p>
<p>Epigenetic modifications contribute to the stability and survival of the plants and their ability to adapt in different environmental conditions.</p>
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<h3>References</h3>
<p><small> Burn, J. et al (1993). DNA methylation, vernalization, and the initiation of flowering. Proc. Natl. Acad. Sci. U.S.A. 90, 287–291. doi: 10.1006/scdb.1996.0055 </small></p>
<p><small> Dukowic-Schulze S, Liu C, Chen C (2017) Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2222-0</small></p>
<p><small> Guo J et al (2017) A histone deacetylase gene, SlHDA3, acts as a negative regulator of fruit ripening and carotenoid accumulation. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2211-3</small></p>
<p><small> Heyman J, et.al (2018) Journal of Cell Science Emerging role of the plant ERF transcription factors in coordinating wound defense responses and repair doi: 10.1242/jcs.208215</small></p>
<p><small> Itabashi E, Osabe K, Fujimoto R, Kakizaki T (2017) Epigenetic regulation of agronomical traits in Brassicaceae. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2223-z</small></p>
<p><small> Kumar V et al (2017) Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2210-4</small></p>
<p><small> Law, J. A., and Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220. doi: 10.1038/nrg2719</small></p>
<p><small> Meyer, P. (2015). Epigenetic variation and environmental change. J. Exp. Bot. 66, 3541–3548. doi: 10.1093/jxb/eru502</small></p>
<p><small> Moazed, D. (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature. doi: 10.1038/nature07756</small></p>
<p><small> Ong-Abdullah et al. (2015). Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525, 533–537. doi: 10.1038/nature15365</small></p>
<p><small> Saéz-Laguna et al. (2014). Epigenetic variability in the genetically uniform forest tree species. PLoS One 9:e103145. doi: 10.1371/journal.pone.0103145</small></p>
<p><small> Sano, H. et al. (1990). A single treatment of rice seedlings with 5-azacytidine induces heritable dwarfism and undermethylation of genomic DNA. Mol. Gen. Genet. 220, 441–447. doi: 10.1007/BF00391751</small></p>
<p><small> Song, J et al (2012). Vernalization – A cold-induced epigenetic switch. J. Cell Sci. 125, 3723–3731. doi: 10.1242/jcs.084764</small></p>
<p><small> Steward, N et al. (2002). Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J. Biol. Chem. 277, 37741–37746. doi: 10.1074/jbc.M204050200</small></p>
<p><small> Vaillant, I., and Paszkowski, J. (2007). Role of histone and DNA methylation in gene regulation. Curr. Opin. Plant Biol. 10, 528–533. doi: 10.1016/j.pbi.2007.06.008</small></p>
<p><small> Zhang, et al. (2006). Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189–1201. doi: 10.1016/j.cell.2006.08.003</small></p>
<p><small> Zhang et al. 2018 Understanding the evolutionary potential of epigenetic variation: a comparison of heritable phenotypic variation in epiRILs, RILs, and natural ecotypes of Arabidopsis thaliana. Heredity 121, 257–265 (2018) doi:10.1038/s41437-018-0095-9</small></p>
<p><small> Zheng X et al (2017) Histone acetylation is involved in GA-mediated 45S rDNA decondensation in maize aleurone layers. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2207-z</small></p>
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<p>Diagenode’s<span> </span><b>IPure</b><b><span> </span>kit<span> </span></b>is the only DNA purification kit using magnetic beads, that is specifically optimized for extracting DNA from<span> </span><b>ChIP</b><b>,<span> </span></b><b>MeDIP</b><span> </span>and<span> </span><b>CUT&Tag</b>. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. This simple and straightforward protocol delivers pure DNA ready for any downstream application (e.g. next generation sequencing). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples.</p>
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<h4>High DNA recovery after purification of ChIP samples using IPure technology</h4>
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<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-B.png" alt="ChIP-seq figure B" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-C.png" alt="ChIP-seq figure C" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><small><strong>Figure 1.</strong> Chromatin Immunoprecipitation has been performed using chromatin from HeLa cells, the iDeal ChIP-seq kit for Transcription Factors (containing the IPure module for DNA purification) and the Diagenode ChIP-seq-grade HDAC1 (A), LSD1 (B) and p53 antibody (C). 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. This figure shows the peak distribution in regions of chromosome 3 (A), chromosome 12 (B) and chromosome 6 (C) respectively.</small></p>
<p></p>
<h2>IPure after CUT&Tag</h2>
<p>Successful CUT&Tag results showing a low background with high region-specific enrichment has been generated using 50.000 of K562 cells, 1 µg of H3K4me3 or H3K27me3 antibody (Diagenode, C15410003 or C15410069, respectively) and proteinA-Tn5 (1:250) (Diagenode, C01070001). 1 µg of IgG (C15410206) was used as negative control. Samples were purified using the IPure kit v2 or phenol-chloroform purification. The below figures present the comparison of two purification methods.</p>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-fig2.png" style="display: block; margin-left: auto; margin-right: auto;" width="400" /></center><center>
<p style="text-align: center;"><small><strong>Figure 2.</strong> Heatmap 3kb upstream and downstream of the TSS for H3K4me3</small></p>
</center>
<p></p>
<p><img src="https://www.diagenode.com/img/product/kits/ipure-fig3.png" style="display: block; margin-left: auto; margin-right: auto;" width="600" /></p>
<p></p>
<center><small><strong>Figure 3.</strong> Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using Diagenode’s pA-Tn5 transposase (Cat. No. C01070002), H3K27me3 antibody (Cat. No. C15410069) and IPure kit v2 vs phenol chloroform purification (PC).</small></center>
<p></p>
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<h2>IPure after MeDIP</h2>
<center><img src="https://www.diagenode.com/img/product/kits/magmedip-seq-figure_multi3.jpg" alt="medip sequencing coverage" width="600" /></center><center></center><center>
<p></p>
<small><strong>Figure 4.</strong> Consistent coverage and methylation detection from different starting amounts of DNA with the Diagenode MagMeDIP-seq Package (including the Ipure kit for DNA purification). Samples containing decreasing starting amounts of DNA (from the top down: 1000 ng (red), 250 ng (blue), 100 ng (green)) originating from human blood were prepared, revealing a consistent coverage profile for the three different starting amounts, which enables reproducible methylation detection. The CpG islands (CGIs) (marked by yellow boxes in the bottom track) are predominantly unmethylated in the human genome, and as expected, we see a depletion of reads at and around CGIs.</small></center>
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<p><strong>Step 1:</strong> Chromatin is decrosslinked and eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added.<br /> <strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet.<br /> <strong>Step 3:</strong> Proteins and remaining buffer are washed away.<br /> <strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
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<p><strong>Step 1:</strong> pA-Tn5 is inactivated and DNA released from the cells. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Proteins and remaining buffer are washed away. <br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).</p>
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'meta_keywords' => 'plant epigenetics, plant ChIP, plant ChIP-seq, Arabidopsis, maize, rice, tomato, poplar',
'meta_description' => 'Optimized extraction of plant chromatin from Arabidopsis,maize,rice,tomato,poplar.Complete ChIP kit including plant-specific control primer pairs and antibody',
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<p style="text-align: justify;">The <strong>Universal Plant ChIP-seq kit</strong> offers the convenience of extracting plant chromatin from a wide variety of plants including Arabidopsis, maize, rice, tomato and poplar. This complete kit has been specifically optimized for <strong>plant chromatin extraction</strong> and includes reagents for chromatin preparation, immunoprecipitation, plant-specific control primer pairs, control antibody, and DNA purification.</p>',
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<li><strong>Universal compatiblity</strong> with a wide variety of plant species</li>
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<h3>Successful ChIP-seq experiments for a variety of plants</h3>
<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Arabidopsis</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG1"> <img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A-small.jpg" /> </a></p>
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<p><small><strong>Figure 1.</strong> ChIP-seq was performed on Arabidopsis thaliana (Col-0) seedlings using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng (green), 500 pg (orange) and 100 pg (red) IP'd DNA and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a public dataset (NCBI GEO Dataset GSM1193621) that we used as an external reference. Enrichments along a wide region of chromosome 5 are uniform regardless of the starting material amount for the preparation of the library.</small></p>
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<div class="small-6 columns">
<h4 class="text-center">Poplar</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG2"><img src="https://www.diagenode.com/img/landing-pages/poplar-small.jpg" /> </a></p>
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<p><small><strong>Figure 3.</strong> ChIP-seq was performed on Populus trichocarpa stem differenciating xylem using the <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with the <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the input and is considered as the background enrichment. The profile in red represents enrichments along a wide region of scaffold 18. Using the same scale, the peaks of the immunoprecipitated samples are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
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<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Tomato</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG3"> <img src="https://www.diagenode.com/img/landing-pages/tomtato-small.jpg" /> </a></p>
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<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 2.</strong> ChIP-seq was performed on Solanum lycopersicum cv. Micro-Tom young leaves using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 750 pg of immunoprecipitated DNA using the Universal Plant ChIP-seq kit (red) and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a dataset obtained from Nguyen et al. 2014 that we used as an external reference. Enrichments are higher and consistent with the reference data along a wide region of chromosome 1.</small></p>
</div>
<div class="small-6 columns">
<h4 class="text-center">Maize</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG4"> <img src="https://www.diagenode.com/img/landing-pages/maize-small.jpg" /> </a></p>
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<p><small><strong>Figure 4.</strong> ChIP-seq was performed on Zea mays cv. B73 inner stem using our <a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">Premium H3K27me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the Input and is considered as the background enrichment. The enrichment in red represents enrichments along a wide region of chromosome 3. Using the same scale, the peaks of the immunoprecipitated sample are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
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<p><strong> </strong></p>
<table style="width: 856px;">
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<tr>
<td style="width: 224px;">
<h4><strong>Plant Species</strong></h4>
</td>
<td style="width: 341px;">
<h4><strong>Validated antibodies</strong></h4>
</td>
<td style="width: 357px;">
<h4><strong>Validated primer pairs</strong></h4>
</td>
</tr>
<tr>
<td style="width: 224px;"><strong>Arabidopsis (<em>Arabidopsis thaliana</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-actin-atg-primer-pair-50-ul">Arabidopsis Actin ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-monoclonal-antibody-classic-50-ug-50-ul">H3K4me3 monoclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-atg-primer-pair-50-ul">Arabidopsis FLC-ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-intron1-primer-pair-50-ul">Arabidopsis FLC-intron1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me3-polyclonal-antibody-classic-sample-size-10-ug">H3K9me3 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9-14ac-polyclonal-antibody-classic-sample-size-10-mg">H3K9/14ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27ac-polyclonal-antibody-premium-sample-size-10-ug">H3K27ac polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Maize (<em>Zea mays</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/maize-B73-inner-stem-ZmB1-UTR-primer-pair-50ul">Maize B73 inner stem ZmB1-UTR primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/Maize-B73-inner-stem-ZmCopia-primer-pair-50ul">Maize B73 inner stem ZmCopia primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Tomato (<em>Solanum lycopersicum</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr2-reg8-primer-pair-50ul">Tomato leaves SlChr2-reg8 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr4-NC1-primer-pair-50ul">Tomato leaves SlChr4-NC1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Rice (<em>Oriza sativa</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsChr4-reg9-primer-pair-50ul">Rice seedlings OsChr4-reg9 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsMADS6-primer-pair-50ul">Rice seedlings OsMADS6 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Poplar (<em>Populus trichocarpa, Populus tremula x alba</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrCopia-orth-primer-pair-50ul">Poplar xylem PtrCopia-orth primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9ac-polyclonal-antibody-classic-sample-size-10-ug">H3K9ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrMYBTF1-primer-pair-50ul">Poplar xylem PtrMYBTF1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
</tbody>
</table>
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<p style="text-align: justify;">The <strong>Universal Plant ChIP-seq kit</strong> offers the convenience of extracting plant chromatin from a wide variety of plants including Arabidopsis, maize, rice, tomato and poplar. This complete kit has been specifically optimized for <strong>plant chromatin extraction</strong> and includes reagents for chromatin preparation, immunoprecipitation, plant-specific control primer pairs, control antibody, and DNA purification.</p>',
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<li><strong>Universal compatiblity</strong> with a wide variety of plant species</li>
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<h3>Successful ChIP-seq experiments for a variety of plants</h3>
<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Arabidopsis</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG1"> <img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A-small.jpg" /> </a></p>
<div id="IMG1" class="reveal-modal" data-reveal="" aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A.png" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 1.</strong> ChIP-seq was performed on Arabidopsis thaliana (Col-0) seedlings using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng (green), 500 pg (orange) and 100 pg (red) IP'd DNA and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a public dataset (NCBI GEO Dataset GSM1193621) that we used as an external reference. Enrichments along a wide region of chromosome 5 are uniform regardless of the starting material amount for the preparation of the library.</small></p>
</div>
<div class="small-6 columns">
<h4 class="text-center">Poplar</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG2"><img src="https://www.diagenode.com/img/landing-pages/poplar-small.jpg" /> </a></p>
<div id="IMG2" class="reveal-modal" data-reveal="" aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/poplar.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 3.</strong> ChIP-seq was performed on Populus trichocarpa stem differenciating xylem using the <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with the <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the input and is considered as the background enrichment. The profile in red represents enrichments along a wide region of scaffold 18. Using the same scale, the peaks of the immunoprecipitated samples are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Tomato</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG3"> <img src="https://www.diagenode.com/img/landing-pages/tomtato-small.jpg" /> </a></p>
<div id="IMG3" class="reveal-modal" data-reveal="" aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/tomtato.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 2.</strong> ChIP-seq was performed on Solanum lycopersicum cv. Micro-Tom young leaves using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 750 pg of immunoprecipitated DNA using the Universal Plant ChIP-seq kit (red) and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a dataset obtained from Nguyen et al. 2014 that we used as an external reference. Enrichments are higher and consistent with the reference data along a wide region of chromosome 1.</small></p>
</div>
<div class="small-6 columns">
<h4 class="text-center">Maize</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG4"> <img src="https://www.diagenode.com/img/landing-pages/maize-small.jpg" /> </a></p>
<div id="IMG4" class="reveal-modal" data-reveal="" aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/maize.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 4.</strong> ChIP-seq was performed on Zea mays cv. B73 inner stem using our <a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">Premium H3K27me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the Input and is considered as the background enrichment. The enrichment in red represents enrichments along a wide region of chromosome 3. Using the same scale, the peaks of the immunoprecipitated sample are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<p><strong> </strong></p>
<table style="width: 856px;">
<tbody>
<tr>
<td style="width: 224px;">
<h4><strong>Plant Species</strong></h4>
</td>
<td style="width: 341px;">
<h4><strong>Validated antibodies</strong></h4>
</td>
<td style="width: 357px;">
<h4><strong>Validated primer pairs</strong></h4>
</td>
</tr>
<tr>
<td style="width: 224px;"><strong>Arabidopsis (<em>Arabidopsis thaliana</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-actin-atg-primer-pair-50-ul">Arabidopsis Actin ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-monoclonal-antibody-classic-50-ug-50-ul">H3K4me3 monoclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-atg-primer-pair-50-ul">Arabidopsis FLC-ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-intron1-primer-pair-50-ul">Arabidopsis FLC-intron1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me3-polyclonal-antibody-classic-sample-size-10-ug">H3K9me3 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9-14ac-polyclonal-antibody-classic-sample-size-10-mg">H3K9/14ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27ac-polyclonal-antibody-premium-sample-size-10-ug">H3K27ac polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Maize (<em>Zea mays</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/maize-B73-inner-stem-ZmB1-UTR-primer-pair-50ul">Maize B73 inner stem ZmB1-UTR primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/Maize-B73-inner-stem-ZmCopia-primer-pair-50ul">Maize B73 inner stem ZmCopia primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Tomato (<em>Solanum lycopersicum</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr2-reg8-primer-pair-50ul">Tomato leaves SlChr2-reg8 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr4-NC1-primer-pair-50ul">Tomato leaves SlChr4-NC1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Rice (<em>Oriza sativa</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsChr4-reg9-primer-pair-50ul">Rice seedlings OsChr4-reg9 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsMADS6-primer-pair-50ul">Rice seedlings OsMADS6 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Poplar (<em>Populus trichocarpa, Populus tremula x alba</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrCopia-orth-primer-pair-50ul">Poplar xylem PtrCopia-orth primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9ac-polyclonal-antibody-classic-sample-size-10-ug">H3K9ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrMYBTF1-primer-pair-50ul">Poplar xylem PtrMYBTF1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
</tbody>
</table>
<p><strong></strong></p>
<p><strong></strong></p>',
