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<p><small><strong>Figure 1 ChIP-seq results obtained with the Diagenode monoclonal antibody directed against TBP </strong><br />ChIP was performed with 5 μg of the Diagenode antibody against TBP (Cat. No. C15200002) on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022) on the IP-Star automated system. The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoters of the active GAPDH and c-fos genes, used as positive control targets, and for a region 1 kb upstream of the GAPDH promoter and the coding region of the inactive MB gene, used as negative control targets (figure 2A). The IP’d DNA was subsequently analysed with an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2 shows the peak distribution in 50 kb regions surrounding the GAPDH, c-fos, ACTB and MCL1 genes (figure 2B, C, D and E, respectively). These results clearly show a localisation of TBP at the promoters of actively transcribed genes.</small></p>
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<p><small><strong>Figure 2 ChIP results obtained with the Diagenode monoclonal antibody against TBP </strong><br />ChIP assays were performed using U2OS cells, the Diagenode antibody directed against TBP (Cat. No. C15200002) and optimized primer sets for qPCR. Sheared chromatin from 1x10e6 cells and 4 μg of antibody were used per ChIP experiment. QPCR was performed with primers for the promoter of the c-fos and GAPDH genes (Cat. No. C17011004 and C17011001), a region 0.5 and 1 kb upstream of the GAPDH promoter (Cat. No. C17011002 and C17011003), respectively, and for exon 2 of the myoglobin gene (cat. No. C17011006) as a negative control. Figure 1 shows the recovery (the relative amount of immunoprecipitated DNA compared to input DNA) and the occupancy (ratio +/- control target). These results demonstrate the occupancy of both promoters by TBP.</small></p>
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<p><small><strong> Figure 3. Western blot analysis using the Diagenode monoclonal antibody directed against TBP</strong><br />Whole cell extracts (40 μg) from HeLa cells transfected with TBP siRNA (lane 2) and from an untransfected control (lane 1) were analysed by Western blot using the Diagenode antibody against TBP (Cat. No. C15200002) diluted 1:500 in TBSTween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-1.png" alt="TBP Antibody ChIP Grade" style="display: block; margin-left: auto; margin-right: auto;" /></div>
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<p><small><strong>Figure 1 ChIP-seq results obtained with the Diagenode monoclonal antibody directed against TBP </strong><br />ChIP was performed with 5 μg of the Diagenode antibody against TBP (Cat. No. C15200002) on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022) on the IP-Star automated system. The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoters of the active GAPDH and c-fos genes, used as positive control targets, and for a region 1 kb upstream of the GAPDH promoter and the coding region of the inactive MB gene, used as negative control targets (figure 2A). The IP’d DNA was subsequently analysed with an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2 shows the peak distribution in 50 kb regions surrounding the GAPDH, c-fos, ACTB and MCL1 genes (figure 2B, C, D and E, respectively). These results clearly show a localisation of TBP at the promoters of actively transcribed genes.</small></p>
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<p><small><strong>Figure 2 ChIP results obtained with the Diagenode monoclonal antibody against TBP </strong><br />ChIP assays were performed using U2OS cells, the Diagenode antibody directed against TBP (Cat. No. C15200002) and optimized primer sets for qPCR. Sheared chromatin from 1x10e6 cells and 4 μg of antibody were used per ChIP experiment. QPCR was performed with primers for the promoter of the c-fos and GAPDH genes (Cat. No. C17011004 and C17011001), a region 0.5 and 1 kb upstream of the GAPDH promoter (Cat. No. C17011002 and C17011003), respectively, and for exon 2 of the myoglobin gene (cat. No. C17011006) as a negative control. Figure 1 shows the recovery (the relative amount of immunoprecipitated DNA compared to input DNA) and the occupancy (ratio +/- control target). These results demonstrate the occupancy of both promoters by TBP.</small></p>
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<p><small><strong> Figure 3. Western blot analysis using the Diagenode monoclonal antibody directed against TBP</strong><br />Whole cell extracts (40 μg) from HeLa cells transfected with TBP siRNA (lane 2) and from an untransfected control (lane 1) were analysed by Western blot using the Diagenode antibody against TBP (Cat. No. C15200002) diluted 1:500 in TBSTween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<td>ChIP/ChIP-seq <sup>*</sup></td>
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<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-1.png" alt="TBP Antibody ChIP Grade" style="display: block; margin-left: auto; margin-right: auto;" /></div>
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<p><small><strong>Figure 1 ChIP-seq results obtained with the Diagenode monoclonal antibody directed against TBP </strong><br />ChIP was performed with 5 μg of the Diagenode antibody against TBP (Cat. No. C15200002) on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022) on the IP-Star automated system. The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoters of the active GAPDH and c-fos genes, used as positive control targets, and for a region 1 kb upstream of the GAPDH promoter and the coding region of the inactive MB gene, used as negative control targets (figure 2A). The IP’d DNA was subsequently analysed with an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2 shows the peak distribution in 50 kb regions surrounding the GAPDH, c-fos, ACTB and MCL1 genes (figure 2B, C, D and E, respectively). These results clearly show a localisation of TBP at the promoters of actively transcribed genes.</small></p>
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<div class="small-12 columns">A. <img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-2.png" alt="TBP Antibody - ChIP-seq Grade" style="display: block; margin-left: auto; margin-right: auto;" /><br /> B. <img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-3.png" alt="TBP Antibody for ChIP-seq" style="display: block; margin-left: auto; margin-right: auto;" /><br /> C. <img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-4.png" alt="TBP Antibody for ChIP-seq assay" style="display: block; margin-left: auto; margin-right: auto;" /><br /> D. <img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-5.png" alt="TBP Antibody validated in ChIP-seq" style="display: block; margin-left: auto; margin-right: auto;" /></div>
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<p><small><strong>Figure 2 ChIP results obtained with the Diagenode monoclonal antibody against TBP </strong><br />ChIP assays were performed using U2OS cells, the Diagenode antibody directed against TBP (Cat. No. C15200002) and optimized primer sets for qPCR. Sheared chromatin from 1x10e6 cells and 4 μg of antibody were used per ChIP experiment. QPCR was performed with primers for the promoter of the c-fos and GAPDH genes (Cat. No. C17011004 and C17011001), a region 0.5 and 1 kb upstream of the GAPDH promoter (Cat. No. C17011002 and C17011003), respectively, and for exon 2 of the myoglobin gene (cat. No. C17011006) as a negative control. Figure 1 shows the recovery (the relative amount of immunoprecipitated DNA compared to input DNA) and the occupancy (ratio +/- control target). These results demonstrate the occupancy of both promoters by TBP.</small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15200002-wb.png" alt="TBP Antibody validated in Western Blot" style="display: block; margin-left: auto; margin-right: auto;" /></p>
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<p><small><strong> Figure 3. Western blot analysis using the Diagenode monoclonal antibody directed against TBP</strong><br />Whole cell extracts (40 μg) from HeLa cells transfected with TBP siRNA (lane 2) and from an untransfected control (lane 1) were analysed by Western blot using the Diagenode antibody against TBP (Cat. No. C15200002) diluted 1:500 in TBSTween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<p>Learn more about: <a href="https://www.diagenode.com/applications/western-blot">Loading control, MW marker visualization</a><em>. <br /></em></p>
<p><em></em>Check our selection of antibodies validated in Western blot.</p>',
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<div class="small-10 columns">
<h3>Epigenetic antibodies you can trust!</h3>
<p>Antibody quality is essential for assay success. Diagenode offers antibodies that are actually validated and have been widely used and published by the scientific community. Now we are adding a new level of siRNA knockdown validation to assure the specificity of our non-histone antibodies.</p>
<p><strong>Short interfering RNA (siRNA)</strong> degrades target mRNA, followed by the knock-down of protein production. If the antibody that recognizes the protein of interest is specific, the Western blot of siRNA-treated cells will show a significant reduction of signal vs. untreated cells.</p>