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<p style="text-align: justify;"><span>Previous name of the kit: Chromatin Shearing Optimization Kit (Universal Plant ChIP-seq kit)<br /></span></p>
<p style="text-align: justify;"><span>The first critical step of a successful ChIP experiment is the best preparation of sheared chromatin. This <strong>Chromatin EasyShear Kit</strong> is designed to be used in conjunction with the <strong>Universal Plant ChIP-seq kit</strong> and contains the right level of <strong>detergent</strong> for extraction of highest quality plant chromatin for ChIP. In addition, the signature</span><span> crosslinking containers of this kit provide a simple and reliable method for fixation. The content of this kit is enough to perform 12 chromatin extractions.<br /></span></p>
<p style="text-align: justify;"><span>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</span></p>
<p style="text-align: justify;"><span>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></span></p>',
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'meta_title' => 'Chromatin Shearing Optimization Kit (Universal Plant ChIP-seq kit) | Diagenode',
'meta_keywords' => 'chromatin shearing, plant epigenetics, plant ChIP, plant ChIP-seq, Arabidopsis, maize, rice, tomato, poplar',
'meta_description' => 'Chromatin Shearing Optimization Kit designed to be used in conjunction with the Universal Plant ChIP-seq kit, providing high quality plant chromatin for ChIP',
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'id' => '2268',
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'name' => 'H3K27me3 Antibody',
'description' => '<p>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 27</strong> (<strong>H3K27me3</strong>), using a KLH-conjugated synthetic peptide.</p>',
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<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig1.png" alt="H3K27me3 Antibody ChIP Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2.png" alt="H3K27me3 Antibody for ChIP" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 1 million cells. The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation. A titration consisting of 0.5, 1, 2 and 5 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control.</small></p>
<p><small><strong>Figure 1A.</strong> Quantitative PCR was performed with primers specific for the promoter of the active GAPDH and EIF4A2 genes, used as negative controls, and for the inactive TSH2B and MYT1 genes, used as positive controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
<p><small><strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K27me1, H3K27me2, H3K27me3, H3K4me3, H3K9me3 and H3K36me3 modifications and the unmodified H3K27 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K27me3 modification.</small></p>
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</div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2a.png" alt="H3K27me3 Antibody ChIP-seq Grade" /></p>
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<div class="extra-spaced"></div>
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<div class="extra-spaced"></div>
<div class="row">
<div class="small-12 columns">
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2b.png" alt="H3K27me3 Antibody for ChIP-seq" /></p>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2c.png" alt="H3K27me3 Antibody for ChIP-seq assay" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2d.png" alt="H3K27me3 Antibody validated in ChIP-seq" /></p>
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</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP was performed on sheared chromatin from 1 million HeLa cells using 1 µg of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2 shows the enrichment in genomic regions of chromosome 6 and 20, surrounding the TSH2B and MYT1 positive control genes (fig 2A and 2B, respectively), and in two genomic regions of chromosome 1 and X (figure 2C and D).</small></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3A.png" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3B.png" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27me3 (cat. No. C15410195) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions on chromosome and 13 and 20 (figure 3A and B, respectively).</small></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-ELISA-Fig4.png" alt="H3K27me3 Antibody ELISA Validation " /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K27me3 (Cat. No. C15410195). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:3,000.</small></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
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<div class="extra-spaced"></div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-DB-Fig5a.png" alt="H3K27me3 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) with peptides containing other modifications of histone H3 and H4 and the unmodified H3K27 sequence. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:5,000. Figure 5 shows a high specificity of the antibody for the modification of interest. Please note that the antibody also recognizes the modification if S28 is phosphorylated.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-WB-Fig6.png" alt="H3K27me3 Antibody validated in Western Blot" /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27me3</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27me3 (cat. No. C15410195) diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-IF-Fig7.png" alt="H3K27me3 Antibody validated for Immunofluorescence" /></p>
</div>
</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27me3</strong><br />Human HeLa cells were stained with the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K27me3 antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.</small></p>
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'meta_description' => 'H3K27me3 (Histone H3 trimethylated at lysine 27) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, CUT&Tag, ELISA, DB, WB and IF. Specificity confirmed by Peptide array assay. Batch-specific data available on the website. Sample size available.',
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'name' => 'Auto Universal Plant ChIP-seq kit',
'description' => '<p style="text-align: justify;">The <strong>Auto Universal Plant ChIP-seq</strong> kit offers the convenience of extracting plant chromatin from a wide variety of plants including Arabidopsis, maize, rice, tomato and poplar and has been validated for the <strong>IP-Star® automated system</strong>. This complete kit has been specifically optimized for <strong>plant chromatin extraction</strong> and includes reagents for chromatin preparation, immunoprecipitation, plant-specific control primer pairs, control antibody, and DNA purification.</p>',
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<ul>
<li><strong>Universal compatiblity</strong> with a wide variety of plant species</li>
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<h3>Successful ChIP-seq experiments for a variety of plants</h3>
<div class="row">
<div class="small-6 columns"><center>Arabidopsis</center><center><img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A.png" /></center>
<p><small><strong>Figure 1.</strong> ChIP-seq was performed on Arabidopsis thaliana (Col-0) seedlings using our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng (green), 500 pg (orange) and 100 pg (red) IP'd DNA and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a public dataset (NCBI GEO Dataset GSM1193621) that we used as an external reference. Enrichments along a wide region of chromosome 5 are uniform regardless of the starting material amount for the preparation of the library.</small></p>
</div>
<div class="small-6 columns"><center>Poplar</center><center><img src="https://www.diagenode.com/img/landing-pages/poplar.jpg" /></center>
<p><small><strong>Figure 3.</strong> ChIP-seq was performed on Populus trichocarpa stem differenciating xylem using the Premium H3K4me3 ChIP-seq grade antibody. Libraries were prepared with the <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the input and is considered as the background enrichment. The profile in red represents enrichments along a wide region of scaffold 18. Using the same scale, the peaks of the immunoprecipitated samples are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns"><center>Tomato</center><center><img src="https://www.diagenode.com/img/landing-pages/tomtato.jpg" /></center>
<p><small><strong>Figure 2.</strong> ChIP-seq was performed on Solanum lycopersicum cv. Micro-Tom young leaves using our Premium H3K4me3 ChIP-seq grade antibody. Librairies were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Librairy Preparation™ kit</a> from 750 pg of immunoprecipitated DNA using the Universal Plant ChIP-seq kit (red) and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a dataset obtained from Nguyen et al. 2014 that we used as an external reference. Enrichments are higher and consistent with the reference data along a wide region of chromosome 1.</small></p>
</div>
<div class="small-6 columns"><center>Maize</center><center><img src="https://www.diagenode.com/img/landing-pages/maize.jpg" /></center>
<p><small><strong>Figure 4.</strong> ChIP-seq was performed on Zea mays cv. B73 inner stem using our Premium H3K27me3 ChIP-seq grade antibody. Librairies were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Librairy Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the Input and is considered as the background enrichment. The enrichment in red represents enrichments along a wide region of chromosome 3. Using the same scale, the peaks of the immunoprecipitated sample are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<table style="width: 856px;">
<tbody>
<tr>
<td style="width: 224px;">
<h4><strong>Plant Species</strong></h4>
</td>
<td style="width: 341px;">
<h4><strong>Validated antibodies</strong></h4>
</td>
<td style="width: 357px;">
<h4><strong>Validated primer pairs</strong></h4>
</td>
</tr>
<tr>
<td style="width: 224px;"><strong>Arabidopsis (<em>Arabidopsis thaliana</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-actin-atg-primer-pair-50-ul">Arabidopsis Actin ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-monoclonal-antibody-classic-50-ug-50-ul">H3K4me3 monoclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-atg-primer-pair-50-ul">Arabidopsis FLC-ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-intron1-primer-pair-50-ul">Arabidopsis FLC-intron1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me3-polyclonal-antibody-classic-sample-size-10-ug">H3K9me3 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9-14ac-polyclonal-antibody-classic-sample-size-10-mg">H3K9/14ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27ac-polyclonal-antibody-premium-sample-size-10-ug">H3K27ac polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Maize (<em>Zea mays</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/maize-B73-inner-stem-ZmB1-UTR-primer-pair-50ul">Maize B73 inner stem ZmB1-UTR primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/Maize-B73-inner-stem-ZmCopia-primer-pair-50ul">Maize B73 inner stem ZmCopia primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Tomato (<em>Solanum lycopersicum</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr2-reg8-primer-pair-50ul">Tomato leaves SlChr2-reg8 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr4-NC1-primer-pair-50ul">Tomato leaves SlChr4-NC1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Rice (<em>Oriza sativa</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsChr4-reg9-primer-pair-50ul">Rice seedlings OsChr4-reg9 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsMADS6-primer-pair-50ul">Rice seedlings OsMADS6 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Poplar (<em>Populus trichocarpa, Populus tremula x alba</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrCopia-orth-primer-pair-50ul">Poplar xylem PtrCopia-orth primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9ac-polyclonal-antibody-classic-sample-size-10-ug">H3K9ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrMYBTF1-primer-pair-50ul">Poplar xylem PtrMYBTF1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
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<p>Diagenode’s<span> </span><b>IPure</b><b><span> </span>kit<span> </span></b>is the only DNA purification kit using magnetic beads, that is specifically optimized for extracting DNA from<span> </span><b>ChIP</b><b>,<span> </span></b><b>MeDIP</b><span> </span>and<span> </span><b>CUT&Tag</b>. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. This simple and straightforward protocol delivers pure DNA ready for any downstream application (e.g. next generation sequencing). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples.</p>
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<h4>High DNA recovery after purification of ChIP samples using IPure technology</h4>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-chromatin-function.png" width="500" /></center>
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<p><small>ChIP assays were performed using different amounts of U2OS cells and the H3K9me3 antibody (Cat. No.<span> </span><span>C15410056</span>; 2 g/IP). <span>The purified DNA was eluted in 50 µl of water and quantified with a Nanodrop.</span></small></p>
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<p><strong>Benefits of the IPure kit:</strong></p>
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<li style="text-align: left;">Provides pure DNA for any downstream application (e. g. Next generation sequencing)</li>
<li style="text-align: left;">Non-toxic</li>
<li style="text-align: left;">Fast & easy to use</li>
<li style="text-align: left;">Optimized for DNA purification after ChIP, MeDIP and CUT&Tag</li>
<li style="text-align: left;">Compatible with automation</li>
<li style="text-align: left;">Validated on the IP-Star Compact</li>
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'info1' => '<h2>IPure after ChIP</h2>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-A.png" alt="ChIP-seq figure A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-B.png" alt="ChIP-seq figure B" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-C.png" alt="ChIP-seq figure C" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><small><strong>Figure 1.</strong> Chromatin Immunoprecipitation has been performed using chromatin from HeLa cells, the iDeal ChIP-seq kit for Transcription Factors (containing the IPure module for DNA purification) and the Diagenode ChIP-seq-grade HDAC1 (A), LSD1 (B) and p53 antibody (C). 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. This figure shows the peak distribution in regions of chromosome 3 (A), chromosome 12 (B) and chromosome 6 (C) respectively.</small></p>
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<h2>IPure after CUT&Tag</h2>
<p>Successful CUT&Tag results showing a low background with high region-specific enrichment has been generated using 50.000 of K562 cells, 1 µg of H3K4me3 or H3K27me3 antibody (Diagenode, C15410003 or C15410069, respectively) and proteinA-Tn5 (1:250) (Diagenode, C01070001). 1 µg of IgG (C15410206) was used as negative control. Samples were purified using the IPure kit v2 or phenol-chloroform purification. The below figures present the comparison of two purification methods.</p>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-fig2.png" style="display: block; margin-left: auto; margin-right: auto;" width="400" /></center><center>
<p style="text-align: center;"><small><strong>Figure 2.</strong> Heatmap 3kb upstream and downstream of the TSS for H3K4me3</small></p>
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<p><img src="https://www.diagenode.com/img/product/kits/ipure-fig3.png" style="display: block; margin-left: auto; margin-right: auto;" width="600" /></p>
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<center><small><strong>Figure 3.</strong> Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using Diagenode’s pA-Tn5 transposase (Cat. No. C01070002), H3K27me3 antibody (Cat. No. C15410069) and IPure kit v2 vs phenol chloroform purification (PC).</small></center>
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<h2>IPure after MeDIP</h2>
<center><img src="https://www.diagenode.com/img/product/kits/magmedip-seq-figure_multi3.jpg" alt="medip sequencing coverage" width="600" /></center><center></center><center>
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<small><strong>Figure 4.</strong> Consistent coverage and methylation detection from different starting amounts of DNA with the Diagenode MagMeDIP-seq Package (including the Ipure kit for DNA purification). Samples containing decreasing starting amounts of DNA (from the top down: 1000 ng (red), 250 ng (blue), 100 ng (green)) originating from human blood were prepared, revealing a consistent coverage profile for the three different starting amounts, which enables reproducible methylation detection. The CpG islands (CGIs) (marked by yellow boxes in the bottom track) are predominantly unmethylated in the human genome, and as expected, we see a depletion of reads at and around CGIs.</small></center>
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<h5><strong>IPure after ChIP</strong></h5>
<p><strong>Step 1:</strong> Chromatin is decrosslinked and eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added.<br /> <strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet.<br /> <strong>Step 3:</strong> Proteins and remaining buffer are washed away.<br /> <strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after MeDIP</strong></h5>
<p><strong>Step 1:</strong> DNA is eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Remaining buffer are washed away.<br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after CUT&Tag</strong></h5>
<p><strong>Step 1:</strong> pA-Tn5 is inactivated and DNA released from the cells. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Proteins and remaining buffer are washed away. <br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).</p>
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<div class="large-12 columns">Chromatin Immunoprecipitation (ChIP) coupled with high-throughput massively parallel sequencing as a detection method (ChIP-seq) has become one of the primary methods for epigenomics researchers, namely to investigate protein-DNA interaction on a genome-wide scale. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</div>
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<h5 class="large-12 columns"><strong></strong></h5>
<h5 class="large-12 columns"><strong>The ChIP-seq workflow</strong></h5>
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<li class="large-12 columns"><strong>Chromatin IP</strong>: Capture protein-DNA complexes with <strong><a href="../categories/chip-seq-grade-antibodies">specific ChIP-seq grade antibodies</a></strong> against the histone or transcription factor of interest</li>
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<li class="large-12 columns"><strong>Bioinformatic analysis</strong>: Perform r<span style="font-weight: 400;">ead filtering and trimming</span>, r<span style="font-weight: 400;">ead specific alignment, enrichment specific peak calling, QC metrics, multi-sample cross-comparison etc. </span></li>
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<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns"><a href="../pages/which-kit-to-choose"><img alt="" src="https://www.diagenode.com/img/banners/banner-decide.png" /></a></div>
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<p class="text-justify">Chromatin Immunoprecipitation (ChIP) coupled with quantitative PCR can be used to investigate protein-DNA interaction at known genomic binding sites. if sites are not known, qPCR primers can also be designed against potential regulatory regions such as promoters. ChIP-qPCR is advantageous in studies that focus on specific genes and potential regulatory regions across differing experimental conditions as the cost of performing real-time PCR is minimal. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</p>
<p class="text-justify"><strong>The ChIP-qPCR workflow</strong></p>
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<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns"><a href="https://www.diagenode.com/pages/which-kit-to-choose"><img src="https://www.diagenode.com/img/banners/banner-decide.png" alt="" /></a></div>
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'modified' => '2017-06-02 10:49:03',
'created' => '2017-05-19 15:13:11',
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[maximum depth reached]
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'Image' => array(
(int) 0 => array(
'id' => '1775',
'name' => 'product/kits/chip-kit-icon.png',
'alt' => 'ChIP kit icon',
'modified' => '2018-04-17 11:52:29',
'created' => '2018-03-15 15:50:34',
'ProductsImage' => array(
[maximum depth reached]
)
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'Protocol' => array(),
'Publication' => array(
(int) 0 => array(
'id' => '4692',
'name' => 'Temporal modification of H3K9/14ac and H3K4me3 histone marksmediates mechano-responsive gene expression during the accommodationprocess in poplar',
'authors' => 'Ghosh R. et al.',
'description' => '<p>Plants can attenuate their molecular response to repetitive mechanical stimulation as a function of their mechanical history. For instance, a single bending of stem is sufficient to attenuate the gene expression in poplar plants to the subsequent mechanical stimulation, and the state of desensitization can last for several days. The role of histone modifications in memory gene expression and modulating plant response to abiotic or biotic signals is well known. However, such information is still lacking to explain the attenuated expression pattern of mechano-responsive genes in plants under repetitive stimulation. Using poplar as a model plant in this study, we first measured the global level of H3K9/14ac and H3K4me3 marks in the bent stem. The result shows that a single mild bending of the stem for 6 seconds is sufficient to alter the global level of the H3K9/14ac mark in poplar, highlighting the fact that plants are extremely sensitive to mechanical signals. Next, we analyzed the temporal dynamics of these two active histone marks at attenuated (PtaZFP2, PtaXET6, and PtaACA13) and non-attenuated (PtaHRD) mechano-responsive loci during the desensitization and resensitization phases. Enrichment of H3K9/14ac and H3K4me3 in the regulatory region of attenuated genes correlates well with their transient expression pattern after the first bending. Moreover, the levels of H3K4me3 correlate well with their expression pattern after the second bending at desensitization (3 days after the first bending) as well as resensitization (5 days after the first bending) phases. On the other hand, H3K9/14ac status correlates only with their attenuated expression pattern at the desensitization phase. The expression efficiency of the attenuated genes was restored after the second bending in the histone deacetylase inhibitor-treated plants. While both histone modifications contribute to the expression of attenuated genes, mechanostimulated expression of the non-attenuated PtaHRD gene seems to be H3K4me3 dependent.</p>',
'date' => '2023-02-01',
'pmid' => 'https://doi.org/10.1101%2F2023.02.12.526104',
'doi' => '10.1101/2023.02.12.526104',
'modified' => '2023-04-14 09:20:38',
'created' => '2023-02-28 12:19:11',
'ProductsPublication' => array(
[maximum depth reached]
)
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(int) 1 => array(
'id' => '4498',
'name' => 'Winter warming post floral initiation delays flowering via bud dormancyactivation and affects yield in a winter annual crop.',
'authors' => 'Lu Xiang et al.',
'description' => '<p>Winter annual life history is conferred by the requirement for vernalization to promote the floral transition and control the timing of flowering. Here we show using winter oilseed rape that flowering time is controlled by inflorescence bud dormancy in addition to vernalization. Winter warming treatments given to plants in the laboratory and field increase flower bud abscisic acid levels and delay flowering in spring. We show that the promotive effect of chilling reproductive tissues on flowering time is associated with the activity of two FLC genes specifically silenced in response to winter temperatures in developing inflorescences, coupled with activation of a BRANCHED1-dependent bud dormancy transcriptional module. We show that adequate winter chilling is required for normal inflorescence development and high yields in addition to the control of flowering time. Because warming during winter flower development is associated with yield losses at the landscape scale, our work suggests that bud dormancy activation may be important for effects of climate change on winter arable crop yields.</p>',
'date' => '2022-09-01',
'pmid' => 'https://doi.org/10.1073%2Fpnas',
'doi' => '10.1073/pnas.2204355119',
'modified' => '2022-11-21 10:28:36',
'created' => '2022-11-15 09:26:20',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'id' => '4218',
'name' => 'AUXIN RESPONSE FACTOR 16 (StARF16) regulates defense gene StNPR1 upon infection with necrotrophic pathogen in potato.',
'authors' => 'Kalsi HS et al.',
'description' => '<p><span>We demonstrate a new regulatory mechanism in the jasmonic acid (JA) and salicylic acid (SA) mediated crosstalk in potato defense response, wherein, miR160 target StARF16 (a gene involved in growth and development) binds to the promoter of StNPR1 (a defense gene) and negatively regulates its expression to suppress the SA pathway. Overall, our study establishes the importance of StARF16 in regulation of StNPR1 during JA mediated defense response upon necrotrophic pathogen interaction. Plants employ antagonistic crosstalk between salicylic acid (SA) and jasmonic acid (JA) to effectively defend them from pathogens. During biotrophic pathogen attack, SA pathway activates and suppresses the JA pathway via NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1). However, upon necrotrophic pathogen attack, how JA-mediated defense response suppresses the SA pathway, is still not well-understood. Recently StARF10 (AUXIN RESPONSE FACTOR), a miR160 target, has been shown to regulate SA and binds to the promoter of StGH3.6 (GRETCHEN HAGEN3), a gene proposed to maintain the balance between the free SA and auxin in plants. In the current study, we investigated the role of StARF16 (a miR160 target) in the regulation of the defense gene StNPR1 in potato upon activation of the JA pathway. We observed that a negative correlation exists between StNPR1 and StARF16 upon infection with the pathogen. The results were further confirmed through the exogenous application of SA and JA. Using yeast one-hybrid assay, we demonstrated that StARF16 binds to the StNPR1 promoter through putative ARF binding sites. Additionally, through protoplast transfection and chromatin immunoprecipitation experiments, we showed that StARF16 could bind to the StNPR1 promoter and regulate its expression. Co-transfection assays using promoter deletion constructs established that ARF binding sites are present in the 2.6 kb sequence upstream to the StNPR1 gene and play a key role in its regulation during infection. In summary, we demonstrate the importance of StARF16 in the regulation of StNPR1, and thus SA pathway, during JA-mediated defense response upon necrotrophic pathogen interaction.</span></p>',
'date' => '2022-04-05',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/35380408/',
'doi' => '10.1007/s11103-022-01261-0',
'modified' => '2022-04-15 13:14:24',
'created' => '2022-04-15 13:13:23',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'id' => '4564',
'name' => 'GIF1 controls ear inflorescence architecture and floral development byregulating key genes in hormone biosynthesis and meristem determinacy inmaize.',
'authors' => 'Li Manfei et al. ',
'description' => '<p>BACKGROUND: Inflorescence architecture and floral development in flowering plants are determined by genetic control of meristem identity, determinacy, and maintenance. The ear inflorescence meristem in maize (Zea mays) initiates short branch meristems called spikelet pair meristems, thus unlike the tassel inflorescence, the ears lack long branches. Maize growth-regulating factor (GRF)-interacting factor1 (GIF1) regulates branching and size of meristems in the tassel inflorescence by binding to Unbranched3. However, the regulatory pathway of gif1 in ear meristems is relatively unknown. RESULT: In this study, we found that loss-of-function gif1 mutants had highly branched ears, and these extra branches repeatedly produce more branches and florets with unfused carpels and an indeterminate floral apex. In addition, GIF1 interacted in vivo with nine GRFs, subunits of the SWI/SNF chromatin-remodeling complex, and hormone biosynthesis-related proteins. Furthermore, key meristem-determinacy gene RAMOSA2 (RA2) and CLAVATA signaling-related gene CLV3/ENDOSPERM SURROUNDING REGION (ESR) 4a (CLE4a) were directly bound and regulated by GIF1 in the ear inflorescence. CONCLUSIONS: Our findings suggest that GIF1 working together with GRFs recruits SWI/SNF chromatin-remodeling ATPases to influence DNA accessibility in the regions that contain genes involved in hormone biosynthesis, meristem identity and determinacy, thus driving the fate of axillary meristems and floral organ primordia in the ear-inflorescence of maize.</p>',
'date' => '2022-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35303806',
'doi' => '10.1186/s12870-022-03517-9',
'modified' => '2022-11-24 09:10:14',
'created' => '2022-11-24 08:49:52',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'id' => '4250',
'name' => 'Chromosomal variations of species revealed by FISH with rDNAs andcentromeric histone H3 variant associated DNAs',
'authors' => 'Liu Mao-Sen et al.',
'description' => '<p>Lycoris species have various chromosome numbers and karyotypes, but all have a constant total number of chromosome major arms. In addition to three fundamental types, including metacentric (M-), telocentric (T-), and acrocentric (A-) chromosomes, chromosomes in various morphology and size were also observed in natural populations. Both fusion and fission translocation have been considered as main mechanisms leading to the diverse karyotypes among Lycoris species, which suggests the centromere organization playing a role in such arrangements. We detected several chromosomal structure changes in Lycoris including centric fusion, inversion, gene amplification, and segment deletion by using fluorescence in situ hybridization (FISH) probing with rDNAs. An antibody against centromere specific histone H3 (CENH3) of L. aurea (2n = 14, 8M+6T) was raised and used to obtain CENH3-associated DNA sequences of L. aurea by chromatin immunoprecipitation (ChIP) cloning method. Immunostaining with anti-CENH3 antibody could label the centromeres of M-, T-, and A-type chromosomes. Immunostaining also revealed two centromeres on one T-type chromosome and a centromere on individual mini-chromosome. Among 10,000 ChIP clones, 500 clones which showed abundant in L. aurea genome by dot-blotting analysis were FISH mapped on chromosomes to examine their cytological distribution. Five of these 500 clones could generate intense FISH signals at centromeric region on M-type but not T-type chromosomes. FISH signals of these five clones rarely appeared on A-type chromosomes. The five ChIP clones showed similarity in DNA sequences and could generate similar but not identical distribution patterns of FISH signals on individual chromosomes. Furthermore, the distinct distribution patterns of FISH signals on each chromosome generated by these five ChIP clones allow to identify individual chromosome, which is considered difficult by conventional staining approaches. Our results suggest a different organization of centromeres of the three chromosome types in Lycoris species.</p>',
'date' => '2021-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34591908',
'doi' => '10.1371/journal.pone.0258028',
'modified' => '2022-05-20 09:36:20',
'created' => '2022-05-19 10:41:50',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '4346',
'name' => 'Expression of in the Stem Cell Domain Is Required for ItsFunction in the Control of Floral Meristem Activity in Arabidopsis',
'authors' => 'Kwaśniewska K. et al. ',
'description' => '<p>In the model plant Arabidopsis thaliana, the zinc-finger transcription factor KNUCKLES (KNU) plays an important role in the termination of floral meristem activity, a process that is crucial for preventing the overgrowth of flowers. The KNU gene is activated in floral meristems by the floral organ identity factor AGAMOUS (AG), and it has been shown that both AG and KNU act in floral meristem control by directly repressing the stem cell regulator WUSCHEL (WUS), which leads to a loss of stem cell activity. When we re-examined the expression pattern of KNU in floral meristems, we found that KNU is expressed throughout the center of floral meristems, which includes, but is considerably broader than the WUS expression domain. We therefore hypothesized that KNU may have additional functions in the control of floral meristem activity. To test this, we employed a gene perturbation approach and knocked down KNU activity at different times and in different domains of the floral meristem. In these experiments we found that early expression in the stem cell domain, which is characterized by the expression of the key meristem regulatory gene CLAVATA3 (CLV3), is crucial for the establishment of KNU expression. The results of additional genetic and molecular analyses suggest that KNU represses floral meristem activity to a large extent by acting on CLV3. Thus, KNU might need to suppress the expression of several meristem regulators to terminate floral meristem activity efficiently.</p>',
'date' => '2021-07-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34367223',
'doi' => '10.3389/fpls.2021.704351',
'modified' => '2022-08-03 16:54:07',
'created' => '2022-05-19 10:41:50',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'id' => '4080',
'name' => 'Localization and characterization of Citrus centromeres by combining
half-tetrad analysis and CenH3-associated sequence profiling.',
'authors' => 'Xia, Qiang-Ming and Miao, Lu-Ke and Xie, Kai-Dong and Yin, Zhao-Ping and
Wu, Xiao-Meng and Chen, Chun-Li and Grosser, Jude W and Guo, Wen-Wu',
'description' => 'KEY MESSAGE: The physical locations of citrus centromere are revealed
by combining genetic and immunological assays for the first time and nine
citrus centromere-specific markers for cytogenetics are mined. Centromere
localization is challenging, because highly redundant repetitive sequences
in centromeric regions make sequence assembly difficult. Although several
citrus genomes have been released, the centromeric regions and their
characteristics remain to be elucidated. Here, we mapped citrus centromeres
through half-tetrad analysis (HTA) that included the genotyping of 54
tetraploid hybrids derived from 2n megagametophytes of Nadorcott tangor
with 212 single nucleotide polymorphism (SNP) markers. The sizes of
centromeric regions, which estimated based on the heterozygosity
restitution rate pattern along the chromosomes, ranged from 1.12 to
18.19 Mb. We also profiled the binding sequences with the
centromere-specific histone variant CenH3 by chromatin immunoprecipitation
sequencing (ChIP-seq). Based on the positions of the top ten
CenH3-enriched contigs, the sizes of centromeric regions were estimated to
range from 0.01 to 7.60 Mb and were either adjacent to or included in the
centromeric regions identified by HTA. We used DNA probes from two
repeats selected from the centromeric regions and seven CenH3-binding
centromeric repeats to verify centromeric locations by fluorescence in situ
hybridization (FISH). Centromere localization in citrus will contribute
to the mining of centromeric/pericentromeric markers, thus to facilitate
the rapid identification of mechanisms underlying 2n gamete formation and
serve the polyploidy breeding.',
'date' => '2020-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32897396',
'doi' => '10.1007/s00299-020-02587-z',
'modified' => '2021-02-18 10:21:53',
'created' => '2021-02-18 10:21:53',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'id' => '4052',
'name' => 'StE(z)2, a Polycomb group methyltransferase and deposition of H3K27me3 andH3K4me3 regulate the expression of tuberization genes in potato.',
'authors' => 'Kumar, Amit and Kondhare, Kirtikumar R and Malankar, Nilam N and Banerjee,Anjan K',
'description' => '<p>Polycomb Repressive Complex (PRC) group proteins regulate various developmental processes in plants by repressing the target genes via H3K27 trimethylation, whereas their function is antagonized by Trithorax group proteins-mediated H3K4 trimethylation. Tuberization in potato is widely studied, but the role of histone modifications in this process is unknown. Recently, we showed that overexpression of StMSI1 (a PRC2 member) alters the expression of tuberization genes in potato. As MSI1 lacks histone-modification activity, we hypothesized that this altered expression could be caused by another PRC2 member, StE(z)2 (a potential H3K27 methyltransferase in potato). Here, we demonstrate that short-day photoperiod influences StE(z)2 expression in leaf and stolon. Moreover, StE(z)2 overexpression alters plant architecture and reduces tuber yield, whereas its knockdown enhanced the yield. ChIP-sequencing using short-day induced stolons revealed that several tuberization and phytohormone-related genes, such as StBEL5/11/29, StSWEET11B, StGA2OX1 and StPIN1 carry H3K4me3 or H3K27me3 marks and/or are StE(z)2 targets. Interestingly, we noticed that another important tuberization gene, StSP6A is targeted by StE(z)2 in leaves and had increased deposition of H3K27me3 under non-induced (long-day) conditions compared to SD. Overall, we show that StE(z)2 and deposition of H3K27me3 and/or H3K4me3 marks could regulate the expression of key tuberization genes in potato.</p>',
'date' => '2020-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33048134',
'doi' => '10.1093/jxb/eraa468',
'modified' => '2021-02-19 14:55:34',
'created' => '2021-02-18 10:21:53',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 8 => array(
'id' => '3959',
'name' => 'The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2).',
'authors' => 'Velanis CN, Perera P, Thomson B, de Leau E, Liang SC, Hartwig B, Förderer A, Thornton H, Arede P, Chen J, Webb KM, Gümüs S, De Jaeger G, Page CA, Hancock CN, Spanos C, Rappsilber J, Voigt P, Turck F, Wellmer F, Goodrich J',
'description' => '<p>A large fraction of plant genomes is composed of transposable elements (TE), which provide a potential source of novel genes through "domestication"-the process whereby the proteins encoded by TE diverge in sequence, lose their ability to catalyse transposition and instead acquire novel functions for their hosts. In Arabidopsis, ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) arose by domestication of the nuclease component of Harbinger class TE and acquired a new function as a component of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a histone H3K27me3 methyltransferase involved in regulation of host genes and in some cases TE. It was not clear how ALP1 associated with PRC2, nor what the functional consequence was. Here, we identify ALP2 genetically as a suppressor of Polycomb-group (PcG) mutant phenotypes and show that it arose from the second, DNA binding component of Harbinger transposases. Molecular analysis of PcG compromised backgrounds reveals that ALP genes oppose silencing and H3K27me3 deposition at key PcG target genes. Proteomic analysis reveals that ALP1 and ALP2 are components of a variant PRC2 complex that contains the four core components but lacks plant-specific accessory components such as the H3K27me3 reader LIKE HETEROCHROMATION PROTEIN 1 (LHP1). We show that the N-terminus of ALP2 interacts directly with ALP1, whereas the C-terminus of ALP2 interacts with MULTICOPY SUPPRESSOR OF IRA1 (MSI1), a core component of PRC2. Proteomic analysis reveals that in alp2 mutant backgrounds ALP1 protein no longer associates with PRC2, consistent with a role for ALP2 in recruitment of ALP1. We suggest that the propensity of Harbinger TE to insert in gene-rich regions of the genome, together with the modular two component nature of their transposases, has predisposed them for domestication and incorporation into chromatin modifying complexes.</p>',
'date' => '2020-05-01',
'pmid' => 'http://www.pubmed.gov/32463832',
'doi' => '10.1371/journal.pgen.1008681',
'modified' => '2020-08-12 09:51:53',
'created' => '2020-08-10 12:12:25',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'id' => '3880',
'name' => 'REDOX RESPONSIVE TRANSCRIPTION FACTOR1 (RRFT1) is involved in extracellular ATP regulated Arabidopsis thaliana seedling growth.',
'authors' => 'Zhu R, Dong X, Xue Y, Xu J, Zhang A, Feng M, Zhao Q, Xia S, Yin Y, He S, Li Y, Liu T, Kang E, Shang Z',
'description' => '<p>Extracellular ATP (eATP) is an apoplastic signaling molecule that plays essential roles in the growth and development of plants. Arabidopsis seedlings have been reported to respond to eATP, however, the downstream signaling components are still not well understood. Here, we report that an ethylene responsive factor, Redox Responsive Transcription Factor 1 (RRTF1), is involved in eATP-regulated Arabidopsis thaliana seedling growth. Exogenous ATP inhibited green seedling root growth and induced hypocotyl bending of etiolated seedlings. RRTF1 loss-of-function mutant (rrtf1) seedlings showed decreased responses to eATP, while its complementation or overexpression led to recovered or increased eATP responsiveness. RRTF1 was expressed rapidly after eATP stimulation and then migrated into the nuclei of root tip cells. eATP-induced auxin accumulation in root tip or hypocotyl cells was impaired in rrtf1. Chromatin immunoprecipitation (ChIP) and high-throughput sequencing results indicated that eATP induced some genes related to cell growth and development in wild type but not in rrtf1 cells. These results suggest that RRTF1 may be involved in eATP signaling by regulating functional gene expression and cell metabolism in Arabidopsis seedlings.</p>',
'date' => '2020-02-12',
'pmid' => 'http://www.pubmed.gov/32049334',
'doi' => '10.1093/pcp/pcaa014/5734653',
'modified' => '2020-03-20 17:32:29',