<center><img src="https://www.diagenode.com/emailing/images/C15100144-wb.png" alt="" /></center>
<p class="text-center"><small>WB results obtained with the HDAC1 pAb (Cat. No. C15100144) <br />on siRNA transfected cells (lane 2) and on untransfected control cells (lane 1).</small></p>
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<div class="small-2 columns">
<p><img src="https://www.diagenode.com/emailing/images/epi-success-guaranteed-icon.png" alt="Epigenetic success guaranteed" /></p>
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<div class="spaced"></div>
<p style="text-align: left;"><span style="font-weight: 400;">The below list shows our first siRNA validated antibodies. More results - coming soon</span>.</p>',
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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> Expert technical support</span></li>
<li><span style="font-weight: 400;"> Sample sizes available</span></li>
<li><span style="font-weight: 400;"> 100% satisfaction guarantee</span></li>
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'description' => '<p><b>Unparalleled ChIP-Seq results with the most rigorously validated antibodies</b></p>
<p><span style="font-weight: 400;">Diagenode provides leading solutions for epigenetic research. Because ChIP-seq is a widely-used technique, we validate our antibodies in ChIP and ChIP-seq experiments (in addition to conventional methods like Western blot, Dot blot, ELISA, and immunofluorescence) to provide the highest quality antibody. We standardize our validation and production to guarantee high product quality without technical bias. Diagenode guarantees ChIP-seq grade antibody performance under our suggested conditions.</span></p>
<div class="row">
<div class="small-12 medium-9 large-9 columns">
<p><strong>ChIP-seq profile</strong> of active (H3K4me3 and H3K36me3) and inactive (H3K27me3) marks using Diagenode antibodies.</p>
<img src="https://www.diagenode.com/img/categories/antibodies/chip-seq-grade-antibodies.png" /></div>
<div class="small-12 medium-3 large-3 columns">
<p><small> ChIP was performed on sheared chromatin from 100,000 K562 cells using iDeal ChIP-seq kit for Histones (cat. No. C01010051) with 1 µg of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 µg of the antibody against H3K36me3 (cat. No. C15410192). The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. The figure shows the signal distribution along the complete sequence of human chromosome 3, a zoomin to a 10 Mb region and a further zoomin to a 1.5 Mb region. </small></p>
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<p>Diagenode’s highly validated antibodies:</p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
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<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
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<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
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<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
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<div class="small-12 medium-6 large-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" alt="" width="400" height="315" /> </div>
<div class="small-12 medium-6 large-6 columns">
<p></p>
<p></p>
<p></p>
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<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
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'name' => 'Enhanced frequency of transcription pre-initiation complexes assemblyafter exposure to UV irradiation results in increased repair activity andreduced probabilities for mutagenesis.',
'authors' => 'Liakos A. et al.',
'description' => '<p>In addition to being essential for gene expression, transcription is crucial for the maintenance of genome integrity. Here, we undertook a systematic approach, to monitor the assembly kinetics of the pre-initiating RNA Polymerase (Pol) II at promoters at steady state and different stages during recovery from UV irradiation-stress, when pre-initiation and initiation steps have been suggested to be transiently shut down. Taking advantage of the reversible dissociation of pre-initiating Pol II after high salt treatment, we found that de novo recruitment of the available Pol II molecules at active promoters not only persists upon UV at all times tested but occurs significantly faster in the early phase of recovery (2 h) than in unexposed human fibroblasts at the majority of active genes. Our method unveiled groups of genes with significantly different pre-initiation complex (PIC) assembly dynamics after UV that present distinct rates of UV-related mutational signatures in melanoma tumours, providing functional relevance to the importance of keeping transcription initiation active during UV recovery. Our findings uncover novel mechanistic insights further detailing the multilayered transcriptional response to genotoxic stress and link PIC assembly dynamics after exposure to genotoxins with cancer mutational landscapes.</p>',
'date' => '2023-07-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37470822',
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'name' => 'A leukemia-protective germline variant mediates chromatin moduleformation via transcription factor nucleation.',
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'description' => '<p>Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named "variable chromatin modules" (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect a VCM-modulating noncoding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a large change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with subtle, long-range chromatin compaction and robust AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology.</p>',
'date' => '2022-04-01',
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'name' => 'R-Loops Promote Antisense Transcription across the Mammalian Genome',
'authors' => 'Tan-Wong Sue Mei, Dhir Somdutta, Proudfoot Nick J.',
'description' => '<p>Widespread antisense long noncoding RNA (lncRNA) overlap with many protein-coding genes in mammals and emanate from gene promoter, enhancer, and termination regions. However, their origin and biological purpose remain unclear. We show that these antisense lncRNA can be generated by R-loops that form when nascent transcript invades the DNA duplex behind elongating RNA polymerase II (Pol II). Biochemically, R-loops act as intrinsic Pol II promoters to induce de novo RNA synthesis. Furthermore, their removal across the human genome by RNase H1 overexpression causes the selective reduction of antisense transcription. Consequently, we predict that R-loops act to facilitate the synthesis of many gene proximal antisense lncRNA. Not only are R-loops widely associated with DNA damage and repair, but we now show that they have the capacity to promote de novo transcript synthesis that may have aided the evolution of gene regulation.</p>',
'date' => '2019-11-21',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/31679819',
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'authors' => 'Hsu E, Pennella MA, Zemke NR, Eng C, Berk AJ',
'description' => '<p>How histone acetylation promotes transcription is not clearly understood. Here, we confirm an interaction between p300 and the adenovirus 2 large E1A activation domain (AD) and map the interacting regions in E1A by observing colocalization at an integrated array of fusions of LacI-mCherry to E1A fragments with YFP-p300. Viruses with mutations in E1A subdomains were constructed and analyzed for kinetics of early viral RNA expression and association of acetylated H3K9, K18, K27, TBP, and RNA polymerase II (Pol II) across the viral genome. The results indicate that this E1A interaction with p300 is required for H3K18 and H3K27 acetylation at the E2early, E3, and E4 promoters and is required for TBP and Pol II association with the E2early promoter. In contrast, H3K18/27 acetylation was not required for TBP and Pol II association with the E3 and E4 promoters but was required for E4 transcription at a step subsequent to Pol II preinitiation complex assembly. Despite a wealth of data associating promoter and enhancer region histone N-terminal tail lysine acetylation with transcriptional activity, there are relatively few examples of studies that establish causation between these histone posttranslational modifications and transcription. While hypoacetylation of histone H3 lysines 18 and 27 is associated with repression, the step(s) in the overall process of transcription that is blocked at a hypoacetylated promoter is not clearly established in most instances. Studies presented here confirm that the adenovirus 2 large E1A protein activation domain interacts with p300, as reported previously (P. Pelka, J. N. G. Ablack, J. Torchia, A. S. Turnell, R. J. A. Grand, J. S. Mymryk, Nucleic Acids Res 1095-1106, 2009, https://doi.org/10.1093/nar/gkn1057), and that the resulting acetylation of H3K18/27 affects varied steps in transcription at different viral promoters.</p>',
'date' => '2018-09-15',
'pmid' => 'http://www.pubmed.gov/29976669 ',
'doi' => '10.1093/nar/gkn1057),',