'created' => '2020-03-13 13:45:54',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 10 => array(
'id' => '3872',
'name' => 'An inferred fitness consequence map of the rice genome.',
'authors' => 'Joly-Lopez Z, Platts AE, Gulko B, Choi JY, Groen SC, Zhong X, Siepel A, Purugganan MD',
'description' => '<p>The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa). We inferred fitCons scores (ρ) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae. We found ρ to be multimodal, with ~9% of the rice genome falling into classes where more than half of the bases would probably have a fitness consequence if mutated. Around 2% of the rice genome showed evidence of weak negative selection, frequently at candidate regulatory sites, including a novel set of 1,000 potentially active enhancer elements. This fitCons map provides perspective on the evolutionary forces associated with genome diversity, aids in genome annotation and can guide crop breeding programs.</p>',
'date' => '2020-02-02',
'pmid' => 'http://www.pubmed.gov/32042156',
'doi' => '10.1038/s41477-019-0589-3',
'modified' => '2020-03-20 17:43:24',
'created' => '2020-03-13 13:45:54',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 11 => array(
'id' => '3191',
'name' => 'Transcription Factor Interplay between LEAFY and APETALA1/CAULIFLOWER during Floral Initiation',
'authors' => 'Goslin K. et al.',
'description' => '<p>The transcription factors LEAFY (LFY) and APETALA1 (AP1), together with the AP1 paralog CAULIFLOWER (CAL), control the onset of flower development in a partially redundant manner. This redundancy is thought to be mediated, at least in part, through the regulation of a shared set of target genes. However, whether these genes are independently or cooperatively regulated by LFY and AP1/CAL is currently unknown. To better understand the regulatory relationship between LFY and AP1/CAL and to obtain deeper insights into the control of floral initiation, we monitored the activity of LFY in the absence of AP1/CAL function. We found that the regulation of several known LFY target genes is unaffected by AP1/CAL perturbation, while others appear to require AP1/CAL activity. Furthermore, we obtained evidence that LFY and AP1/CAL control the expression of some genes in an antagonistic manner. Notably, these include key regulators of floral initiation such as <i>TERMINAL FLOWER1</i> (<i>TFL1</i>), which had been previously reported to be directly repressed by both LFY and AP1. We show here that <i>TFL1</i> expression is suppressed by AP1 but promoted by LFY. We further demonstrate that LFY has an inhibitory effect on flower formation in the absence of AP1/CAL activity. We propose that LFY and AP1/CAL act as part of an incoherent feed-forward loop, a network motif where two interconnected pathways or transcription factors act in opposite directions on a target gene, to control the establishment of a stable developmental program for the formation of flowers.</p>',
'date' => '2017-06-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28385730',
'doi' => '',
'modified' => '2017-06-19 10:57:08',
'created' => '2017-06-19 10:57:08',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 12 => array(
'id' => '3358',
'name' => 'Characterization of the Polycomb-Group Mark H3K27me3 in Unicellular Algae',
'authors' => 'Mikulski P. et al.',
'description' => '<p>Polycomb Group (PcG) proteins mediate chromatin repression in plants and animals by catalyzing H3K27 methylation and H2AK118/119 mono-ubiquitination through the activity of the Polycomb repressive complex 2 (PRC2) and PRC1, respectively. PcG proteins were extensively studied in higher plants, but their function and target genes in unicellular branches of the green lineage remain largely unknown. To shed light on PcG function and <i>modus operandi</i> in a broad evolutionary context, we demonstrate phylogenetic relationship of core PRC1 and PRC2 proteins and H3K27me3 biochemical presence in several unicellular algae of different phylogenetic subclades. We focus then on one of the species, the model red alga <i>Cyanidioschizon merolae</i>, and show that H3K27me3 occupies both, genes and repetitive elements, and mediates the strength of repression depending on the differential occupancy over gene bodies. Furthermore, we report that H3K27me3 in <i>C. merolae</i> is enriched in telomeric and subtelomeric regions of the chromosomes and has unique preferential binding toward intein-containing genes involved in protein splicing. Thus, our study gives important insight for Polycomb-mediated repression in lower eukaryotes, uncovering a previously unknown link between H3K27me3 targets and protein splicing.</p>',
'date' => '2017-04-26',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28491069',
'doi' => '',
'modified' => '2018-04-05 13:09:46',
'created' => '2018-04-05 13:09:46',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 13 => array(
'id' => '3099',
'name' => 'Nitric oxide modulates histone acetylation at stress genes by inhibition of histone deacetylases',
'authors' => 'Mengel A. et al.',
'description' => '<p>Histone acetylation, which is an important mechanism to regulate gene expression, is controlled by the opposing action of histone acetyltransferases (HATs) and histone deacetylases (HDACs). In animals, several HDACs are subjected to regulation by nitric oxide (NO), in plants however, it is unknown whether NO affects histone acetylation. We found that treatment with the physiological NO-donor S-nitroso-glutathione (GSNO) increased the abundance of several histone acetylation marks in Arabidopsis, which was strongly diminished in the presence of the NO scavenger 2-4-carboxyphenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO). This increase was likely triggered by NO-dependent inhibition of HDAC activity since GSNO and S-nitroso-N-acetyl-DL-penicillamine (SNAP) significantly and reversibly reduced total HDAC activity in vitro (in nuclear extracts) and in vivo (in protoplasts). Next, genome-wide H3K9/14ac profiles in Arabidopsis seedlings were generated by ChIP-sequencing and changes induced by GSNO, GSNO/cPTIO or trichostatin A (HDAC inhibitor) were quantified thereby identifying genes which display putative NO-regulated histone acetylation. Functional classification of these genes revealed that many of them are involved in the plant defense response and the abiotic stress response. Furthermore, salicylic acid (SA), which is the major plant defense hormone against biotrophic pathogens, inhibited HDAC activity and increased histone acetylation by inducing endogenous NO production. These data suggest, that NO affects histone acetylation by targeting and inhibiting HDAC complexes, resulting in the hyperacetylation of specific genes. This mechanism might operate in the plant stress response by facilitating stress-induced transcription of genes.</p>',
'date' => '2016-12-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27980017',
'doi' => '',
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<h2>Epigenetic Regulation in Plants</h2>
<p>Plants utilize a number of gene regulation mechanisms to ensure proper development, function, growth, and survival under different environmental conditions. Plants depend on changes in gene expression to respond to environmental stimuli, in which the full repertoire of histone modifications, DNA methylation, and small ncRNAs play an important role in epigenetic regulation.</p>
<p>Studying the epigenetics of model plants such as Arabidopsis thaliana have allowed researchers to understand pathways that maintain chromatin modifications as well as the mapping of modifications such as DNA methylation on a genome-wide scale. Small RNAs have also been implicated in playing a role in the distribution of chromatin modifications, and RNA may also play a role in the complex epigenetic interactions that occur between homologous sequences (Moazed et al, 2009). In the future, by understanding epigenetic control, researchers can uncover the research necessary to improve plant growth, yields, and transformation efficiency especially in the face of climate change and other environmental factors.</p>
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<h3 style="font-weight: 100; margin-top: 0;">Chromatin</h3>
<p>Chromatin consists of nucleosomes formed by a complex of histone proteins and DNA, which allows the packaging of DNA into the nucleus. The less condensed euchromatin represents transcriptionally active regions, while heterochromatin is usually inactive (Vaillant and Paszkowski, 2007). Chromatin state is known to be influenced by both DNA methylation and histone modifications which in turn impact gene expression and the structure of chromosomes. In a recent study, the role of chromatin modifications during plant reproduction elucidated 3-dimensional chromosome reorganization mediated by histones and DNA methylation (Dukowic-Schulze et al. 2017). In addition, gibberellins have been shown in increasing the level of histone acetylation, which affects regions of chromatin involved in maize seed germination (Zheng et al. 2017). Another study reports a novel function of a tomato histone deacetylase gene in the regulation of fruit ripening (Guo et al. 2017).</p>
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<p>In addition, multigene families encode transcription factors, with members found throughout the genome or clustered on the same chromosome. Numerous DNA binding proteins that interact with plant promoters have been identified -- some are similar to well-characterized transcription factors in animals or yeast, while others are unique to plants. For example, diverse members of the subfamily X of the plant-specific ethylene response factor (ERF) transcription factors coordinate stress signaling with wound repair activation. Tissue repair is also enhanced through a protein complex of ERF and GRAS TFs (Heyman et. al,.2018). A compilation of known plant transcription factors can be found in the plant transcription factor database at http://plntfdb.bio.uni-potsdam.de/v3.0/.</p>
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<h3 style="font-weight: 100; margin-top: 0;">RNA</h3>
<p>Recent research shows that a number of classes of small RNAs are key epigenetic regulators. In many cases, small RNAs have been implicated in DNA methylation and chromatin modification (Meyer, 2015). In addition, the role of small RNAs has been implicated in plant stress tolerance (Kumar et al., 2017). López-Galiano et al also provided insight into a coordinated function of a miRNA gene and histone modifications in regulating the expression of a WRKY transcription factor in response to stress.</p>
<p>RNA interference (RNAi) is another epigenetic mechanism that leads to small RNA generation, which mediates gene silencing at the post-transcriptional level. RNAi technology has immense potential for plant disease resistance.</p>
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<h3 style="font-weight: 100; margin-top: 0;">DNA methylation</h3>
<p>Plants, unlike animals, have three sites that can be methylated G, CHG (H can be A, C, T), and CHH (Law and Jacobsen, 2010). DNA methylation has attracted particular interest. In Arabidopsis, one-third of methylated genes occur in transcribed regions, and 5% of genes are methylated in promoter regions, suggesting that many of these are epigenetically regulated. (Zhang et al., 2006).</p>
<p>There are thousands of differentially methylated regions (DMRs) that influence phenotype by influencing gene expression. The analysis of epigenetic recombinant inbred line (epiRIL) plants from Arabidopsis points to the evidence of the influence of DMRs. An epiRIL results from crossing two genetically identical plants with differing DNA methylation levels (with one parent as a homozygous mutant for an essential DNA methylation maintenance gene). The offspring of these plants have similar genomes that vary only in methylation levels. Many traits have been studied using epiRILs -- flowering time, plant height, and response to abiotic stress, some of which have now been mapped to DMRs (Zhang et al. 2018)</p>
<p>Regulation by DNA methylation has been shown to be important in many aspects of plant development and response such as vernalization, hybrid vigor, and self-incompatibility (Itabashi et al. 2017). For example, vernalization treatments have shown reduced DNA methylation and subsequent initiation of flowering (Burn et al., 1993). Stress can also influence DNA methylation in plants as a response to environmental stimuli. (Steward et al., 2002; Song et al., 2012). A high degree of DNA methylation has also suggested the role in the improvement of plant fitness under different environmental conditions (Saéz-Laguna et al., 2014). In addition, methylation can affect normal fruit and hypomethylation predicts homeotic transformation and loss of fruit yield (Ong-Abdullah et al., 2015)</p>
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<p>DNA demethylation has also been implied in various aspects of plant development including pollen tube formation, embryogenesis, fruit ripening, stomatal development, and nodule formation ( Li et al. 2017). Demethylation of rice genomic DNA caused an altered pattern of gene expression, inducing dwarf plants (Sano et al., 1990).</p>
<p>Epigenetic modifications contribute to the stability and survival of the plants and their ability to adapt in different environmental conditions.</p>
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<h3>References</h3>
<p><small> Burn, J. et al (1993). DNA methylation, vernalization, and the initiation of flowering. Proc. Natl. Acad. Sci. U.S.A. 90, 287–291. doi: 10.1006/scdb.1996.0055 </small></p>
<p><small> Dukowic-Schulze S, Liu C, Chen C (2017) Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2222-0</small></p>
<p><small> Guo J et al (2017) A histone deacetylase gene, SlHDA3, acts as a negative regulator of fruit ripening and carotenoid accumulation. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2211-3</small></p>
<p><small> Heyman J, et.al (2018) Journal of Cell Science Emerging role of the plant ERF transcription factors in coordinating wound defense responses and repair doi: 10.1242/jcs.208215</small></p>
<p><small> Itabashi E, Osabe K, Fujimoto R, Kakizaki T (2017) Epigenetic regulation of agronomical traits in Brassicaceae. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2223-z</small></p>
<p><small> Kumar V et al (2017) Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2210-4</small></p>
<p><small> Law, J. A., and Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220. doi: 10.1038/nrg2719</small></p>
<p><small> Meyer, P. (2015). Epigenetic variation and environmental change. J. Exp. Bot. 66, 3541–3548. doi: 10.1093/jxb/eru502</small></p>
<p><small> Moazed, D. (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature. doi: 10.1038/nature07756</small></p>
<p><small> Ong-Abdullah et al. (2015). Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525, 533–537. doi: 10.1038/nature15365</small></p>
<p><small> Saéz-Laguna et al. (2014). Epigenetic variability in the genetically uniform forest tree species. PLoS One 9:e103145. doi: 10.1371/journal.pone.0103145</small></p>
<p><small> Sano, H. et al. (1990). A single treatment of rice seedlings with 5-azacytidine induces heritable dwarfism and undermethylation of genomic DNA. Mol. Gen. Genet. 220, 441–447. doi: 10.1007/BF00391751</small></p>
<p><small> Song, J et al (2012). Vernalization – A cold-induced epigenetic switch. J. Cell Sci. 125, 3723–3731. doi: 10.1242/jcs.084764</small></p>
<p><small> Steward, N et al. (2002). Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J. Biol. Chem. 277, 37741–37746. doi: 10.1074/jbc.M204050200</small></p>
<p><small> Vaillant, I., and Paszkowski, J. (2007). Role of histone and DNA methylation in gene regulation. Curr. Opin. Plant Biol. 10, 528–533. doi: 10.1016/j.pbi.2007.06.008</small></p>
<p><small> Zhang, et al. (2006). Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189–1201. doi: 10.1016/j.cell.2006.08.003</small></p>
<p><small> Zhang et al. 2018 Understanding the evolutionary potential of epigenetic variation: a comparison of heritable phenotypic variation in epiRILs, RILs, and natural ecotypes of Arabidopsis thaliana. Heredity 121, 257–265 (2018) doi:10.1038/s41437-018-0095-9</small></p>
<p><small> Zheng X et al (2017) Histone acetylation is involved in GA-mediated 45S rDNA decondensation in maize aleurone layers. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2207-z</small></p>
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<p>Diagenode’s<span> </span><b>IPure</b><b><span> </span>kit<span> </span></b>is the only DNA purification kit using magnetic beads, that is specifically optimized for extracting DNA from<span> </span><b>ChIP</b><b>,<span> </span></b><b>MeDIP</b><span> </span>and<span> </span><b>CUT&Tag</b>. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. This simple and straightforward protocol delivers pure DNA ready for any downstream application (e.g. next generation sequencing). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples.</p>
<center>
<h4>High DNA recovery after purification of ChIP samples using IPure technology</h4>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-chromatin-function.png" width="500" /></center>
<p></p>
<p><small>ChIP assays were performed using different amounts of U2OS cells and the H3K9me3 antibody (Cat. No.<span> </span><span>C15410056</span>; 2 g/IP). <span>The purified DNA was eluted in 50 µl of water and quantified with a Nanodrop.</span></small></p>
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<p><strong>Benefits of the IPure kit:</strong></p>
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<li style="text-align: left;">Provides pure DNA for any downstream application (e. g. Next generation sequencing)</li>
<li style="text-align: left;">Non-toxic</li>
<li style="text-align: left;">Fast & easy to use</li>
<li style="text-align: left;">Optimized for DNA purification after ChIP, MeDIP and CUT&Tag</li>
<li style="text-align: left;">Compatible with automation</li>
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<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-A.png" alt="ChIP-seq figure A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-B.png" alt="ChIP-seq figure B" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-C.png" alt="ChIP-seq figure C" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><small><strong>Figure 1.</strong> Chromatin Immunoprecipitation has been performed using chromatin from HeLa cells, the iDeal ChIP-seq kit for Transcription Factors (containing the IPure module for DNA purification) and the Diagenode ChIP-seq-grade HDAC1 (A), LSD1 (B) and p53 antibody (C). 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. This figure shows the peak distribution in regions of chromosome 3 (A), chromosome 12 (B) and chromosome 6 (C) respectively.</small></p>
<p></p>
<h2>IPure after CUT&Tag</h2>
<p>Successful CUT&Tag results showing a low background with high region-specific enrichment has been generated using 50.000 of K562 cells, 1 µg of H3K4me3 or H3K27me3 antibody (Diagenode, C15410003 or C15410069, respectively) and proteinA-Tn5 (1:250) (Diagenode, C01070001). 1 µg of IgG (C15410206) was used as negative control. Samples were purified using the IPure kit v2 or phenol-chloroform purification. The below figures present the comparison of two purification methods.</p>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-fig2.png" style="display: block; margin-left: auto; margin-right: auto;" width="400" /></center><center>
<p style="text-align: center;"><small><strong>Figure 2.</strong> Heatmap 3kb upstream and downstream of the TSS for H3K4me3</small></p>
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<p></p>
<p><img src="https://www.diagenode.com/img/product/kits/ipure-fig3.png" style="display: block; margin-left: auto; margin-right: auto;" width="600" /></p>
<p></p>
<center><small><strong>Figure 3.</strong> Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using Diagenode’s pA-Tn5 transposase (Cat. No. C01070002), H3K27me3 antibody (Cat. No. C15410069) and IPure kit v2 vs phenol chloroform purification (PC).</small></center>
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<h2>IPure after MeDIP</h2>
<center><img src="https://www.diagenode.com/img/product/kits/magmedip-seq-figure_multi3.jpg" alt="medip sequencing coverage" width="600" /></center><center></center><center>
<p></p>
<small><strong>Figure 4.</strong> Consistent coverage and methylation detection from different starting amounts of DNA with the Diagenode MagMeDIP-seq Package (including the Ipure kit for DNA purification). Samples containing decreasing starting amounts of DNA (from the top down: 1000 ng (red), 250 ng (blue), 100 ng (green)) originating from human blood were prepared, revealing a consistent coverage profile for the three different starting amounts, which enables reproducible methylation detection. The CpG islands (CGIs) (marked by yellow boxes in the bottom track) are predominantly unmethylated in the human genome, and as expected, we see a depletion of reads at and around CGIs.</small></center>
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<h3><strong>Workflow description</strong></h3>
<h5><strong>IPure after ChIP</strong></h5>
<p><strong>Step 1:</strong> Chromatin is decrosslinked and eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added.<br /> <strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet.<br /> <strong>Step 3:</strong> Proteins and remaining buffer are washed away.<br /> <strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after MeDIP</strong></h5>
<p><strong>Step 1:</strong> DNA is eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Remaining buffer are washed away.<br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after CUT&Tag</strong></h5>
<p><strong>Step 1:</strong> pA-Tn5 is inactivated and DNA released from the cells. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Proteins and remaining buffer are washed away. <br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).</p>
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'meta_keywords' => 'plant epigenetics, plant ChIP, plant ChIP-seq, Arabidopsis, maize, rice, tomato, poplar',
'meta_description' => 'Optimized extraction of plant chromatin from Arabidopsis,maize,rice,tomato,poplar.Complete ChIP kit including plant-specific control primer pairs and antibody',
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<p style="text-align: justify;">The <strong>Universal Plant ChIP-seq kit</strong> offers the convenience of extracting plant chromatin from a wide variety of plants including Arabidopsis, maize, rice, tomato and poplar. This complete kit has been specifically optimized for <strong>plant chromatin extraction</strong> and includes reagents for chromatin preparation, immunoprecipitation, plant-specific control primer pairs, control antibody, and DNA purification.</p>',
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<li><strong>Universal compatiblity</strong> with a wide variety of plant species</li>
<li>Optimized and <strong>complete kit</strong> for start-to-finish plant ChIP</li>
<li>Includes <strong>plant-specific control</strong> primers and control antibody<strong></strong></li>
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<h3>Successful ChIP-seq experiments for a variety of plants</h3>
<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Arabidopsis</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG1"> <img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A-small.jpg" /> </a></p>
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<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A.png" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 1.</strong> ChIP-seq was performed on Arabidopsis thaliana (Col-0) seedlings using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng (green), 500 pg (orange) and 100 pg (red) IP'd DNA and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a public dataset (NCBI GEO Dataset GSM1193621) that we used as an external reference. Enrichments along a wide region of chromosome 5 are uniform regardless of the starting material amount for the preparation of the library.</small></p>
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<div class="small-6 columns">
<h4 class="text-center">Poplar</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG2"><img src="https://www.diagenode.com/img/landing-pages/poplar-small.jpg" /> </a></p>
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<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 3.</strong> ChIP-seq was performed on Populus trichocarpa stem differenciating xylem using the <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with the <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the input and is considered as the background enrichment. The profile in red represents enrichments along a wide region of scaffold 18. Using the same scale, the peaks of the immunoprecipitated samples are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
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<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Tomato</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG3"> <img src="https://www.diagenode.com/img/landing-pages/tomtato-small.jpg" /> </a></p>
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<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/tomtato.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 2.</strong> ChIP-seq was performed on Solanum lycopersicum cv. Micro-Tom young leaves using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 750 pg of immunoprecipitated DNA using the Universal Plant ChIP-seq kit (red) and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a dataset obtained from Nguyen et al. 2014 that we used as an external reference. Enrichments are higher and consistent with the reference data along a wide region of chromosome 1.</small></p>
</div>
<div class="small-6 columns">
<h4 class="text-center">Maize</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG4"> <img src="https://www.diagenode.com/img/landing-pages/maize-small.jpg" /> </a></p>
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<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/maize.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 4.</strong> ChIP-seq was performed on Zea mays cv. B73 inner stem using our <a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">Premium H3K27me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the Input and is considered as the background enrichment. The enrichment in red represents enrichments along a wide region of chromosome 3. Using the same scale, the peaks of the immunoprecipitated sample are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<p><strong> </strong></p>
<table style="width: 856px;">
<tbody>
<tr>
<td style="width: 224px;">
<h4><strong>Plant Species</strong></h4>
</td>
<td style="width: 341px;">
<h4><strong>Validated antibodies</strong></h4>
</td>
<td style="width: 357px;">
<h4><strong>Validated primer pairs</strong></h4>
</td>
</tr>
<tr>
<td style="width: 224px;"><strong>Arabidopsis (<em>Arabidopsis thaliana</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-actin-atg-primer-pair-50-ul">Arabidopsis Actin ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-monoclonal-antibody-classic-50-ug-50-ul">H3K4me3 monoclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-atg-primer-pair-50-ul">Arabidopsis FLC-ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-intron1-primer-pair-50-ul">Arabidopsis FLC-intron1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me3-polyclonal-antibody-classic-sample-size-10-ug">H3K9me3 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9-14ac-polyclonal-antibody-classic-sample-size-10-mg">H3K9/14ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27ac-polyclonal-antibody-premium-sample-size-10-ug">H3K27ac polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Maize (<em>Zea mays</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/maize-B73-inner-stem-ZmB1-UTR-primer-pair-50ul">Maize B73 inner stem ZmB1-UTR primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/Maize-B73-inner-stem-ZmCopia-primer-pair-50ul">Maize B73 inner stem ZmCopia primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Tomato (<em>Solanum lycopersicum</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr2-reg8-primer-pair-50ul">Tomato leaves SlChr2-reg8 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr4-NC1-primer-pair-50ul">Tomato leaves SlChr4-NC1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Rice (<em>Oriza sativa</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsChr4-reg9-primer-pair-50ul">Rice seedlings OsChr4-reg9 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsMADS6-primer-pair-50ul">Rice seedlings OsMADS6 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Poplar (<em>Populus trichocarpa, Populus tremula x alba</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrCopia-orth-primer-pair-50ul">Poplar xylem PtrCopia-orth primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9ac-polyclonal-antibody-classic-sample-size-10-ug">H3K9ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrMYBTF1-primer-pair-50ul">Poplar xylem PtrMYBTF1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
</tbody>
</table>
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<p style="text-align: justify;">The <strong>Universal Plant ChIP-seq kit</strong> offers the convenience of extracting plant chromatin from a wide variety of plants including Arabidopsis, maize, rice, tomato and poplar. This complete kit has been specifically optimized for <strong>plant chromatin extraction</strong> and includes reagents for chromatin preparation, immunoprecipitation, plant-specific control primer pairs, control antibody, and DNA purification.</p>',
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<h3>Successful ChIP-seq experiments for a variety of plants</h3>
<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Arabidopsis</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG1"> <img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A-small.jpg" /> </a></p>
<div id="IMG1" class="reveal-modal" data-reveal="" aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A.png" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 1.</strong> ChIP-seq was performed on Arabidopsis thaliana (Col-0) seedlings using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng (green), 500 pg (orange) and 100 pg (red) IP'd DNA and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a public dataset (NCBI GEO Dataset GSM1193621) that we used as an external reference. Enrichments along a wide region of chromosome 5 are uniform regardless of the starting material amount for the preparation of the library.</small></p>
</div>
<div class="small-6 columns">
<h4 class="text-center">Poplar</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG2"><img src="https://www.diagenode.com/img/landing-pages/poplar-small.jpg" /> </a></p>
<div id="IMG2" class="reveal-modal" data-reveal="" aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/poplar.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 3.</strong> ChIP-seq was performed on Populus trichocarpa stem differenciating xylem using the <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with the <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the input and is considered as the background enrichment. The profile in red represents enrichments along a wide region of scaffold 18. Using the same scale, the peaks of the immunoprecipitated samples are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<div class="row">
<div class="small-6 columns">
<h4 class="text-center">Tomato</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG3"> <img src="https://www.diagenode.com/img/landing-pages/tomtato-small.jpg" /> </a></p>
<div id="IMG3" class="reveal-modal" data-reveal="" aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/tomtato.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 2.</strong> ChIP-seq was performed on Solanum lycopersicum cv. Micro-Tom young leaves using our <a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 750 pg of immunoprecipitated DNA using the Universal Plant ChIP-seq kit (red) and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a dataset obtained from Nguyen et al. 2014 that we used as an external reference. Enrichments are higher and consistent with the reference data along a wide region of chromosome 1.</small></p>
</div>
<div class="small-6 columns">
<h4 class="text-center">Maize</h4>
<p class="text-center"><a href="#" data-reveal-id="IMG4"> <img src="https://www.diagenode.com/img/landing-pages/maize-small.jpg" /> </a></p>
<div id="IMG4" class="reveal-modal" data-reveal="" aria-labelledby="modalTitle" aria-hidden="true" role="dialog">
<p class="text-center"><img src="https://www.diagenode.com/img/landing-pages/maize.jpg" /></p>
<a class="close-reveal-modal" aria-label="Close">×</a></div>
<p><small><strong>Figure 4.</strong> ChIP-seq was performed on Zea mays cv. B73 inner stem using our <a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-50-mg-27-ml">Premium H3K27me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the Input and is considered as the background enrichment. The enrichment in red represents enrichments along a wide region of chromosome 3. Using the same scale, the peaks of the immunoprecipitated sample are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
</div>
</div>
<p><strong> </strong></p>
<table style="width: 856px;">
<tbody>
<tr>
<td style="width: 224px;">
<h4><strong>Plant Species</strong></h4>
</td>
<td style="width: 341px;">
<h4><strong>Validated antibodies</strong></h4>
</td>
<td style="width: 357px;">
<h4><strong>Validated primer pairs</strong></h4>
</td>
</tr>
<tr>
<td style="width: 224px;"><strong>Arabidopsis (<em>Arabidopsis thaliana</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-actin-atg-primer-pair-50-ul">Arabidopsis Actin ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-monoclonal-antibody-classic-50-ug-50-ul">H3K4me3 monoclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-atg-primer-pair-50-ul">Arabidopsis FLC-ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-intron1-primer-pair-50-ul">Arabidopsis FLC-intron1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me3-polyclonal-antibody-classic-sample-size-10-ug">H3K9me3 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9-14ac-polyclonal-antibody-classic-sample-size-10-mg">H3K9/14ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27ac-polyclonal-antibody-premium-sample-size-10-ug">H3K27ac polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Maize (<em>Zea mays</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/maize-B73-inner-stem-ZmB1-UTR-primer-pair-50ul">Maize B73 inner stem ZmB1-UTR primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/Maize-B73-inner-stem-ZmCopia-primer-pair-50ul">Maize B73 inner stem ZmCopia primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Tomato (<em>Solanum lycopersicum</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr2-reg8-primer-pair-50ul">Tomato leaves SlChr2-reg8 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr4-NC1-primer-pair-50ul">Tomato leaves SlChr4-NC1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Rice (<em>Oriza sativa</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsChr4-reg9-primer-pair-50ul">Rice seedlings OsChr4-reg9 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsMADS6-primer-pair-50ul">Rice seedlings OsMADS6 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Poplar (<em>Populus trichocarpa, Populus tremula x alba</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrCopia-orth-primer-pair-50ul">Poplar xylem PtrCopia-orth primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9ac-polyclonal-antibody-classic-sample-size-10-ug">H3K9ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrMYBTF1-primer-pair-50ul">Poplar xylem PtrMYBTF1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
</tbody>
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<p style="text-align: justify;"><span>Previous name of the kit: Chromatin Shearing Optimization Kit (Universal Plant ChIP-seq kit)<br /></span></p>
<p style="text-align: justify;"><span>The first critical step of a successful ChIP experiment is the best preparation of sheared chromatin. This <strong>Chromatin EasyShear Kit</strong> is designed to be used in conjunction with the <strong>Universal Plant ChIP-seq kit</strong> and contains the right level of <strong>detergent</strong> for extraction of highest quality plant chromatin for ChIP. In addition, the signature</span><span> crosslinking containers of this kit provide a simple and reliable method for fixation. The content of this kit is enough to perform 12 chromatin extractions.<br /></span></p>
<p style="text-align: justify;"><span>Check all <a href="https://www.diagenode.com/en/categories/chromatin-shearing">Chromatin EasyShear Kits</a>.</span></p>
<p style="text-align: justify;"><span>Guide for the optimal chromatin preparation using Chromatin EasyShear Kits – <a href="https://www.diagenode.com/en/pages/chromatin-prep-easyshear-kit-guide">Read more</a></span></p>',
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'name' => 'H3K27me3 Antibody',
'description' => '<p>Polyclonal antibody raised in rabbit against the region of histone <strong>H3 containing the trimethylated lysine 27</strong> (<strong>H3K27me3</strong>), using a KLH-conjugated synthetic peptide.</p>',
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<div class="small-6 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig1.png" alt="H3K27me3 Antibody ChIP Grade" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2.png" alt="H3K27me3 Antibody for ChIP" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 1. ChIP results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP assays were performed using human HeLa cells, the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and optimized PCR primer pairs for qPCR. ChIP was performed with the “iDeal ChIP-seq” kit (Cat. No. C01010051), using sheared chromatin from 1 million cells. The chromatin was spiked with a panel of in vitro assembled nucleosomes, each containing a specific lysine methylation. A titration consisting of 0.5, 1, 2 and 5 µg of antibody per ChIP experiment was analyzed. IgG (1 µg/IP) was used as a negative IP control.</small></p>
<p><small><strong>Figure 1A.</strong> Quantitative PCR was performed with primers specific for the promoter of the active GAPDH and EIF4A2 genes, used as negative controls, and for the inactive TSH2B and MYT1 genes, used as positive controls. The graph shows the recovery, expressed as a % of input (the relative amount of immunoprecipitated DNA compared to input DNA after qPCR analysis).</small></p>
<p><small><strong>Figure 1B.</strong> Recovery of the nucleosomes carrying the H3K27me1, H3K27me2, H3K27me3, H3K4me3, H3K9me3 and H3K36me3 modifications and the unmodified H3K27 as determined by qPCR. The figure clearly shows the antibody is very specific in ChIP for the H3K27me3 modification.</small></p>
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<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2a.png" alt="H3K27me3 Antibody ChIP-seq Grade" /></p>
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<div class="row">
<div class="small-12 columns">
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2b.png" alt="H3K27me3 Antibody for ChIP-seq" /></p>
<p>C. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2c.png" alt="H3K27me3 Antibody for ChIP-seq assay" /></p>
<p>D. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-ChIP-Fig2d.png" alt="H3K27me3 Antibody validated in ChIP-seq" /></p>
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</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 2. ChIP-seq results obtained with the Diagenode antibody directed against H3K27me3</strong><br />ChIP was performed on sheared chromatin from 1 million HeLa cells using 1 µg of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) as described above. The IP'd DNA was subsequently analysed on an Illumina HiSeq. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 50 bp tags were aligned to the human genome using the BWA algorithm. Figure 2 shows the enrichment in genomic regions of chromosome 6 and 20, surrounding the TSH2B and MYT1 positive control genes (fig 2A and 2B, respectively), and in two genomic regions of chromosome 1 and X (figure 2C and D).</small></p>
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<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="extra-spaced"></div>
<div class="row">
<div class="small-12 columns">
<p>A. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3A.png" /></p>
<p>B. <img src="https://www.diagenode.com/img/product/antibodies/C15410195-CUTTAG-Fig3B.png" /></p>
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</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 3. Cut&Tag results obtained with the Diagenode antibody directed against H3K27me3</strong><br />CUT&TAG (Kaya-Okur, H.S., Nat Commun 10, 1930, 2019) was performed on 50,000 K562 cells using 1 µg of the Diagenode antibody against H3K27me3 (cat. No. C15410195) and the Diagenode pA-Tn5 transposase (C01070001). The libraries were subsequently analysed on an Illumina NextSeq 500 sequencer (2x75 paired-end reads) according to the manufacturer's instructions. The tags were aligned to the human genome (hg19) using the BWA algorithm. Figure 3 shows the peak distribution in 2 genomic regions on chromosome and 13 and 20 (figure 3A and B, respectively).</small></p>
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<div class="extra-spaced"></div>
<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-ELISA-Fig4.png" alt="H3K27me3 Antibody ELISA Validation " /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 4. Determination of the antibody titer</strong><br />To determine the titer of the antibody, an ELISA was performed using a serial dilution of the Diagenode antibody directed against H3K27me3 (Cat. No. C15410195). The antigen used was a peptide containing the histone modification of interest. By plotting the absorbance against the antibody dilution (Figure 4), the titer of the antibody was estimated to be 1:3,000.</small></p>
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<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-DB-Fig5a.png" alt="H3K27me3 Antibody Dot Blot Validation " /></p>
</div>