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'description' => '<p>Chromosome condensation is a hallmark of mitosis in eukaryotes and is a prerequisite for faithful segregation of genetic material to daughter cells. Here we show that condensin, which is essential for assembling condensed chromosomes, helps to preclude the detrimental effects of gene transcription on mitotic condensation. ChIP-seq profiling reveals that the fission yeast condensin preferentially binds to active protein-coding genes in a transcription-dependent manner during mitosis. Pharmacological and genetic attenuation of transcription largely rescue bulk chromosome segregation defects observed in condensin mutants. We also demonstrate that condensin is associated with and reduces unwound DNA segments generated by transcription, providing a direct link between an in vitro activity of condensin and its in vivo function. The human condensin isoform condensin I also binds to unwound DNA regions at the transcription start sites of active genes, implying that our findings uncover a fundamental feature of condensin complexes.</p>',
'date' => '2015-07-23',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/26204128',
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'name' => 'A pro-apoptotic function of iASPP by stabilizing p300 and CBP through inhibition of BRMS1 E3 ubiquitin ligase activity.',
'authors' => 'Kramer D, Schön M, Bayerlová M, Bleckmann A, Schön MP, Zörnig M, Dobbelstein M',
'description' => 'The p53 family and its cofactors are potent inducers of apoptosis and form a barrier to cancer. Here, we investigated the impact of the supposedly inhibitory member of the apoptosis-stimulating protein of p53, iASPP, on the activity of the p53 homolog TAp73, and its cofactors p300 and CBP. We found that iASPP interacted with and stabilized the histone acetyltransferase p300 and its homolog CBP upon cisplatin treatment. Vice versa, iASPP depletion by shRNA resulted in decreased amounts of p300 and CBP, impaired binding of p300 and TAp73 to target site promoters, reduced induction of pro-apoptotic TAp73 target genes, and impaired apoptosis. Mechanistically, we observed that the p300-regulatory E3 ubiquitin ligase BRMS1 could rescue the degradation of p300 and CBP in cisplatin-treated, iASPP-depleted cells. This argues that iASPP stabilizes p300 and CBP by interfering with their BRMS1-mediated ubiquitination, thereby contributing to apoptotic susceptibility. In line, iASPP overexpression partially abolished the interaction of BRMS1 and CBP upon DNA damage. Reduced levels of iASPP mRNA and protein as well as CBP protein were observed in human melanoma compared with normal skin tissue and benign melanocytic nevi. In line with our findings, iASPP overexpression or knockdown of BRMS1 each augmented p300/CBP levels in melanoma cell lines, thereby enhancing apoptosis upon DNA damage. Taken together, destabilization of p300/CBP by downregulation of iASPP expression levels appears to represent a molecular mechanism that contributes to chemoresistance in melanoma cells.',
'date' => '2015-02-12',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25675294',
'doi' => '',
'modified' => '2015-07-24 15:39:05',
'created' => '2015-07-24 15:39:05',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'id' => '2424',
'name' => 'The unfolded protein response and the phosphorylations of activating transcription factor 2 in the trans-activation of il23a promoter produced by β-glucans.',
'authors' => 'Rodríguez M, Domingo E, Alonso S, Frade JG, Eiros J, Crespo MS, Fernández N',
'description' => 'Current views on the control of IL-23 production focus on the regulation of il23a, the gene encoding IL-23 p19, by NF-κB in combination with other transcription factors. C/EBP homologous protein (CHOP), X2-Box-binding protein 1 (XBP1), activator protein 1 (AP1), SMAD, CCAAT/enhancer-binding protein (C/EBPβ), and cAMP-response element-binding protein (CREB) have been involved in response to LPS, but no data are available regarding the mechanism triggered by the fungal mimic and β-glucan-containing stimulus zymosan, which produces IL-23 and to a low extent the related cytokine IL-12 p70. Zymosan induced the mobilization of CHOP from the nuclear fractions to phagocytic vesicles. Hypha-forming Candida also induced the nuclear disappearance of CHOP. Assay of transcription factor binding to the il23a promoter showed an increase of Thr(P)-71-Thr(P)-69-activating transcription factor 2 (ATF2) binding in response to zymosan. PKC and PKA/mitogen- and stress-activated kinase inhibitors down-regulated Thr(P)-71-ATF2 binding to the il23a promoter and il23a mRNA expression. Consistent with the current concept of complementary phosphorylations on N-terminal Thr-71 and Thr-69 of ATF2 by ERK and p38 MAPK, MEK, and p38 MAPK inhibitors blunted Thr(P)-69-ATF2 binding. Knockdown of atf2 mRNA with siRNA correlated with inhibition of il23a mRNA, but it did not affect the expression of il12/23b and il10 mRNA. These data indicate the following: (i) zymosan decreases nuclear proapoptotic CHOP, most likely by promoting its accumulation in phagocytic vesicles; (ii) zymosan-induced il23a mRNA expression is best explained through coordinated κB- and ATF2-dependent transcription; and (iii) il23a expression relies on complementary phosphorylation of ATF2 on Thr-69 and Thr-71 dependent on PKC and MAPK activities.',
'date' => '2014-08-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24982422',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'id' => '997',
'name' => 'ERG and FLI1 binding sites demarcate targets for aberrant epigenetic regulation by AML1-ETO in acute myeloid leukemia.',
'authors' => 'Martens JH, Mandoli A, Simmer F, Wierenga BJ, Saeed S, Singh AA, Altucci L, Vellenga E, Stunnenberg HG',
'description' => '<p>ERG and FLI1 are closely related members of the ETS family of transcription factors and have been identified as essential factors for the function and maintenance of normal hematopoietic stem cells. Here, genome-wide analysis revealed that both ERG and FLI1 occupy similar genomic regions as AML1-ETO in t(8;21) AMLs and identified ERG/FLI1 as proteins that facilitate binding of oncofusion protein complexes. In addition, we demonstrate that ERG and FLI1 bind the RUNX1 promoter and that shRNA mediated silencing of ERG leads to reduced expression of RUNX1 and AML1-ETO, consistent with a role of ERG in transcriptional activation of these proteins. Finally, we identify H3 acetylation as the epigenetic mark preferentially associated with ETS factor binding. This intimate connection between ERG/FLI1 binding and H3 acetylation implies that one of the molecular strategies of oncofusion proteins such as AML1-ETO and PML-RARα involves the targeting of histone deacetylase activities to ERG/FLI1 bound hematopoietic regulatory sites. Together these results highlight the dual importance of ETS factors in t(8;21) leukemogenesis, both as transcriptional regulators of the oncofusion protein itself as well as proteins that facilitate AML1-ETO binding.</p>',
'date' => '2012-09-14',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22983443',
'doi' => '',
'modified' => '2016-05-03 12:14:08',
'created' => '2015-07-24 15:38:59',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 8 => array(
'id' => '795',
'name' => 'Recruitment of histone deacetylase 3 to the interferon-a gene promoters attenuates interferon expression.',
'authors' => 'Génin P, Lin R, Hiscott J, Civas A',
'description' => 'BACKGROUND: Induction of Type I Interferon (IFN) genes constitutes an essential step leading to innate immune responses during virus infection. Sendai virus (SeV) infection of B lymphoid Namalwa cells transiently induces the transcriptional expression of multiple IFN-A genes. Although transcriptional activation of IFN-A genes has been extensively studied, the mechanism responsible for the attenuation of their expression remains to be determined. PRINCIPAL FINDINGS: In this study, we demonstrate that virus infection of Namalwa cells induces transient recruitment of HDAC3 (histone deacetylase 3) to IFN-A promoters. Analysis of chromatin-protein association by Chip-QPCR demonstrated that recruitment of interferon regulatory factor (IRF)3 and IRF7, as well as TBP correlated with enhanced histone H3K9 and H3K14 acetylation, whereas recruitment of HDAC3 correlated with inhibition of histone H3K9/K14 acetylation, removal of IRF7 and TATA-binding protein (TBP) from IFN-A promoters and inhibition of virus-induced IFN-A gene transcription. Additionally, HDAC3 overexpression reduced, and HDAC3 depletion by siRNA enhanced IFN-A gene expression. Furthermore, activation of IRF7 enhanced histone H3K9/K14 acetylation and IFN-A gene expression, whereas activation of both IRF7 and IRF3 led to recruitment of HDAC3 to the IFN-A gene promoters, resulting in impaired histone H3K9 acetylation and attenuation of IFN-A gene transcription. CONCLUSION: Altogether these data indicate that reversal of histone H3K9/K14 acetylation by HDAC3 is required for attenuation of IFN-A gene transcription during viral infection.',
'date' => '2012-06-07',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22685561',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'id' => '253',
'name' => 'Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes.',
'authors' => 'Rao NA, McCalman MT, Moulos P, Francoijs KJ, Chatziioannou A, Kolisis FN, Alexis MN, Mitsiou DJ, Stunnenberg HG',
'description' => 'Glucocorticoid receptor (GR) exerts anti-inflammatory action in part by antagonizing proinflammatory transcription factors such as the nuclear factor kappa-b (NFKB). Here, we assess the crosstalk of activated GR and RELA (p65, major NFKB component) by global identification of their binding sites and target genes. We show that coactivation of GR and p65 alters the repertoire of regulated genes and results in their association with novel sites in a mutually dependent manner. These novel sites predominantly cluster with p65 target genes that are antagonized by activated GR and vice versa. Our data show that coactivation of GR and NFKB alters signaling pathways that are regulated by each factor separately and provide insight into the networks underlying the GR and NFKB crosstalk.',
'date' => '2011-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21750107',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 10 => array(
'id' => '680',
'name' => 'Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters.',
'authors' => 'Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C, Eick D, Gut I, Ferrier P, Andrau JC',
'description' => 'Recent work has shown that RNA polymerase (Pol) II can be recruited to and transcribe distal regulatory regions. Here we analyzed transcription initiation and elongation through genome-wide localization of Pol II, general transcription factors (GTFs) and active chromatin in developing T cells. We show that Pol II and GTFs are recruited to known T cell-specific enhancers. We extend this observation to many new putative enhancers, a majority of which can be transcribed with or without polyadenylation. Importantly, we also identify genomic features called transcriptional initiation platforms (TIPs) that are characterized by large areas of Pol II and GTF recruitment at promoters, intergenic and intragenic regions. TIPs show variable widths (0.4-10 kb) and correlate with high CpG content and increased tissue specificity at promoters. Finally, we also report differential recruitment of TFIID and other GTFs at promoters and enhancers. Overall, we propose that TIPs represent important new regulatory hallmarks of the genome.',
'date' => '2011-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21765417',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 11 => array(
'id' => '290',
'name' => 'Role of p53 serine 46 in p53 target gene regulation.',
'authors' => 'Smeenk L, van Heeringen SJ, Koeppel M, Gilbert B, Janssen-Megens E, Stunnenberg HG, Lohrum M',
'description' => 'The tumor suppressor p53 plays a crucial role in cellular growth control inducing a plethora of different response pathways. The molecular mechanisms that discriminate between the distinct p53-responses have remained largely elusive. Here, we have analyzed the p53-regulated pathways induced by Actinomycin D and Etoposide treatment resulting in more growth arrested versus apoptotic cells respectively. We found that the genome-wide p53 DNA-binding patterns are almost identical upon both treatments notwithstanding transcriptional differences that we observed in global transcriptome analysis. To assess the role of post-translational modifications in target gene choice and activation we investigated the genome-wide level of phosphorylation of Serine 46 of p53 bound to DNA (p53-pS46) and of Serine 15 (p53-pS15). Interestingly, the extent of S46 phosphorylation of p53 bound to DNA is considerably higher in cells directed towards apoptosis while the degree of phosphorylation at S15 remains highly similar. Moreover, our data suggest that following different chemotherapeutical treatments, the amount of chromatin-associated p53 phosphorylated at S46 but not at pS15 is higher on certain apoptosis related target genes. Our data provide evidence that cell fate decisions are not made primarily on the level of general p53 DNA-binding and that post-translationally modified p53 can have distinct DNA-binding characteristics.',
'date' => '2011-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21394211',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 12 => array(
'id' => '512',
'name' => 'Control of the differentiation of regulatory T cells and T(H)17 cells by the DNA-binding inhibitor Id3.',
'authors' => 'Maruyama T, Li J, Vaque JP, Konkel JE, Wang W, Zhang B, Zhang P, Zamarron BF, Yu D, Wu Y, Zhuang Y, Gutkind JS, Chen W',
'description' => 'The molecular mechanisms that direct transcription of the gene encoding the transcription factor Foxp3 in CD4(+) T cells remain ill-defined. We show here that deletion of the DNA-binding inhibitor Id3 resulted in the defective generation of Foxp3(+) regulatory T cells (T(reg) cells). We identify two transforming growth factor-β1 (TGF-β1)-dependent mechanisms that were vital for activation of Foxp3 transcription and were defective in Id3(-/-) CD4(+) T cells. Enhanced binding of the transcription factor E2A to the Foxp3 promoter promoted Foxp3 transcription. Id3 was required for relief of inhibition by the transcription factor GATA-3 at the Foxp3 promoter. Furthermore, Id3(-/-) T cells showed greater differentiation into the T(H)17 subset of helper T cells in vitro and in a mouse asthma model. Therefore, a network of factors acts in a TGF-β-dependent manner to control Foxp3 expression and inhibit the development of T(H)17 cells.',
'date' => '2010-12-05',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21131965',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 13 => array(
'id' => '117',
'name' => 'High-resolution analysis of epigenetic changes associated with X inactivation.',
'authors' => 'Marks H, Chow JC, Denissov S, Françoijs KJ, Brockdorff N, Heard E, Stunnenberg HG',
'description' => 'Differentiation of female murine ES cells triggers silencing of one X chromosome through X-chromosome inactivation (XCI). Immunofluorescence studies showed that soon after Xist RNA coating the inactive X (Xi) undergoes many heterochromatic changes, including the acquisition of H3K27me3. However, the mechanisms that lead to the establishment of heterochromatin remain unclear. We first analyze chromatin changes by ChIP-chip, as well as RNA expression, around the X-inactivation center (Xic) in female and male ES cells, and their day 4 and 10 differentiated derivatives. A dynamic epigenetic landscape is observed within the Xic locus. Tsix repression is accompanied by deposition of H3K27me3 at its promoter during differentiation of both female and male cells. However, only in female cells does an active epigenetic landscape emerge at the Xist locus, concomitant with high Xist expression. Several regions within and around the Xic show unsuspected chromatin changes, and we define a series of unusual loci containing highly enriched H3K27me3. Genome-wide ChIP-seq analyses show a female-specific quantitative increase of H3K27me3 across the X chromosome as XCI proceeds in differentiating female ES cells. Using female ES cells with nonrandom XCI and polymorphic X chromosomes, we demonstrate that this increase is specific to the Xi by allele-specific SNP mapping of the ChIP-seq tags. H3K27me3 becomes evenly associated with the Xi in a chromosome-wide fashion. A selective and robust increase of H3K27me3 and concomitant decrease in H3K4me3 is observed over active genes. This indicates that deposition of H3K27me3 during XCI is tightly associated with the act of silencing of individual genes across the Xi.',
'date' => '2009-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19581487',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 14 => array(
'id' => '89',
'name' => 'TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation.',
'authors' => 'Pitulescu ME, Teichmann M, Luo L, Kessel M',
'description' => 'BACKGROUND: The re-replication inhibitor Geminin binds to several transcription factors including homeodomain proteins, and to members of the polycomb and the SWI/SNF complexes. RESULTS: Here we describe the TATA-binding protein-like factor-interacting protein (TIPT) isoform 2, as a strong binding partner of Geminin. TIPT2 is widely expressed in mouse embryonic and adult tissues, residing both in cyto- and nucleoplasma, and enriched in the nucleolus. Like Geminin, also TIPT2 interacts with several polycomb factors, with the general transcription factor TBP (TATA box binding protein), and with the related protein TBPL1 (TRF2). TIPT2 synergizes with geminin and TBP in the activation of TATA box-containing promoters, and with TBPL1 and geminin in the activation of the TATA-less NF1 promoter. Geminin and TIPT2 were detected in the chromatin near TBP/TBPL1 binding sites. CONCLUSION: Together, our study introduces a novel transcriptional regulator and its function in cooperation with chromatin associated factors and the basal transcription machinery.',
'date' => '2009-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19515240',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 15 => array(
'id' => '844',
'name' => 'Identification of novel functional TBP-binding sites and general factor repertoires',
'authors' => 'Denissov S, van Driel M, Voit R, Hekkelman M, Hulsen T, Hernandez N, Grummt I, Wehrens R, Stunnenberg H.',