<div class="small-6 columns">
<p><small><strong>Figure 5. Cross reactivity tests using the Diagenode antibody directed against H3K27me3</strong><br />A Dot Blot analysis was performed to test the cross reactivity of the Diagenode antibody against H3K27me3 (Cat. No. C15410195) with peptides containing other modifications of histone H3 and H4 and the unmodified H3K27 sequence. One hundred to 0.2 pmol of the peptide containing the respective histone modification were spotted on a membrane. The antibody was used at a dilution of 1:5,000. Figure 5 shows a high specificity of the antibody for the modification of interest. Please note that the antibody also recognizes the modification if S28 is phosphorylated.</small></p>
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<div class="row">
<div class="small-6 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-WB-Fig6.png" alt="H3K27me3 Antibody validated in Western Blot" /></p>
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<div class="small-6 columns">
<p><small><strong>Figure 6. Western blot analysis using the Diagenode antibody directed against H3K27me3</strong><br />Western blot was performed on whole cell (25 µg, lane 1) and histone extracts (15 µg, lane 2) from HeLa cells, and on 1 µg of recombinant histone H2A, H2B, H3 and H4 (lane 3, 4, 5 and 6, respectively) using the Diagenode antibody against H3K27me3 (cat. No. C15410195) diluted 1:500 in TBS-Tween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<div class="row">
<div class="small-12 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15410195-IF-Fig7.png" alt="H3K27me3 Antibody validated for Immunofluorescence" /></p>
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</div>
<div class="row">
<div class="small-12 columns">
<p><small><strong>Figure 7. Immunofluorescence using the Diagenode antibody directed against H3K27me3</strong><br />Human HeLa cells were stained with the Diagenode antibody against H3K27me3 (Cat. No. C15410195) and with DAPI. Cells were fixed with 4% formaldehyde for 10’ and blocked with PBS/TX-100 containing 5% normal goat serum and 1% BSA. The cells were immunofluorescently labelled with the H3K27me3 antibody (left) diluted 1:200 in blocking solution followed by an anti-rabbit antibody conjugated to Alexa488. The middle panel shows staining of the nuclei with DAPI. A merge of the two stainings is shown on the right.</small></p>
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'meta_description' => 'H3K27me3 (Histone H3 trimethylated at lysine 27) Polyclonal Antibody validated in ChIP-seq, ChIP-qPCR, CUT&Tag, ELISA, DB, WB and IF. Specificity confirmed by Peptide array assay. Batch-specific data available on the website. Sample size available.',
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'description' => '<p style="text-align: justify;">The <strong>Auto Universal Plant ChIP-seq</strong> kit offers the convenience of extracting plant chromatin from a wide variety of plants including Arabidopsis, maize, rice, tomato and poplar and has been validated for the <strong>IP-Star® automated system</strong>. This complete kit has been specifically optimized for <strong>plant chromatin extraction</strong> and includes reagents for chromatin preparation, immunoprecipitation, plant-specific control primer pairs, control antibody, and DNA purification.</p>',
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<ul>
<li><strong>Universal compatiblity</strong> with a wide variety of plant species</li>
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<h3>Successful ChIP-seq experiments for a variety of plants</h3>
<div class="row">
<div class="small-6 columns"><center>Arabidopsis</center><center><img src="https://www.diagenode.com/img/landing-pages/Plant-ChIP-figure-3-A.png" /></center>
<p><small><strong>Figure 1.</strong> ChIP-seq was performed on Arabidopsis thaliana (Col-0) seedlings using our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">Premium H3K4me3 ChIP-seq grade antibody</a>. Libraries were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng (green), 500 pg (orange) and 100 pg (red) IP'd DNA and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a public dataset (NCBI GEO Dataset GSM1193621) that we used as an external reference. Enrichments along a wide region of chromosome 5 are uniform regardless of the starting material amount for the preparation of the library.</small></p>
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<div class="small-6 columns"><center>Poplar</center><center><img src="https://www.diagenode.com/img/landing-pages/poplar.jpg" /></center>
<p><small><strong>Figure 3.</strong> ChIP-seq was performed on Populus trichocarpa stem differenciating xylem using the Premium H3K4me3 ChIP-seq grade antibody. Libraries were prepared with the <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Library Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the input and is considered as the background enrichment. The profile in red represents enrichments along a wide region of scaffold 18. Using the same scale, the peaks of the immunoprecipitated samples are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
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</div>
<div class="row">
<div class="small-6 columns"><center>Tomato</center><center><img src="https://www.diagenode.com/img/landing-pages/tomtato.jpg" /></center>
<p><small><strong>Figure 2.</strong> ChIP-seq was performed on Solanum lycopersicum cv. Micro-Tom young leaves using our Premium H3K4me3 ChIP-seq grade antibody. Librairies were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Librairy Preparation™ kit</a> from 750 pg of immunoprecipitated DNA using the Universal Plant ChIP-seq kit (red) and sequenced on an Illumina® HiSeq 2500. The enrichment in blue represents a dataset obtained from Nguyen et al. 2014 that we used as an external reference. Enrichments are higher and consistent with the reference data along a wide region of chromosome 1.</small></p>
</div>
<div class="small-6 columns"><center>Maize</center><center><img src="https://www.diagenode.com/img/landing-pages/maize.jpg" /></center>
<p><small><strong>Figure 4.</strong> ChIP-seq was performed on Zea mays cv. B73 inner stem using our Premium H3K27me3 ChIP-seq grade antibody. Librairies were prepared with our <a href="https://www.diagenode.com/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns">MicroPlex Librairy Preparation™ kit</a> from 1 ng of immunoprecipitated DNA using the Universal Plant ChIP-seq kit and 1 ng of Input and sequenced on an Illumina® HiSeq 2500. The enrichment in green represents the Input and is considered as the background enrichment. The enrichment in red represents enrichments along a wide region of chromosome 3. Using the same scale, the peaks of the immunoprecipitated sample are significantly higher than those of the input, indicating a successful ChIP-seq experiment.</small></p>
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<tbody>
<tr>
<td style="width: 224px;">
<h4><strong>Plant Species</strong></h4>
</td>
<td style="width: 341px;">
<h4><strong>Validated antibodies</strong></h4>
</td>
<td style="width: 357px;">
<h4><strong>Validated primer pairs</strong></h4>
</td>
</tr>
<tr>
<td style="width: 224px;"><strong>Arabidopsis (<em>Arabidopsis thaliana</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-actin-atg-primer-pair-50-ul">Arabidopsis Actin ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-monoclonal-antibody-classic-50-ug-50-ul">H3K4me3 monoclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-atg-primer-pair-50-ul">Arabidopsis FLC-ATG primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/arabidopsis-flc-intron1-primer-pair-50-ul">Arabidopsis FLC-intron1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me3-polyclonal-antibody-classic-sample-size-10-ug">H3K9me3 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9-14ac-polyclonal-antibody-classic-sample-size-10-mg">H3K9/14ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27ac-polyclonal-antibody-premium-sample-size-10-ug">H3K27ac polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Maize (<em>Zea mays</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/maize-B73-inner-stem-ZmB1-UTR-primer-pair-50ul">Maize B73 inner stem ZmB1-UTR primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/Maize-B73-inner-stem-ZmCopia-primer-pair-50ul">Maize B73 inner stem ZmCopia primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Tomato (<em>Solanum lycopersicum</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr2-reg8-primer-pair-50ul">Tomato leaves SlChr2-reg8 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/tomato-leaves-SlChr4-NC1-primer-pair-50ul">Tomato leaves SlChr4-NC1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Rice (<em>Oriza sativa</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsChr4-reg9-primer-pair-50ul">Rice seedlings OsChr4-reg9 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9me2-polyclonal-antibody-classic-50-ug-44-ul">H3K9me2 polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/rice-seedlings-OsMADS6-primer-pair-50ul">Rice seedlings OsMADS6 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k36me3-polyclonal-antibody-premium-sample-size-10-ug">H3K36me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"><strong>Poplar (<em>Populus trichocarpa, Populus tremula x alba</em>)</strong></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k4me3-polyclonal-antibody-premium-sample-size-10-ug">H3K4me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrCopia-orth-primer-pair-50ul">Poplar xylem PtrCopia-orth primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k9ac-polyclonal-antibody-classic-sample-size-10-ug">H3K9ac polyclonal antibody - Classic</a></td>
<td style="width: 357px;"><a href="https://www.diagenode.com/p/poplar-xylem-PtrMYBTF1-primer-pair-50ul">Poplar xylem PtrMYBTF1 primer pair</a></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3pan-monoclonal-antibody-classic-50-mg-100-ml">H3pan monoclonal antibody - Classic</a></td>
<td style="width: 357px;"></td>
</tr>
<tr>
<td style="width: 224px;"></td>
<td style="width: 341px;"><a href="https://www.diagenode.com/p/h3k27me3-polyclonal-antibody-premium-sample-size-10-ug">H3K27me3 polyclonal antibody - Premium</a></td>
<td style="width: 357px;"></td>
</tr>
</tbody>
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'meta_title' => 'Auto Universal Plant ChIP-seq kit | Diagenode',
'meta_keywords' => 'plant epigenetics, plant ChIP, plant ChIP-seq, Arabidopsis, maize, rice, tomato, poplar, automated system, automation, IP-Star',
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<p>Diagenode’s<span> </span><b>IPure</b><b><span> </span>kit<span> </span></b>is the only DNA purification kit using magnetic beads, that is specifically optimized for extracting DNA from<span> </span><b>ChIP</b><b>,<span> </span></b><b>MeDIP</b><span> </span>and<span> </span><b>CUT&Tag</b>. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. This simple and straightforward protocol delivers pure DNA ready for any downstream application (e.g. next generation sequencing). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples.</p>
<center>
<h4>High DNA recovery after purification of ChIP samples using IPure technology</h4>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-chromatin-function.png" width="500" /></center>
<p></p>
<p><small>ChIP assays were performed using different amounts of U2OS cells and the H3K9me3 antibody (Cat. No.<span> </span><span>C15410056</span>; 2 g/IP). <span>The purified DNA was eluted in 50 µl of water and quantified with a Nanodrop.</span></small></p>
<p></p>
<p><strong>Benefits of the IPure kit:</strong></p>
<ul>
<li style="text-align: left;">Provides pure DNA for any downstream application (e. g. Next generation sequencing)</li>
<li style="text-align: left;">Non-toxic</li>
<li style="text-align: left;">Fast & easy to use</li>
<li style="text-align: left;">Optimized for DNA purification after ChIP, MeDIP and CUT&Tag</li>
<li style="text-align: left;">Compatible with automation</li>
<li style="text-align: left;">Validated on the IP-Star Compact</li>
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'info1' => '<h2>IPure after ChIP</h2>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-A.png" alt="ChIP-seq figure A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-B.png" alt="ChIP-seq figure B" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-C.png" alt="ChIP-seq figure C" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><small><strong>Figure 1.</strong> Chromatin Immunoprecipitation has been performed using chromatin from HeLa cells, the iDeal ChIP-seq kit for Transcription Factors (containing the IPure module for DNA purification) and the Diagenode ChIP-seq-grade HDAC1 (A), LSD1 (B) and p53 antibody (C). 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. This figure shows the peak distribution in regions of chromosome 3 (A), chromosome 12 (B) and chromosome 6 (C) respectively.</small></p>
<p></p>
<h2>IPure after CUT&Tag</h2>
<p>Successful CUT&Tag results showing a low background with high region-specific enrichment has been generated using 50.000 of K562 cells, 1 µg of H3K4me3 or H3K27me3 antibody (Diagenode, C15410003 or C15410069, respectively) and proteinA-Tn5 (1:250) (Diagenode, C01070001). 1 µg of IgG (C15410206) was used as negative control. Samples were purified using the IPure kit v2 or phenol-chloroform purification. The below figures present the comparison of two purification methods.</p>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-fig2.png" style="display: block; margin-left: auto; margin-right: auto;" width="400" /></center><center>
<p style="text-align: center;"><small><strong>Figure 2.</strong> Heatmap 3kb upstream and downstream of the TSS for H3K4me3</small></p>
</center>
<p></p>
<p><img src="https://www.diagenode.com/img/product/kits/ipure-fig3.png" style="display: block; margin-left: auto; margin-right: auto;" width="600" /></p>
<p></p>
<center><small><strong>Figure 3.</strong> Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using Diagenode’s pA-Tn5 transposase (Cat. No. C01070002), H3K27me3 antibody (Cat. No. C15410069) and IPure kit v2 vs phenol chloroform purification (PC).</small></center>
<p></p>
<p></p>
<h2>IPure after MeDIP</h2>
<center><img src="https://www.diagenode.com/img/product/kits/magmedip-seq-figure_multi3.jpg" alt="medip sequencing coverage" width="600" /></center><center></center><center>
<p></p>
<small><strong>Figure 4.</strong> Consistent coverage and methylation detection from different starting amounts of DNA with the Diagenode MagMeDIP-seq Package (including the Ipure kit for DNA purification). Samples containing decreasing starting amounts of DNA (from the top down: 1000 ng (red), 250 ng (blue), 100 ng (green)) originating from human blood were prepared, revealing a consistent coverage profile for the three different starting amounts, which enables reproducible methylation detection. The CpG islands (CGIs) (marked by yellow boxes in the bottom track) are predominantly unmethylated in the human genome, and as expected, we see a depletion of reads at and around CGIs.</small></center>
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<p><img src="https://www.diagenode.com/img/product/kits/workflow-ipure-cuttag.png" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<h3><strong>Workflow description</strong></h3>
<h5><strong>IPure after ChIP</strong></h5>
<p><strong>Step 1:</strong> Chromatin is decrosslinked and eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added.<br /> <strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet.<br /> <strong>Step 3:</strong> Proteins and remaining buffer are washed away.<br /> <strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after MeDIP</strong></h5>
<p><strong>Step 1:</strong> DNA is eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Remaining buffer are washed away.<br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after CUT&Tag</strong></h5>
<p><strong>Step 1:</strong> pA-Tn5 is inactivated and DNA released from the cells. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Proteins and remaining buffer are washed away. <br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).</p>
<p></p>
<p></p>
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'meta_title' => 'IPure kit v2 | Diagenode',
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<div class="large-12 columns">Chromatin Immunoprecipitation (ChIP) coupled with high-throughput massively parallel sequencing as a detection method (ChIP-seq) has become one of the primary methods for epigenomics researchers, namely to investigate protein-DNA interaction on a genome-wide scale. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</div>
<div class="large-12 columns"></div>
<h5 class="large-12 columns"><strong></strong></h5>
<h5 class="large-12 columns"><strong>The ChIP-seq workflow</strong></h5>
<div class="small-12 medium-12 large-12 columns text-center"><br /><img src="https://www.diagenode.com/img/chip-seq-diagram.png" /></div>
<div class="large-12 columns"><br />
<ol>
<li class="large-12 columns"><strong>Chromatin preparation: </strong>Crosslink chromatin-bound proteins (histones or transcription factors) to DNA followed by cell lysis.</li>
<li class="large-12 columns"><strong>Chromatin shearing:</strong> Fragment chromatin by sonication to desired fragment size (100-500 bp)</li>
<li class="large-12 columns"><strong>Chromatin IP</strong>: Capture protein-DNA complexes with <strong><a href="../categories/chip-seq-grade-antibodies">specific ChIP-seq grade antibodies</a></strong> against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: Reverse cross-links, elute, and purify </li>
<li class="large-12 columns"><strong>NGS Library Preparation</strong>: Ligate adapters and amplify IP'd material</li>
<li class="large-12 columns"><strong>Bioinformatic analysis</strong>: Perform r<span style="font-weight: 400;">ead filtering and trimming</span>, r<span style="font-weight: 400;">ead specific alignment, enrichment specific peak calling, QC metrics, multi-sample cross-comparison etc. </span></li>
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<div class="row" style="margin-top: 32px;">
<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns"><a href="../pages/which-kit-to-choose"><img alt="" src="https://www.diagenode.com/img/banners/banner-decide.png" /></a></div>
<div class="small-6 medium-6 large-6 columns"><a href="../pages/chip-kit-customizer-1"><img alt="" src="https://www.diagenode.com/img/banners/banner-customizer.png" /></a></div>
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'meta_description' => 'Diagenode offers wide range of kits and antibodies for Chromatin Immunoprecipitation Sequencing (ChIP-Seq) and also provides Bioruptor for chromatin shearing',
'meta_title' => 'Chromatin Immunoprecipitation - ChIP-seq Kits - Dna methylation | Diagenode',
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<div class="small-12 medium-12 large-12 columns text-justify">
<p class="text-justify">Chromatin Immunoprecipitation (ChIP) coupled with quantitative PCR can be used to investigate protein-DNA interaction at known genomic binding sites. if sites are not known, qPCR primers can also be designed against potential regulatory regions such as promoters. ChIP-qPCR is advantageous in studies that focus on specific genes and potential regulatory regions across differing experimental conditions as the cost of performing real-time PCR is minimal. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</p>
<p class="text-justify"><strong>The ChIP-qPCR workflow</strong></p>
</div>
<div class="small-12 medium-12 large-12 columns text-center"><br /> <img src="https://www.diagenode.com/img/chip-qpcr-diagram.png" /></div>
<div class="small-12 medium-12 large-12 columns"><br />
<ol>
<li class="large-12 columns"><strong>Chromatin preparation: </strong>cell fixation (cross-linking) of chromatin-bound proteins such as histones or transcription factors to DNA followed by cell lysis.</li>
<li class="large-12 columns"><strong>Chromatin shearing: </strong>fragmentation of chromatin<strong> </strong>by sonication down to desired fragment size (100-500 bp)</li>
<li class="large-12 columns"><strong>Chromatin IP</strong>: protein-DNA complexe capture using<strong> <a href="https://www.diagenode.com/en/categories/chip-grade-antibodies">specific ChIP-grade antibodies</a></strong> against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: chromatin reverse cross-linking and elution followed by purification<strong> </strong></li>
<li class="large-12 columns"><strong>qPCR and analysis</strong>: using previously designed primers to amplify IP'd material at specific loci</li>
</ol>
</div>
</div>
<div class="row" style="margin-top: 32px;">
<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
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'id' => '4692',
'name' => 'Temporal modification of H3K9/14ac and H3K4me3 histone marksmediates mechano-responsive gene expression during the accommodationprocess in poplar',
'authors' => 'Ghosh R. et al.',