'description' => 'Our current knowledge of the general factor requirement in transcription by the three mammalian RNA polymerases is based on a small number of model promoters. Here, we present a comprehensive chromatin immunoprecipitation (ChIP)-on-chip analysis for 28 transcription factors on a large set of known and novel TATA-binding protein (TBP)-binding sites experimentally identified via ChIP cloning. A large fraction of identified TBP-binding sites is located in introns or lacks a gene/mRNA annotation and is found to direct transcription. Integrated analysis of the ChIP-on-chip data and functional studies revealed that TAF12 hitherto regarded as RNA polymerase II (RNAP II)-specific was found to be also involved in RNAP I transcription. Distinct profiles for general transcription factors and TAF-containing complexes were uncovered for RNAP II promoters located in CpG and non-CpG islands suggesting distinct transcription initiation pathways. Our study broadens the spectrum of general transcription factor function and uncovers a plethora of novel, functional TBP-binding sites in the human genome.',
'date' => '2007-02-21',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/17268553',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
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[maximum depth reached]
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<p><small><strong>Figure 2 ChIP results obtained with the Diagenode monoclonal antibody against TBP </strong><br />ChIP assays were performed using U2OS cells, the Diagenode antibody directed against TBP (Cat. No. C15200002) and optimized primer sets for qPCR. Sheared chromatin from 1x10e6 cells and 4 μg of antibody were used per ChIP experiment. QPCR was performed with primers for the promoter of the c-fos and GAPDH genes (Cat. No. C17011004 and C17011001), a region 0.5 and 1 kb upstream of the GAPDH promoter (Cat. No. C17011002 and C17011003), respectively, and for exon 2 of the myoglobin gene (cat. No. C17011006) as a negative control. Figure 1 shows the recovery (the relative amount of immunoprecipitated DNA compared to input DNA) and the occupancy (ratio +/- control target). These results demonstrate the occupancy of both promoters by TBP.</small></p>
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<p><small><strong> Figure 3. Western blot analysis using the Diagenode monoclonal antibody directed against TBP</strong><br />Whole cell extracts (40 μg) from HeLa cells transfected with TBP siRNA (lane 2) and from an untransfected control (lane 1) were analysed by Western blot using the Diagenode antibody against TBP (Cat. No. C15200002) diluted 1:500 in TBSTween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<p><small><strong>Figure 1 ChIP-seq results obtained with the Diagenode monoclonal antibody directed against TBP </strong><br />ChIP was performed with 5 μg of the Diagenode antibody against TBP (Cat. No. C15200002) on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022) on the IP-Star automated system. The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoters of the active GAPDH and c-fos genes, used as positive control targets, and for a region 1 kb upstream of the GAPDH promoter and the coding region of the inactive MB gene, used as negative control targets (figure 2A). The IP’d DNA was subsequently analysed with an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2 shows the peak distribution in 50 kb regions surrounding the GAPDH, c-fos, ACTB and MCL1 genes (figure 2B, C, D and E, respectively). These results clearly show a localisation of TBP at the promoters of actively transcribed genes.</small></p>
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<p><small><strong>Figure 2 ChIP results obtained with the Diagenode monoclonal antibody against TBP </strong><br />ChIP assays were performed using U2OS cells, the Diagenode antibody directed against TBP (Cat. No. C15200002) and optimized primer sets for qPCR. Sheared chromatin from 1x10e6 cells and 4 μg of antibody were used per ChIP experiment. QPCR was performed with primers for the promoter of the c-fos and GAPDH genes (Cat. No. C17011004 and C17011001), a region 0.5 and 1 kb upstream of the GAPDH promoter (Cat. No. C17011002 and C17011003), respectively, and for exon 2 of the myoglobin gene (cat. No. C17011006) as a negative control. Figure 1 shows the recovery (the relative amount of immunoprecipitated DNA compared to input DNA) and the occupancy (ratio +/- control target). These results demonstrate the occupancy of both promoters by TBP.</small></p>
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<div class="row">
<div class="small-3 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15200002-wb.png" alt="TBP Antibody validated in Western Blot" style="display: block; margin-left: auto; margin-right: auto;" /></p>
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<div class="small-9 columns">
<p><small><strong> Figure 3. Western blot analysis using the Diagenode monoclonal antibody directed against TBP</strong><br />Whole cell extracts (40 μg) from HeLa cells transfected with TBP siRNA (lane 2) and from an untransfected control (lane 1) were analysed by Western blot using the Diagenode antibody against TBP (Cat. No. C15200002) diluted 1:500 in TBSTween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<td>ChIP/ChIP-seq <sup>*</sup></td>
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<p><span>Monoclonal antibody raised in mouse against the amino-terminal domain of human <strong>TBP (TATA box binding protein).</strong></span></p>',
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<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-1.png" alt="TBP Antibody ChIP Grade" style="display: block; margin-left: auto; margin-right: auto;" /></div>
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<p><small><strong>Figure 1 ChIP-seq results obtained with the Diagenode monoclonal antibody directed against TBP </strong><br />ChIP was performed with 5 μg of the Diagenode antibody against TBP (Cat. No. C15200002) on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022) on the IP-Star automated system. The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoters of the active GAPDH and c-fos genes, used as positive control targets, and for a region 1 kb upstream of the GAPDH promoter and the coding region of the inactive MB gene, used as negative control targets (figure 2A). The IP’d DNA was subsequently analysed with an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2 shows the peak distribution in 50 kb regions surrounding the GAPDH, c-fos, ACTB and MCL1 genes (figure 2B, C, D and E, respectively). These results clearly show a localisation of TBP at the promoters of actively transcribed genes.</small></p>
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<div class="small-12 columns">A. <img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-2.png" alt="TBP Antibody - ChIP-seq Grade" style="display: block; margin-left: auto; margin-right: auto;" /><br /> B. <img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-3.png" alt="TBP Antibody for ChIP-seq" style="display: block; margin-left: auto; margin-right: auto;" /><br /> C. <img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-4.png" alt="TBP Antibody for ChIP-seq assay" style="display: block; margin-left: auto; margin-right: auto;" /><br /> D. <img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-5.png" alt="TBP Antibody validated in ChIP-seq" style="display: block; margin-left: auto; margin-right: auto;" /></div>
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<p><small><strong>Figure 2 ChIP results obtained with the Diagenode monoclonal antibody against TBP </strong><br />ChIP assays were performed using U2OS cells, the Diagenode antibody directed against TBP (Cat. No. C15200002) and optimized primer sets for qPCR. Sheared chromatin from 1x10e6 cells and 4 μg of antibody were used per ChIP experiment. QPCR was performed with primers for the promoter of the c-fos and GAPDH genes (Cat. No. C17011004 and C17011001), a region 0.5 and 1 kb upstream of the GAPDH promoter (Cat. No. C17011002 and C17011003), respectively, and for exon 2 of the myoglobin gene (cat. No. C17011006) as a negative control. Figure 1 shows the recovery (the relative amount of immunoprecipitated DNA compared to input DNA) and the occupancy (ratio +/- control target). These results demonstrate the occupancy of both promoters by TBP.</small></p>
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<div class="row">
<div class="small-3 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15200002-wb.png" alt="TBP Antibody validated in Western Blot" style="display: block; margin-left: auto; margin-right: auto;" /></p>
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<p><small><strong> Figure 3. Western blot analysis using the Diagenode monoclonal antibody directed against TBP</strong><br />Whole cell extracts (40 μg) from HeLa cells transfected with TBP siRNA (lane 2) and from an untransfected control (lane 1) were analysed by Western blot using the Diagenode antibody against TBP (Cat. No. C15200002) diluted 1:500 in TBSTween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<p>Learn more about: <a href="https://www.diagenode.com/applications/western-blot">Loading control, MW marker visualization</a><em>. <br /></em></p>
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<div class="small-10 columns">
<h3>Epigenetic antibodies you can trust!</h3>
<p>Antibody quality is essential for assay success. Diagenode offers antibodies that are actually validated and have been widely used and published by the scientific community. Now we are adding a new level of siRNA knockdown validation to assure the specificity of our non-histone antibodies.</p>
<p><strong>Short interfering RNA (siRNA)</strong> degrades target mRNA, followed by the knock-down of protein production. If the antibody that recognizes the protein of interest is specific, the Western blot of siRNA-treated cells will show a significant reduction of signal vs. untreated cells.</p>
<center><img src="https://www.diagenode.com/emailing/images/C15100144-wb.png" alt="" /></center>
<p class="text-center"><small>WB results obtained with the HDAC1 pAb (Cat. No. C15100144) <br />on siRNA transfected cells (lane 2) and on untransfected control cells (lane 1).</small></p>
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<p><img src="https://www.diagenode.com/emailing/images/epi-success-guaranteed-icon.png" alt="Epigenetic success guaranteed" /></p>
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<p style="text-align: left;"><span style="font-weight: 400;">The below list shows our first siRNA validated antibodies. More results - coming soon</span>.</p>',
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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
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<p><span style="font-weight: 400;">Diagenode provides leading solutions for epigenetic research. Because ChIP-seq is a widely-used technique, we validate our antibodies in ChIP and ChIP-seq experiments (in addition to conventional methods like Western blot, Dot blot, ELISA, and immunofluorescence) to provide the highest quality antibody. We standardize our validation and production to guarantee high product quality without technical bias. Diagenode guarantees ChIP-seq grade antibody performance under our suggested conditions.</span></p>
<div class="row">
<div class="small-12 medium-9 large-9 columns">
<p><strong>ChIP-seq profile</strong> of active (H3K4me3 and H3K36me3) and inactive (H3K27me3) marks using Diagenode antibodies.</p>
<img src="https://www.diagenode.com/img/categories/antibodies/chip-seq-grade-antibodies.png" /></div>
<div class="small-12 medium-3 large-3 columns">
<p><small> ChIP was performed on sheared chromatin from 100,000 K562 cells using iDeal ChIP-seq kit for Histones (cat. No. C01010051) with 1 µg of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 µg of the antibody against H3K36me3 (cat. No. C15410192). The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. The figure shows the signal distribution along the complete sequence of human chromosome 3, a zoomin to a 10 Mb region and a further zoomin to a 1.5 Mb region. </small></p>
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<p>Diagenode’s highly validated antibodies:</p>
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<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
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<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
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<div class="small-12 medium-6 large-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" alt="" width="400" height="315" /> </div>
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<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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'name' => 'Antibodies you can trust',
'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
'image_id' => null,
'type' => 'Poster',
'url' => 'files/posters/Antibodies_you_can_trust_Poster.pdf',
'slug' => 'antibodies-you-can-trust-poster',
'meta_keywords' => '',
'meta_description' => '',
'modified' => '2015-10-01 20:18:31',
'created' => '2015-07-03 16:05:15',
'ProductsDocument' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'id' => '38',
'name' => 'Epigenetic Antibodies Brochure',
'description' => '<p>More than in any other immuoprecipitation assays, quality antibodies are critical tools in many epigenetics experiments. Since 10 years, Diagenode has developed the most stringent quality production available on the market for antibodies exclusively focused on epigenetic uses. All our antibodies have been qualified to work in epigenetic applications.</p>',
'image_id' => null,
'type' => 'Brochure',
'url' => 'files/brochures/Epigenetic_Antibodies_Brochure.pdf',
'slug' => 'epigenetic-antibodies-brochure',
'meta_keywords' => '',
'meta_description' => '',
'modified' => '2016-06-15 11:24:06',
'created' => '2015-07-03 16:05:27',
'ProductsDocument' => array(
[maximum depth reached]
)
)
),
'Feature' => array(),
'Image' => array(
(int) 0 => array(
'id' => '1783',
'name' => 'product/antibodies/chipseq-grade-ab-icon.png',
'alt' => 'ChIP-seq Grade',
'modified' => '2020-11-27 07:04:40',
'created' => '2018-03-15 15:54:09',
'ProductsImage' => array(
[maximum depth reached]
)
)
),
'Promotion' => array(),
'Protocol' => array(),
'Publication' => array(
(int) 0 => array(
'id' => '4834',
'name' => 'Enhanced frequency of transcription pre-initiation complexes assemblyafter exposure to UV irradiation results in increased repair activity andreduced probabilities for mutagenesis.',
'authors' => 'Liakos A. et al.',
'description' => '<p>In addition to being essential for gene expression, transcription is crucial for the maintenance of genome integrity. Here, we undertook a systematic approach, to monitor the assembly kinetics of the pre-initiating RNA Polymerase (Pol) II at promoters at steady state and different stages during recovery from UV irradiation-stress, when pre-initiation and initiation steps have been suggested to be transiently shut down. Taking advantage of the reversible dissociation of pre-initiating Pol II after high salt treatment, we found that de novo recruitment of the available Pol II molecules at active promoters not only persists upon UV at all times tested but occurs significantly faster in the early phase of recovery (2 h) than in unexposed human fibroblasts at the majority of active genes. Our method unveiled groups of genes with significantly different pre-initiation complex (PIC) assembly dynamics after UV that present distinct rates of UV-related mutational signatures in melanoma tumours, providing functional relevance to the importance of keeping transcription initiation active during UV recovery. Our findings uncover novel mechanistic insights further detailing the multilayered transcriptional response to genotoxic stress and link PIC assembly dynamics after exposure to genotoxins with cancer mutational landscapes.</p>',
'date' => '2023-07-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37470822',
'doi' => '10.1093/nar/gkad593',
'modified' => '2023-08-01 13:47:31',
'created' => '2023-08-01 15:59:38',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'id' => '4559',
'name' => 'A leukemia-protective germline variant mediates chromatin moduleformation via transcription factor nucleation.',
'authors' => 'Llimos G. et al.',
'description' => '<p>Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named "variable chromatin modules" (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect a VCM-modulating noncoding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a large change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with subtle, long-range chromatin compaction and robust AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology.</p>',
'date' => '2022-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35440565',
'doi' => '10.1038/s41467-022-29625-6',
'modified' => '2022-11-24 10:00:25',
'created' => '2022-11-24 08:49:52',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'id' => '3805',
'name' => 'R-Loops Promote Antisense Transcription across the Mammalian Genome',
'authors' => 'Tan-Wong Sue Mei, Dhir Somdutta, Proudfoot Nick J.',
'description' => '<p>Widespread antisense long noncoding RNA (lncRNA) overlap with many protein-coding genes in mammals and emanate from gene promoter, enhancer, and termination regions. However, their origin and biological purpose remain unclear. We show that these antisense lncRNA can be generated by R-loops that form when nascent transcript invades the DNA duplex behind elongating RNA polymerase II (Pol II). Biochemically, R-loops act as intrinsic Pol II promoters to induce de novo RNA synthesis. Furthermore, their removal across the human genome by RNase H1 overexpression causes the selective reduction of antisense transcription. Consequently, we predict that R-loops act to facilitate the synthesis of many gene proximal antisense lncRNA. Not only are R-loops widely associated with DNA damage and repair, but we now show that they have the capacity to promote de novo transcript synthesis that may have aided the evolution of gene regulation.</p>',
'date' => '2019-11-21',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/31679819',
'doi' => '10.1016/j.molcel.2019.10.002',
'modified' => '2019-12-05 11:23:13',