'description' => '<p>Plants can attenuate their molecular response to repetitive mechanical stimulation as a function of their mechanical history. For instance, a single bending of stem is sufficient to attenuate the gene expression in poplar plants to the subsequent mechanical stimulation, and the state of desensitization can last for several days. The role of histone modifications in memory gene expression and modulating plant response to abiotic or biotic signals is well known. However, such information is still lacking to explain the attenuated expression pattern of mechano-responsive genes in plants under repetitive stimulation. Using poplar as a model plant in this study, we first measured the global level of H3K9/14ac and H3K4me3 marks in the bent stem. The result shows that a single mild bending of the stem for 6 seconds is sufficient to alter the global level of the H3K9/14ac mark in poplar, highlighting the fact that plants are extremely sensitive to mechanical signals. Next, we analyzed the temporal dynamics of these two active histone marks at attenuated (PtaZFP2, PtaXET6, and PtaACA13) and non-attenuated (PtaHRD) mechano-responsive loci during the desensitization and resensitization phases. Enrichment of H3K9/14ac and H3K4me3 in the regulatory region of attenuated genes correlates well with their transient expression pattern after the first bending. Moreover, the levels of H3K4me3 correlate well with their expression pattern after the second bending at desensitization (3 days after the first bending) as well as resensitization (5 days after the first bending) phases. On the other hand, H3K9/14ac status correlates only with their attenuated expression pattern at the desensitization phase. The expression efficiency of the attenuated genes was restored after the second bending in the histone deacetylase inhibitor-treated plants. While both histone modifications contribute to the expression of attenuated genes, mechanostimulated expression of the non-attenuated PtaHRD gene seems to be H3K4me3 dependent.</p>',
'date' => '2023-02-01',
'pmid' => 'https://doi.org/10.1101%2F2023.02.12.526104',
'doi' => '10.1101/2023.02.12.526104',
'modified' => '2023-04-14 09:20:38',
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(int) 1 => array(
'id' => '4498',
'name' => 'Winter warming post floral initiation delays flowering via bud dormancyactivation and affects yield in a winter annual crop.',
'authors' => 'Lu Xiang et al.',
'description' => '<p>Winter annual life history is conferred by the requirement for vernalization to promote the floral transition and control the timing of flowering. Here we show using winter oilseed rape that flowering time is controlled by inflorescence bud dormancy in addition to vernalization. Winter warming treatments given to plants in the laboratory and field increase flower bud abscisic acid levels and delay flowering in spring. We show that the promotive effect of chilling reproductive tissues on flowering time is associated with the activity of two FLC genes specifically silenced in response to winter temperatures in developing inflorescences, coupled with activation of a BRANCHED1-dependent bud dormancy transcriptional module. We show that adequate winter chilling is required for normal inflorescence development and high yields in addition to the control of flowering time. Because warming during winter flower development is associated with yield losses at the landscape scale, our work suggests that bud dormancy activation may be important for effects of climate change on winter arable crop yields.</p>',
'date' => '2022-09-01',
'pmid' => 'https://doi.org/10.1073%2Fpnas',
'doi' => '10.1073/pnas.2204355119',
'modified' => '2022-11-21 10:28:36',
'created' => '2022-11-15 09:26:20',
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'id' => '4218',
'name' => 'AUXIN RESPONSE FACTOR 16 (StARF16) regulates defense gene StNPR1 upon infection with necrotrophic pathogen in potato.',
'authors' => 'Kalsi HS et al.',
'description' => '<p><span>We demonstrate a new regulatory mechanism in the jasmonic acid (JA) and salicylic acid (SA) mediated crosstalk in potato defense response, wherein, miR160 target StARF16 (a gene involved in growth and development) binds to the promoter of StNPR1 (a defense gene) and negatively regulates its expression to suppress the SA pathway. Overall, our study establishes the importance of StARF16 in regulation of StNPR1 during JA mediated defense response upon necrotrophic pathogen interaction. Plants employ antagonistic crosstalk between salicylic acid (SA) and jasmonic acid (JA) to effectively defend them from pathogens. During biotrophic pathogen attack, SA pathway activates and suppresses the JA pathway via NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1). However, upon necrotrophic pathogen attack, how JA-mediated defense response suppresses the SA pathway, is still not well-understood. Recently StARF10 (AUXIN RESPONSE FACTOR), a miR160 target, has been shown to regulate SA and binds to the promoter of StGH3.6 (GRETCHEN HAGEN3), a gene proposed to maintain the balance between the free SA and auxin in plants. In the current study, we investigated the role of StARF16 (a miR160 target) in the regulation of the defense gene StNPR1 in potato upon activation of the JA pathway. We observed that a negative correlation exists between StNPR1 and StARF16 upon infection with the pathogen. The results were further confirmed through the exogenous application of SA and JA. Using yeast one-hybrid assay, we demonstrated that StARF16 binds to the StNPR1 promoter through putative ARF binding sites. Additionally, through protoplast transfection and chromatin immunoprecipitation experiments, we showed that StARF16 could bind to the StNPR1 promoter and regulate its expression. Co-transfection assays using promoter deletion constructs established that ARF binding sites are present in the 2.6 kb sequence upstream to the StNPR1 gene and play a key role in its regulation during infection. In summary, we demonstrate the importance of StARF16 in the regulation of StNPR1, and thus SA pathway, during JA-mediated defense response upon necrotrophic pathogen interaction.</span></p>',
'date' => '2022-04-05',
'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/35380408/',
'doi' => '10.1007/s11103-022-01261-0',
'modified' => '2022-04-15 13:14:24',
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(int) 3 => array(
'id' => '4564',
'name' => 'GIF1 controls ear inflorescence architecture and floral development byregulating key genes in hormone biosynthesis and meristem determinacy inmaize.',
'authors' => 'Li Manfei et al. ',
'description' => '<p>BACKGROUND: Inflorescence architecture and floral development in flowering plants are determined by genetic control of meristem identity, determinacy, and maintenance. The ear inflorescence meristem in maize (Zea mays) initiates short branch meristems called spikelet pair meristems, thus unlike the tassel inflorescence, the ears lack long branches. Maize growth-regulating factor (GRF)-interacting factor1 (GIF1) regulates branching and size of meristems in the tassel inflorescence by binding to Unbranched3. However, the regulatory pathway of gif1 in ear meristems is relatively unknown. RESULT: In this study, we found that loss-of-function gif1 mutants had highly branched ears, and these extra branches repeatedly produce more branches and florets with unfused carpels and an indeterminate floral apex. In addition, GIF1 interacted in vivo with nine GRFs, subunits of the SWI/SNF chromatin-remodeling complex, and hormone biosynthesis-related proteins. Furthermore, key meristem-determinacy gene RAMOSA2 (RA2) and CLAVATA signaling-related gene CLV3/ENDOSPERM SURROUNDING REGION (ESR) 4a (CLE4a) were directly bound and regulated by GIF1 in the ear inflorescence. CONCLUSIONS: Our findings suggest that GIF1 working together with GRFs recruits SWI/SNF chromatin-remodeling ATPases to influence DNA accessibility in the regions that contain genes involved in hormone biosynthesis, meristem identity and determinacy, thus driving the fate of axillary meristems and floral organ primordia in the ear-inflorescence of maize.</p>',
'date' => '2022-03-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35303806',
'doi' => '10.1186/s12870-022-03517-9',
'modified' => '2022-11-24 09:10:14',
'created' => '2022-11-24 08:49:52',
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(int) 4 => array(
'id' => '4250',
'name' => 'Chromosomal variations of species revealed by FISH with rDNAs andcentromeric histone H3 variant associated DNAs',
'authors' => 'Liu Mao-Sen et al.',
'description' => '<p>Lycoris species have various chromosome numbers and karyotypes, but all have a constant total number of chromosome major arms. In addition to three fundamental types, including metacentric (M-), telocentric (T-), and acrocentric (A-) chromosomes, chromosomes in various morphology and size were also observed in natural populations. Both fusion and fission translocation have been considered as main mechanisms leading to the diverse karyotypes among Lycoris species, which suggests the centromere organization playing a role in such arrangements. We detected several chromosomal structure changes in Lycoris including centric fusion, inversion, gene amplification, and segment deletion by using fluorescence in situ hybridization (FISH) probing with rDNAs. An antibody against centromere specific histone H3 (CENH3) of L. aurea (2n = 14, 8M+6T) was raised and used to obtain CENH3-associated DNA sequences of L. aurea by chromatin immunoprecipitation (ChIP) cloning method. Immunostaining with anti-CENH3 antibody could label the centromeres of M-, T-, and A-type chromosomes. Immunostaining also revealed two centromeres on one T-type chromosome and a centromere on individual mini-chromosome. Among 10,000 ChIP clones, 500 clones which showed abundant in L. aurea genome by dot-blotting analysis were FISH mapped on chromosomes to examine their cytological distribution. Five of these 500 clones could generate intense FISH signals at centromeric region on M-type but not T-type chromosomes. FISH signals of these five clones rarely appeared on A-type chromosomes. The five ChIP clones showed similarity in DNA sequences and could generate similar but not identical distribution patterns of FISH signals on individual chromosomes. Furthermore, the distinct distribution patterns of FISH signals on each chromosome generated by these five ChIP clones allow to identify individual chromosome, which is considered difficult by conventional staining approaches. Our results suggest a different organization of centromeres of the three chromosome types in Lycoris species.</p>',
'date' => '2021-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34591908',
'doi' => '10.1371/journal.pone.0258028',
'modified' => '2022-05-20 09:36:20',
'created' => '2022-05-19 10:41:50',
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(int) 5 => array(
'id' => '4346',
'name' => 'Expression of in the Stem Cell Domain Is Required for ItsFunction in the Control of Floral Meristem Activity in Arabidopsis',
'authors' => 'Kwaśniewska K. et al. ',
'description' => '<p>In the model plant Arabidopsis thaliana, the zinc-finger transcription factor KNUCKLES (KNU) plays an important role in the termination of floral meristem activity, a process that is crucial for preventing the overgrowth of flowers. The KNU gene is activated in floral meristems by the floral organ identity factor AGAMOUS (AG), and it has been shown that both AG and KNU act in floral meristem control by directly repressing the stem cell regulator WUSCHEL (WUS), which leads to a loss of stem cell activity. When we re-examined the expression pattern of KNU in floral meristems, we found that KNU is expressed throughout the center of floral meristems, which includes, but is considerably broader than the WUS expression domain. We therefore hypothesized that KNU may have additional functions in the control of floral meristem activity. To test this, we employed a gene perturbation approach and knocked down KNU activity at different times and in different domains of the floral meristem. In these experiments we found that early expression in the stem cell domain, which is characterized by the expression of the key meristem regulatory gene CLAVATA3 (CLV3), is crucial for the establishment of KNU expression. The results of additional genetic and molecular analyses suggest that KNU represses floral meristem activity to a large extent by acting on CLV3. Thus, KNU might need to suppress the expression of several meristem regulators to terminate floral meristem activity efficiently.</p>',
'date' => '2021-07-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34367223',
'doi' => '10.3389/fpls.2021.704351',
'modified' => '2022-08-03 16:54:07',
'created' => '2022-05-19 10:41:50',
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(int) 6 => array(
'id' => '4080',
'name' => 'Localization and characterization of Citrus centromeres by combining
half-tetrad analysis and CenH3-associated sequence profiling.',
'authors' => 'Xia, Qiang-Ming and Miao, Lu-Ke and Xie, Kai-Dong and Yin, Zhao-Ping and
Wu, Xiao-Meng and Chen, Chun-Li and Grosser, Jude W and Guo, Wen-Wu',
'description' => 'KEY MESSAGE: The physical locations of citrus centromere are revealed
by combining genetic and immunological assays for the first time and nine
citrus centromere-specific markers for cytogenetics are mined. Centromere
localization is challenging, because highly redundant repetitive sequences
in centromeric regions make sequence assembly difficult. Although several
citrus genomes have been released, the centromeric regions and their
characteristics remain to be elucidated. Here, we mapped citrus centromeres
through half-tetrad analysis (HTA) that included the genotyping of 54
tetraploid hybrids derived from 2n megagametophytes of Nadorcott tangor
with 212 single nucleotide polymorphism (SNP) markers. The sizes of
centromeric regions, which estimated based on the heterozygosity
restitution rate pattern along the chromosomes, ranged from 1.12 to
18.19 Mb. We also profiled the binding sequences with the
centromere-specific histone variant CenH3 by chromatin immunoprecipitation
sequencing (ChIP-seq). Based on the positions of the top ten
CenH3-enriched contigs, the sizes of centromeric regions were estimated to
range from 0.01 to 7.60 Mb and were either adjacent to or included in the
centromeric regions identified by HTA. We used DNA probes from two
repeats selected from the centromeric regions and seven CenH3-binding
centromeric repeats to verify centromeric locations by fluorescence in situ
hybridization (FISH). Centromere localization in citrus will contribute
to the mining of centromeric/pericentromeric markers, thus to facilitate
the rapid identification of mechanisms underlying 2n gamete formation and
serve the polyploidy breeding.',
'date' => '2020-12-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32897396',
'doi' => '10.1007/s00299-020-02587-z',
'modified' => '2021-02-18 10:21:53',
'created' => '2021-02-18 10:21:53',
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(int) 7 => array(
'id' => '4052',
'name' => 'StE(z)2, a Polycomb group methyltransferase and deposition of H3K27me3 andH3K4me3 regulate the expression of tuberization genes in potato.',
'authors' => 'Kumar, Amit and Kondhare, Kirtikumar R and Malankar, Nilam N and Banerjee,Anjan K',
'description' => '<p>Polycomb Repressive Complex (PRC) group proteins regulate various developmental processes in plants by repressing the target genes via H3K27 trimethylation, whereas their function is antagonized by Trithorax group proteins-mediated H3K4 trimethylation. Tuberization in potato is widely studied, but the role of histone modifications in this process is unknown. Recently, we showed that overexpression of StMSI1 (a PRC2 member) alters the expression of tuberization genes in potato. As MSI1 lacks histone-modification activity, we hypothesized that this altered expression could be caused by another PRC2 member, StE(z)2 (a potential H3K27 methyltransferase in potato). Here, we demonstrate that short-day photoperiod influences StE(z)2 expression in leaf and stolon. Moreover, StE(z)2 overexpression alters plant architecture and reduces tuber yield, whereas its knockdown enhanced the yield. ChIP-sequencing using short-day induced stolons revealed that several tuberization and phytohormone-related genes, such as StBEL5/11/29, StSWEET11B, StGA2OX1 and StPIN1 carry H3K4me3 or H3K27me3 marks and/or are StE(z)2 targets. Interestingly, we noticed that another important tuberization gene, StSP6A is targeted by StE(z)2 in leaves and had increased deposition of H3K27me3 under non-induced (long-day) conditions compared to SD. Overall, we show that StE(z)2 and deposition of H3K27me3 and/or H3K4me3 marks could regulate the expression of key tuberization genes in potato.</p>',
'date' => '2020-10-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33048134',
'doi' => '10.1093/jxb/eraa468',
'modified' => '2021-02-19 14:55:34',
'created' => '2021-02-18 10:21:53',
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[maximum depth reached]
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),
(int) 8 => array(
'id' => '3959',
'name' => 'The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2).',
'authors' => 'Velanis CN, Perera P, Thomson B, de Leau E, Liang SC, Hartwig B, Förderer A, Thornton H, Arede P, Chen J, Webb KM, Gümüs S, De Jaeger G, Page CA, Hancock CN, Spanos C, Rappsilber J, Voigt P, Turck F, Wellmer F, Goodrich J',
'description' => '<p>A large fraction of plant genomes is composed of transposable elements (TE), which provide a potential source of novel genes through "domestication"-the process whereby the proteins encoded by TE diverge in sequence, lose their ability to catalyse transposition and instead acquire novel functions for their hosts. In Arabidopsis, ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) arose by domestication of the nuclease component of Harbinger class TE and acquired a new function as a component of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a histone H3K27me3 methyltransferase involved in regulation of host genes and in some cases TE. It was not clear how ALP1 associated with PRC2, nor what the functional consequence was. Here, we identify ALP2 genetically as a suppressor of Polycomb-group (PcG) mutant phenotypes and show that it arose from the second, DNA binding component of Harbinger transposases. Molecular analysis of PcG compromised backgrounds reveals that ALP genes oppose silencing and H3K27me3 deposition at key PcG target genes. Proteomic analysis reveals that ALP1 and ALP2 are components of a variant PRC2 complex that contains the four core components but lacks plant-specific accessory components such as the H3K27me3 reader LIKE HETEROCHROMATION PROTEIN 1 (LHP1). We show that the N-terminus of ALP2 interacts directly with ALP1, whereas the C-terminus of ALP2 interacts with MULTICOPY SUPPRESSOR OF IRA1 (MSI1), a core component of PRC2. Proteomic analysis reveals that in alp2 mutant backgrounds ALP1 protein no longer associates with PRC2, consistent with a role for ALP2 in recruitment of ALP1. We suggest that the propensity of Harbinger TE to insert in gene-rich regions of the genome, together with the modular two component nature of their transposases, has predisposed them for domestication and incorporation into chromatin modifying complexes.</p>',
'date' => '2020-05-01',
'pmid' => 'http://www.pubmed.gov/32463832',
'doi' => '10.1371/journal.pgen.1008681',
'modified' => '2020-08-12 09:51:53',
'created' => '2020-08-10 12:12:25',
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(int) 9 => array(
'id' => '3880',
'name' => 'REDOX RESPONSIVE TRANSCRIPTION FACTOR1 (RRFT1) is involved in extracellular ATP regulated Arabidopsis thaliana seedling growth.',
'authors' => 'Zhu R, Dong X, Xue Y, Xu J, Zhang A, Feng M, Zhao Q, Xia S, Yin Y, He S, Li Y, Liu T, Kang E, Shang Z',
'description' => '<p>Extracellular ATP (eATP) is an apoplastic signaling molecule that plays essential roles in the growth and development of plants. Arabidopsis seedlings have been reported to respond to eATP, however, the downstream signaling components are still not well understood. Here, we report that an ethylene responsive factor, Redox Responsive Transcription Factor 1 (RRTF1), is involved in eATP-regulated Arabidopsis thaliana seedling growth. Exogenous ATP inhibited green seedling root growth and induced hypocotyl bending of etiolated seedlings. RRTF1 loss-of-function mutant (rrtf1) seedlings showed decreased responses to eATP, while its complementation or overexpression led to recovered or increased eATP responsiveness. RRTF1 was expressed rapidly after eATP stimulation and then migrated into the nuclei of root tip cells. eATP-induced auxin accumulation in root tip or hypocotyl cells was impaired in rrtf1. Chromatin immunoprecipitation (ChIP) and high-throughput sequencing results indicated that eATP induced some genes related to cell growth and development in wild type but not in rrtf1 cells. These results suggest that RRTF1 may be involved in eATP signaling by regulating functional gene expression and cell metabolism in Arabidopsis seedlings.</p>',
'date' => '2020-02-12',
'pmid' => 'http://www.pubmed.gov/32049334',
'doi' => '10.1093/pcp/pcaa014/5734653',
'modified' => '2020-03-20 17:32:29',
'created' => '2020-03-13 13:45:54',
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(int) 10 => array(
'id' => '3872',
'name' => 'An inferred fitness consequence map of the rice genome.',
'authors' => 'Joly-Lopez Z, Platts AE, Gulko B, Choi JY, Groen SC, Zhong X, Siepel A, Purugganan MD',
'description' => '<p>The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa). We inferred fitCons scores (ρ) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae. We found ρ to be multimodal, with ~9% of the rice genome falling into classes where more than half of the bases would probably have a fitness consequence if mutated. Around 2% of the rice genome showed evidence of weak negative selection, frequently at candidate regulatory sites, including a novel set of 1,000 potentially active enhancer elements. This fitCons map provides perspective on the evolutionary forces associated with genome diversity, aids in genome annotation and can guide crop breeding programs.</p>',
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'description' => '<p>The transcription factors LEAFY (LFY) and APETALA1 (AP1), together with the AP1 paralog CAULIFLOWER (CAL), control the onset of flower development in a partially redundant manner. This redundancy is thought to be mediated, at least in part, through the regulation of a shared set of target genes. However, whether these genes are independently or cooperatively regulated by LFY and AP1/CAL is currently unknown. To better understand the regulatory relationship between LFY and AP1/CAL and to obtain deeper insights into the control of floral initiation, we monitored the activity of LFY in the absence of AP1/CAL function. We found that the regulation of several known LFY target genes is unaffected by AP1/CAL perturbation, while others appear to require AP1/CAL activity. Furthermore, we obtained evidence that LFY and AP1/CAL control the expression of some genes in an antagonistic manner. Notably, these include key regulators of floral initiation such as <i>TERMINAL FLOWER1</i> (<i>TFL1</i>), which had been previously reported to be directly repressed by both LFY and AP1. We show here that <i>TFL1</i> expression is suppressed by AP1 but promoted by LFY. We further demonstrate that LFY has an inhibitory effect on flower formation in the absence of AP1/CAL activity. We propose that LFY and AP1/CAL act as part of an incoherent feed-forward loop, a network motif where two interconnected pathways or transcription factors act in opposite directions on a target gene, to control the establishment of a stable developmental program for the formation of flowers.</p>',
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<p><img src="https://www.diagenode.com/img/areas/plant.jpg" /></p>
</div>
<div class="extra-spaced">
<h2>Epigenetic Regulation in Plants</h2>
<p>Plants utilize a number of gene regulation mechanisms to ensure proper development, function, growth, and survival under different environmental conditions. Plants depend on changes in gene expression to respond to environmental stimuli, in which the full repertoire of histone modifications, DNA methylation, and small ncRNAs play an important role in epigenetic regulation.</p>
<p>Studying the epigenetics of model plants such as Arabidopsis thaliana have allowed researchers to understand pathways that maintain chromatin modifications as well as the mapping of modifications such as DNA methylation on a genome-wide scale. Small RNAs have also been implicated in playing a role in the distribution of chromatin modifications, and RNA may also play a role in the complex epigenetic interactions that occur between homologous sequences (Moazed et al, 2009). In the future, by understanding epigenetic control, researchers can uncover the research necessary to improve plant growth, yields, and transformation efficiency especially in the face of climate change and other environmental factors.</p>
</div>
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<p><img src="https://www.diagenode.com/img/areas/chromatin-and-transcription-factors.jpg" /></p>
</div>
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<h3 style="font-weight: 100; margin-top: 0;">Chromatin</h3>
<p>Chromatin consists of nucleosomes formed by a complex of histone proteins and DNA, which allows the packaging of DNA into the nucleus. The less condensed euchromatin represents transcriptionally active regions, while heterochromatin is usually inactive (Vaillant and Paszkowski, 2007). Chromatin state is known to be influenced by both DNA methylation and histone modifications which in turn impact gene expression and the structure of chromosomes. In a recent study, the role of chromatin modifications during plant reproduction elucidated 3-dimensional chromosome reorganization mediated by histones and DNA methylation (Dukowic-Schulze et al. 2017). In addition, gibberellins have been shown in increasing the level of histone acetylation, which affects regions of chromatin involved in maize seed germination (Zheng et al. 2017). Another study reports a novel function of a tomato histone deacetylase gene in the regulation of fruit ripening (Guo et al. 2017).</p>
</div>
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<p><img src="https://www.diagenode.com/img/areas/cherry-tomato-common-grape-vine-ripening-fruit-vegetable-cherry-tomatoes.jpg" /></p>
</div>
<div class="small-12 medium-9 large-9 columns">
<p>In addition, multigene families encode transcription factors, with members found throughout the genome or clustered on the same chromosome. Numerous DNA binding proteins that interact with plant promoters have been identified -- some are similar to well-characterized transcription factors in animals or yeast, while others are unique to plants. For example, diverse members of the subfamily X of the plant-specific ethylene response factor (ERF) transcription factors coordinate stress signaling with wound repair activation. Tissue repair is also enhanced through a protein complex of ERF and GRAS TFs (Heyman et. al,.2018). A compilation of known plant transcription factors can be found in the plant transcription factor database at http://plntfdb.bio.uni-potsdam.de/v3.0/.</p>
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</div>
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<p><img src="https://www.diagenode.com/img/areas/rna-strand.jpg" /></p>
</div>
<div class="small-12 medium-9 large-9 columns">
<h3 style="font-weight: 100; margin-top: 0;">RNA</h3>
<p>Recent research shows that a number of classes of small RNAs are key epigenetic regulators. In many cases, small RNAs have been implicated in DNA methylation and chromatin modification (Meyer, 2015). In addition, the role of small RNAs has been implicated in plant stress tolerance (Kumar et al., 2017). López-Galiano et al also provided insight into a coordinated function of a miRNA gene and histone modifications in regulating the expression of a WRKY transcription factor in response to stress.</p>
<p>RNA interference (RNAi) is another epigenetic mechanism that leads to small RNA generation, which mediates gene silencing at the post-transcriptional level. RNAi technology has immense potential for plant disease resistance.</p>
</div>
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<p><img src="https://www.diagenode.com/img/areas/dna-methylation.jpg" /></p>
</div>
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<h3 style="font-weight: 100; margin-top: 0;">DNA methylation</h3>
<p>Plants, unlike animals, have three sites that can be methylated G, CHG (H can be A, C, T), and CHH (Law and Jacobsen, 2010). DNA methylation has attracted particular interest. In Arabidopsis, one-third of methylated genes occur in transcribed regions, and 5% of genes are methylated in promoter regions, suggesting that many of these are epigenetically regulated. (Zhang et al., 2006).</p>
<p>There are thousands of differentially methylated regions (DMRs) that influence phenotype by influencing gene expression. The analysis of epigenetic recombinant inbred line (epiRIL) plants from Arabidopsis points to the evidence of the influence of DMRs. An epiRIL results from crossing two genetically identical plants with differing DNA methylation levels (with one parent as a homozygous mutant for an essential DNA methylation maintenance gene). The offspring of these plants have similar genomes that vary only in methylation levels. Many traits have been studied using epiRILs -- flowering time, plant height, and response to abiotic stress, some of which have now been mapped to DMRs (Zhang et al. 2018)</p>
<p>Regulation by DNA methylation has been shown to be important in many aspects of plant development and response such as vernalization, hybrid vigor, and self-incompatibility (Itabashi et al. 2017). For example, vernalization treatments have shown reduced DNA methylation and subsequent initiation of flowering (Burn et al., 1993). Stress can also influence DNA methylation in plants as a response to environmental stimuli. (Steward et al., 2002; Song et al., 2012). A high degree of DNA methylation has also suggested the role in the improvement of plant fitness under different environmental conditions (Saéz-Laguna et al., 2014). In addition, methylation can affect normal fruit and hypomethylation predicts homeotic transformation and loss of fruit yield (Ong-Abdullah et al., 2015)</p>
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<p>DNA demethylation has also been implied in various aspects of plant development including pollen tube formation, embryogenesis, fruit ripening, stomatal development, and nodule formation ( Li et al. 2017). Demethylation of rice genomic DNA caused an altered pattern of gene expression, inducing dwarf plants (Sano et al., 1990).</p>
<p>Epigenetic modifications contribute to the stability and survival of the plants and their ability to adapt in different environmental conditions.</p>
</div>
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<h3>Diagenode products for your epigenomics research in plants</h3>
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<h3 class="text-center"><a href="https://www.diagenode.com/en/categories/chromatin-function">Chromatin analysis</a></h3>
<center><a href="https://www.diagenode.com/en/categories/chromatin-function"><img src="https://www.diagenode.com/img/cancer/chromatin-icon.png" /></a></center>
<p class="text-left">Understand the role of chromatin in plant function and development</p>
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<li><a href="https://www.diagenode.com/en/categories/chromatin-function">Learn about our chromatin analysis products</a></li>
<li><a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns"> Learn about the Universal Plant ChIP Kit</a></li>
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<h3 class="text-center"><a href="https://www.diagenode.com/en/categories/dna-methylation" style="color: #30415c;">DNA methylation</a></h3>
<center><a href="https://www.diagenode.com/en/categories/dna-methylation"><img src="https://www.diagenode.com/img/cancer/dna-icon.png" /></a></center>
<p class="text-left">DNA methylation and demethylation and the effects on plant response and function</p>
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<li><a href="https://www.diagenode.com/en/categories/dna-methylation">Discover DNA methylation analysis solutions at any resolution</a></li>
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<h3 class="text-center"><span class="darkgrey">Non-coding RNAs</span></h3>
<center><img src="https://www.diagenode.com/img/cancer/non-coding-icon.png" /></center>
<p class="text-left">Discover noncoding RNAs in the regulation of gene expression in plants</p>
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<li><a href="https://www.diagenode.com/en/categories/Library-preparation-for-RNA-seq">Library prep for RNA-seq studies for ncRNAs</a></li>
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<h3>References</h3>
<p><small> Burn, J. et al (1993). DNA methylation, vernalization, and the initiation of flowering. Proc. Natl. Acad. Sci. U.S.A. 90, 287–291. doi: 10.1006/scdb.1996.0055 </small></p>
<p><small> Dukowic-Schulze S, Liu C, Chen C (2017) Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2222-0</small></p>
<p><small> Guo J et al (2017) A histone deacetylase gene, SlHDA3, acts as a negative regulator of fruit ripening and carotenoid accumulation. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2211-3</small></p>
<p><small> Heyman J, et.al (2018) Journal of Cell Science Emerging role of the plant ERF transcription factors in coordinating wound defense responses and repair doi: 10.1242/jcs.208215</small></p>
<p><small> Itabashi E, Osabe K, Fujimoto R, Kakizaki T (2017) Epigenetic regulation of agronomical traits in Brassicaceae. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2223-z</small></p>
<p><small> Kumar V et al (2017) Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2210-4</small></p>
<p><small> Law, J. A., and Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220. doi: 10.1038/nrg2719</small></p>
<p><small> Meyer, P. (2015). Epigenetic variation and environmental change. J. Exp. Bot. 66, 3541–3548. doi: 10.1093/jxb/eru502</small></p>
<p><small> Moazed, D. (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature. doi: 10.1038/nature07756</small></p>
<p><small> Ong-Abdullah et al. (2015). Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525, 533–537. doi: 10.1038/nature15365</small></p>
<p><small> Saéz-Laguna et al. (2014). Epigenetic variability in the genetically uniform forest tree species. PLoS One 9:e103145. doi: 10.1371/journal.pone.0103145</small></p>
<p><small> Sano, H. et al. (1990). A single treatment of rice seedlings with 5-azacytidine induces heritable dwarfism and undermethylation of genomic DNA. Mol. Gen. Genet. 220, 441–447. doi: 10.1007/BF00391751</small></p>
<p><small> Song, J et al (2012). Vernalization – A cold-induced epigenetic switch. J. Cell Sci. 125, 3723–3731. doi: 10.1242/jcs.084764</small></p>
<p><small> Steward, N et al. (2002). Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J. Biol. Chem. 277, 37741–37746. doi: 10.1074/jbc.M204050200</small></p>
<p><small> Vaillant, I., and Paszkowski, J. (2007). Role of histone and DNA methylation in gene regulation. Curr. Opin. Plant Biol. 10, 528–533. doi: 10.1016/j.pbi.2007.06.008</small></p>
<p><small> Zhang, et al. (2006). Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189–1201. doi: 10.1016/j.cell.2006.08.003</small></p>
<p><small> Zhang et al. 2018 Understanding the evolutionary potential of epigenetic variation: a comparison of heritable phenotypic variation in epiRILs, RILs, and natural ecotypes of Arabidopsis thaliana. Heredity 121, 257–265 (2018) doi:10.1038/s41437-018-0095-9</small></p>
<p><small> Zheng X et al (2017) Histone acetylation is involved in GA-mediated 45S rDNA decondensation in maize aleurone layers. Plant Cell Rep. https://dx.doi.org/10.1007/s00299-017-2207-z</small></p>
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<p>Diagenode’s<span> </span><b>IPure</b><b><span> </span>kit<span> </span></b>is the only DNA purification kit using magnetic beads, that is specifically optimized for extracting DNA from<span> </span><b>ChIP</b><b>,<span> </span></b><b>MeDIP</b><span> </span>and<span> </span><b>CUT&Tag</b>. The use of the magnetic beads allows for a clear separation of DNA and increases therefore the reproducibility of your DNA purification. This simple and straightforward protocol delivers pure DNA ready for any downstream application (e.g. next generation sequencing). Comparing to phenol-chloroform extraction, the IPure technology has the advantage of being nontoxic and much easier to be carried out on multiple samples.</p>
<center>
<h4>High DNA recovery after purification of ChIP samples using IPure technology</h4>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-chromatin-function.png" width="500" /></center>
<p></p>
<p><small>ChIP assays were performed using different amounts of U2OS cells and the H3K9me3 antibody (Cat. No.<span> </span><span>C15410056</span>; 2 g/IP). <span>The purified DNA was eluted in 50 µl of water and quantified with a Nanodrop.</span></small></p>
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<p><strong>Benefits of the IPure kit:</strong></p>
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<li style="text-align: left;">Provides pure DNA for any downstream application (e. g. Next generation sequencing)</li>
<li style="text-align: left;">Non-toxic</li>
<li style="text-align: left;">Fast & easy to use</li>
<li style="text-align: left;">Optimized for DNA purification after ChIP, MeDIP and CUT&Tag</li>
<li style="text-align: left;">Compatible with automation</li>
<li style="text-align: left;">Validated on the IP-Star Compact</li>
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'info1' => '<h2>IPure after ChIP</h2>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-A.png" alt="ChIP-seq figure A" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-B.png" alt="ChIP-seq figure B" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><img src="https://www.diagenode.com/img/product/kits/ideal-TF-chip-seq-C.png" alt="ChIP-seq figure C" style="display: block; margin-left: auto; margin-right: auto;" /></p>
<p><small><strong>Figure 1.</strong> Chromatin Immunoprecipitation has been performed using chromatin from HeLa cells, the iDeal ChIP-seq kit for Transcription Factors (containing the IPure module for DNA purification) and the Diagenode ChIP-seq-grade HDAC1 (A), LSD1 (B) and p53 antibody (C). 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. This figure shows the peak distribution in regions of chromosome 3 (A), chromosome 12 (B) and chromosome 6 (C) respectively.</small></p>
<p></p>
<h2>IPure after CUT&Tag</h2>
<p>Successful CUT&Tag results showing a low background with high region-specific enrichment has been generated using 50.000 of K562 cells, 1 µg of H3K4me3 or H3K27me3 antibody (Diagenode, C15410003 or C15410069, respectively) and proteinA-Tn5 (1:250) (Diagenode, C01070001). 1 µg of IgG (C15410206) was used as negative control. Samples were purified using the IPure kit v2 or phenol-chloroform purification. The below figures present the comparison of two purification methods.</p>
<center><img src="https://www.diagenode.com/img/product/kits/ipure-fig2.png" style="display: block; margin-left: auto; margin-right: auto;" width="400" /></center><center>
<p style="text-align: center;"><small><strong>Figure 2.</strong> Heatmap 3kb upstream and downstream of the TSS for H3K4me3</small></p>
</center>
<p></p>
<p><img src="https://www.diagenode.com/img/product/kits/ipure-fig3.png" style="display: block; margin-left: auto; margin-right: auto;" width="600" /></p>
<p></p>
<center><small><strong>Figure 3.</strong> Integrative genomics viewer (IGV) visualization of CUT&Tag experiments using Diagenode’s pA-Tn5 transposase (Cat. No. C01070002), H3K27me3 antibody (Cat. No. C15410069) and IPure kit v2 vs phenol chloroform purification (PC).</small></center>
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<h2>IPure after MeDIP</h2>
<center><img src="https://www.diagenode.com/img/product/kits/magmedip-seq-figure_multi3.jpg" alt="medip sequencing coverage" width="600" /></center><center></center><center>
<p></p>
<small><strong>Figure 4.</strong> Consistent coverage and methylation detection from different starting amounts of DNA with the Diagenode MagMeDIP-seq Package (including the Ipure kit for DNA purification). Samples containing decreasing starting amounts of DNA (from the top down: 1000 ng (red), 250 ng (blue), 100 ng (green)) originating from human blood were prepared, revealing a consistent coverage profile for the three different starting amounts, which enables reproducible methylation detection. The CpG islands (CGIs) (marked by yellow boxes in the bottom track) are predominantly unmethylated in the human genome, and as expected, we see a depletion of reads at and around CGIs.</small></center>
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<h3><strong>Workflow description</strong></h3>
<h5><strong>IPure after ChIP</strong></h5>
<p><strong>Step 1:</strong> Chromatin is decrosslinked and eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added.<br /> <strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet.<br /> <strong>Step 3:</strong> Proteins and remaining buffer are washed away.<br /> <strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after MeDIP</strong></h5>
<p><strong>Step 1:</strong> DNA is eluted from beads (magnetic or agarose) which are discarded. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Remaining buffer are washed away.<br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).<br /><br /><br /></p>
<h5><strong>IPure after CUT&Tag</strong></h5>
<p><strong>Step 1:</strong> pA-Tn5 is inactivated and DNA released from the cells. <strong>Magnetic beads</strong> <strong>for purification</strong> are added. <br /><strong>Step 2:</strong> Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet. <br /><strong>Step 3:</strong> Proteins and remaining buffer are washed away. <br /><strong>Step 4:</strong> DNA is eluted from magnetic beads, which are discarded. Purified DNA is ready for any downstream application (NGS, qPCR, amplification, microarray).</p>
<p></p>
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