'created' => '2019-12-02 15:25:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'id' => '3415',
'name' => 'Adenovirus E1A Activation Domain Regulates H3 Acetylation Affecting Varied Steps in Transcription at Different Viral Promoters.',
'authors' => 'Hsu E, Pennella MA, Zemke NR, Eng C, Berk AJ',
'description' => '<p>How histone acetylation promotes transcription is not clearly understood. Here, we confirm an interaction between p300 and the adenovirus 2 large E1A activation domain (AD) and map the interacting regions in E1A by observing colocalization at an integrated array of fusions of LacI-mCherry to E1A fragments with YFP-p300. Viruses with mutations in E1A subdomains were constructed and analyzed for kinetics of early viral RNA expression and association of acetylated H3K9, K18, K27, TBP, and RNA polymerase II (Pol II) across the viral genome. The results indicate that this E1A interaction with p300 is required for H3K18 and H3K27 acetylation at the E2early, E3, and E4 promoters and is required for TBP and Pol II association with the E2early promoter. In contrast, H3K18/27 acetylation was not required for TBP and Pol II association with the E3 and E4 promoters but was required for E4 transcription at a step subsequent to Pol II preinitiation complex assembly. Despite a wealth of data associating promoter and enhancer region histone N-terminal tail lysine acetylation with transcriptional activity, there are relatively few examples of studies that establish causation between these histone posttranslational modifications and transcription. While hypoacetylation of histone H3 lysines 18 and 27 is associated with repression, the step(s) in the overall process of transcription that is blocked at a hypoacetylated promoter is not clearly established in most instances. Studies presented here confirm that the adenovirus 2 large E1A protein activation domain interacts with p300, as reported previously (P. Pelka, J. N. G. Ablack, J. Torchia, A. S. Turnell, R. J. A. Grand, J. S. Mymryk, Nucleic Acids Res 1095-1106, 2009, https://doi.org/10.1093/nar/gkn1057), and that the resulting acetylation of H3K18/27 affects varied steps in transcription at different viral promoters.</p>',
'date' => '2018-09-15',
'pmid' => 'http://www.pubmed.gov/29976669 ',
'doi' => '10.1093/nar/gkn1057),',
'modified' => '2018-12-31 11:29:42',
'created' => '2018-12-04 09:51:07',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'id' => '2872',
'name' => 'Condensin targets and reduces unwound DNA structures associated with transcription in mitotic chromosome condensation',
'authors' => 'Sutani T, Sakata T, Nakato R, Masuda K, Ishibashi M, Yamashita D, Suzuki Y, Hirano T, Bando M, Shirahige K',
'description' => '<p>Chromosome condensation is a hallmark of mitosis in eukaryotes and is a prerequisite for faithful segregation of genetic material to daughter cells. Here we show that condensin, which is essential for assembling condensed chromosomes, helps to preclude the detrimental effects of gene transcription on mitotic condensation. ChIP-seq profiling reveals that the fission yeast condensin preferentially binds to active protein-coding genes in a transcription-dependent manner during mitosis. Pharmacological and genetic attenuation of transcription largely rescue bulk chromosome segregation defects observed in condensin mutants. We also demonstrate that condensin is associated with and reduces unwound DNA segments generated by transcription, providing a direct link between an in vitro activity of condensin and its in vivo function. The human condensin isoform condensin I also binds to unwound DNA regions at the transcription start sites of active genes, implying that our findings uncover a fundamental feature of condensin complexes.</p>',
'date' => '2015-07-23',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/26204128',
'doi' => '10.1038/ncomms8815',
'modified' => '2016-03-25 11:03:02',
'created' => '2016-03-25 11:03:02',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '2593',
'name' => 'A pro-apoptotic function of iASPP by stabilizing p300 and CBP through inhibition of BRMS1 E3 ubiquitin ligase activity.',
'authors' => 'Kramer D, Schön M, Bayerlová M, Bleckmann A, Schön MP, Zörnig M, Dobbelstein M',
'description' => 'The p53 family and its cofactors are potent inducers of apoptosis and form a barrier to cancer. Here, we investigated the impact of the supposedly inhibitory member of the apoptosis-stimulating protein of p53, iASPP, on the activity of the p53 homolog TAp73, and its cofactors p300 and CBP. We found that iASPP interacted with and stabilized the histone acetyltransferase p300 and its homolog CBP upon cisplatin treatment. Vice versa, iASPP depletion by shRNA resulted in decreased amounts of p300 and CBP, impaired binding of p300 and TAp73 to target site promoters, reduced induction of pro-apoptotic TAp73 target genes, and impaired apoptosis. Mechanistically, we observed that the p300-regulatory E3 ubiquitin ligase BRMS1 could rescue the degradation of p300 and CBP in cisplatin-treated, iASPP-depleted cells. This argues that iASPP stabilizes p300 and CBP by interfering with their BRMS1-mediated ubiquitination, thereby contributing to apoptotic susceptibility. In line, iASPP overexpression partially abolished the interaction of BRMS1 and CBP upon DNA damage. Reduced levels of iASPP mRNA and protein as well as CBP protein were observed in human melanoma compared with normal skin tissue and benign melanocytic nevi. In line with our findings, iASPP overexpression or knockdown of BRMS1 each augmented p300/CBP levels in melanoma cell lines, thereby enhancing apoptosis upon DNA damage. Taken together, destabilization of p300/CBP by downregulation of iASPP expression levels appears to represent a molecular mechanism that contributes to chemoresistance in melanoma cells.',
'date' => '2015-02-12',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25675294',
'doi' => '',
'modified' => '2015-07-24 15:39:05',
'created' => '2015-07-24 15:39:05',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'id' => '2424',
'name' => 'The unfolded protein response and the phosphorylations of activating transcription factor 2 in the trans-activation of il23a promoter produced by β-glucans.',
'authors' => 'Rodríguez M, Domingo E, Alonso S, Frade JG, Eiros J, Crespo MS, Fernández N',
'description' => 'Current views on the control of IL-23 production focus on the regulation of il23a, the gene encoding IL-23 p19, by NF-κB in combination with other transcription factors. C/EBP homologous protein (CHOP), X2-Box-binding protein 1 (XBP1), activator protein 1 (AP1), SMAD, CCAAT/enhancer-binding protein (C/EBPβ), and cAMP-response element-binding protein (CREB) have been involved in response to LPS, but no data are available regarding the mechanism triggered by the fungal mimic and β-glucan-containing stimulus zymosan, which produces IL-23 and to a low extent the related cytokine IL-12 p70. Zymosan induced the mobilization of CHOP from the nuclear fractions to phagocytic vesicles. Hypha-forming Candida also induced the nuclear disappearance of CHOP. Assay of transcription factor binding to the il23a promoter showed an increase of Thr(P)-71-Thr(P)-69-activating transcription factor 2 (ATF2) binding in response to zymosan. PKC and PKA/mitogen- and stress-activated kinase inhibitors down-regulated Thr(P)-71-ATF2 binding to the il23a promoter and il23a mRNA expression. Consistent with the current concept of complementary phosphorylations on N-terminal Thr-71 and Thr-69 of ATF2 by ERK and p38 MAPK, MEK, and p38 MAPK inhibitors blunted Thr(P)-69-ATF2 binding. Knockdown of atf2 mRNA with siRNA correlated with inhibition of il23a mRNA, but it did not affect the expression of il12/23b and il10 mRNA. These data indicate the following: (i) zymosan decreases nuclear proapoptotic CHOP, most likely by promoting its accumulation in phagocytic vesicles; (ii) zymosan-induced il23a mRNA expression is best explained through coordinated κB- and ATF2-dependent transcription; and (iii) il23a expression relies on complementary phosphorylation of ATF2 on Thr-69 and Thr-71 dependent on PKC and MAPK activities.',
'date' => '2014-08-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24982422',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'id' => '997',
'name' => 'ERG and FLI1 binding sites demarcate targets for aberrant epigenetic regulation by AML1-ETO in acute myeloid leukemia.',
'authors' => 'Martens JH, Mandoli A, Simmer F, Wierenga BJ, Saeed S, Singh AA, Altucci L, Vellenga E, Stunnenberg HG',
'description' => '<p>ERG and FLI1 are closely related members of the ETS family of transcription factors and have been identified as essential factors for the function and maintenance of normal hematopoietic stem cells. Here, genome-wide analysis revealed that both ERG and FLI1 occupy similar genomic regions as AML1-ETO in t(8;21) AMLs and identified ERG/FLI1 as proteins that facilitate binding of oncofusion protein complexes. In addition, we demonstrate that ERG and FLI1 bind the RUNX1 promoter and that shRNA mediated silencing of ERG leads to reduced expression of RUNX1 and AML1-ETO, consistent with a role of ERG in transcriptional activation of these proteins. Finally, we identify H3 acetylation as the epigenetic mark preferentially associated with ETS factor binding. This intimate connection between ERG/FLI1 binding and H3 acetylation implies that one of the molecular strategies of oncofusion proteins such as AML1-ETO and PML-RARα involves the targeting of histone deacetylase activities to ERG/FLI1 bound hematopoietic regulatory sites. Together these results highlight the dual importance of ETS factors in t(8;21) leukemogenesis, both as transcriptional regulators of the oncofusion protein itself as well as proteins that facilitate AML1-ETO binding.</p>',
'date' => '2012-09-14',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22983443',
'doi' => '',
'modified' => '2016-05-03 12:14:08',
'created' => '2015-07-24 15:38:59',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 8 => array(
'id' => '795',
'name' => 'Recruitment of histone deacetylase 3 to the interferon-a gene promoters attenuates interferon expression.',
'authors' => 'Génin P, Lin R, Hiscott J, Civas A',
'description' => 'BACKGROUND: Induction of Type I Interferon (IFN) genes constitutes an essential step leading to innate immune responses during virus infection. Sendai virus (SeV) infection of B lymphoid Namalwa cells transiently induces the transcriptional expression of multiple IFN-A genes. Although transcriptional activation of IFN-A genes has been extensively studied, the mechanism responsible for the attenuation of their expression remains to be determined. PRINCIPAL FINDINGS: In this study, we demonstrate that virus infection of Namalwa cells induces transient recruitment of HDAC3 (histone deacetylase 3) to IFN-A promoters. Analysis of chromatin-protein association by Chip-QPCR demonstrated that recruitment of interferon regulatory factor (IRF)3 and IRF7, as well as TBP correlated with enhanced histone H3K9 and H3K14 acetylation, whereas recruitment of HDAC3 correlated with inhibition of histone H3K9/K14 acetylation, removal of IRF7 and TATA-binding protein (TBP) from IFN-A promoters and inhibition of virus-induced IFN-A gene transcription. Additionally, HDAC3 overexpression reduced, and HDAC3 depletion by siRNA enhanced IFN-A gene expression. Furthermore, activation of IRF7 enhanced histone H3K9/K14 acetylation and IFN-A gene expression, whereas activation of both IRF7 and IRF3 led to recruitment of HDAC3 to the IFN-A gene promoters, resulting in impaired histone H3K9 acetylation and attenuation of IFN-A gene transcription. CONCLUSION: Altogether these data indicate that reversal of histone H3K9/K14 acetylation by HDAC3 is required for attenuation of IFN-A gene transcription during viral infection.',
'date' => '2012-06-07',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22685561',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'id' => '253',
'name' => 'Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes.',
'authors' => 'Rao NA, McCalman MT, Moulos P, Francoijs KJ, Chatziioannou A, Kolisis FN, Alexis MN, Mitsiou DJ, Stunnenberg HG',
'description' => 'Glucocorticoid receptor (GR) exerts anti-inflammatory action in part by antagonizing proinflammatory transcription factors such as the nuclear factor kappa-b (NFKB). Here, we assess the crosstalk of activated GR and RELA (p65, major NFKB component) by global identification of their binding sites and target genes. We show that coactivation of GR and p65 alters the repertoire of regulated genes and results in their association with novel sites in a mutually dependent manner. These novel sites predominantly cluster with p65 target genes that are antagonized by activated GR and vice versa. Our data show that coactivation of GR and NFKB alters signaling pathways that are regulated by each factor separately and provide insight into the networks underlying the GR and NFKB crosstalk.',
'date' => '2011-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21750107',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 10 => array(
'id' => '680',
'name' => 'Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters.',
'authors' => 'Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C, Eick D, Gut I, Ferrier P, Andrau JC',
'description' => 'Recent work has shown that RNA polymerase (Pol) II can be recruited to and transcribe distal regulatory regions. Here we analyzed transcription initiation and elongation through genome-wide localization of Pol II, general transcription factors (GTFs) and active chromatin in developing T cells. We show that Pol II and GTFs are recruited to known T cell-specific enhancers. We extend this observation to many new putative enhancers, a majority of which can be transcribed with or without polyadenylation. Importantly, we also identify genomic features called transcriptional initiation platforms (TIPs) that are characterized by large areas of Pol II and GTF recruitment at promoters, intergenic and intragenic regions. TIPs show variable widths (0.4-10 kb) and correlate with high CpG content and increased tissue specificity at promoters. Finally, we also report differential recruitment of TFIID and other GTFs at promoters and enhancers. Overall, we propose that TIPs represent important new regulatory hallmarks of the genome.',
'date' => '2011-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21765417',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 11 => array(
'id' => '290',
'name' => 'Role of p53 serine 46 in p53 target gene regulation.',
'authors' => 'Smeenk L, van Heeringen SJ, Koeppel M, Gilbert B, Janssen-Megens E, Stunnenberg HG, Lohrum M',
'description' => 'The tumor suppressor p53 plays a crucial role in cellular growth control inducing a plethora of different response pathways. The molecular mechanisms that discriminate between the distinct p53-responses have remained largely elusive. Here, we have analyzed the p53-regulated pathways induced by Actinomycin D and Etoposide treatment resulting in more growth arrested versus apoptotic cells respectively. We found that the genome-wide p53 DNA-binding patterns are almost identical upon both treatments notwithstanding transcriptional differences that we observed in global transcriptome analysis. To assess the role of post-translational modifications in target gene choice and activation we investigated the genome-wide level of phosphorylation of Serine 46 of p53 bound to DNA (p53-pS46) and of Serine 15 (p53-pS15). Interestingly, the extent of S46 phosphorylation of p53 bound to DNA is considerably higher in cells directed towards apoptosis while the degree of phosphorylation at S15 remains highly similar. Moreover, our data suggest that following different chemotherapeutical treatments, the amount of chromatin-associated p53 phosphorylated at S46 but not at pS15 is higher on certain apoptosis related target genes. Our data provide evidence that cell fate decisions are not made primarily on the level of general p53 DNA-binding and that post-translationally modified p53 can have distinct DNA-binding characteristics.',
'date' => '2011-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21394211',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 12 => array(
'id' => '512',
'name' => 'Control of the differentiation of regulatory T cells and T(H)17 cells by the DNA-binding inhibitor Id3.',
'authors' => 'Maruyama T, Li J, Vaque JP, Konkel JE, Wang W, Zhang B, Zhang P, Zamarron BF, Yu D, Wu Y, Zhuang Y, Gutkind JS, Chen W',
'description' => 'The molecular mechanisms that direct transcription of the gene encoding the transcription factor Foxp3 in CD4(+) T cells remain ill-defined. We show here that deletion of the DNA-binding inhibitor Id3 resulted in the defective generation of Foxp3(+) regulatory T cells (T(reg) cells). We identify two transforming growth factor-β1 (TGF-β1)-dependent mechanisms that were vital for activation of Foxp3 transcription and were defective in Id3(-/-) CD4(+) T cells. Enhanced binding of the transcription factor E2A to the Foxp3 promoter promoted Foxp3 transcription. Id3 was required for relief of inhibition by the transcription factor GATA-3 at the Foxp3 promoter. Furthermore, Id3(-/-) T cells showed greater differentiation into the T(H)17 subset of helper T cells in vitro and in a mouse asthma model. Therefore, a network of factors acts in a TGF-β-dependent manner to control Foxp3 expression and inhibit the development of T(H)17 cells.',
'date' => '2010-12-05',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21131965',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 13 => array(
'id' => '117',
'name' => 'High-resolution analysis of epigenetic changes associated with X inactivation.',
'authors' => 'Marks H, Chow JC, Denissov S, Françoijs KJ, Brockdorff N, Heard E, Stunnenberg HG',
'description' => 'Differentiation of female murine ES cells triggers silencing of one X chromosome through X-chromosome inactivation (XCI). Immunofluorescence studies showed that soon after Xist RNA coating the inactive X (Xi) undergoes many heterochromatic changes, including the acquisition of H3K27me3. However, the mechanisms that lead to the establishment of heterochromatin remain unclear. We first analyze chromatin changes by ChIP-chip, as well as RNA expression, around the X-inactivation center (Xic) in female and male ES cells, and their day 4 and 10 differentiated derivatives. A dynamic epigenetic landscape is observed within the Xic locus. Tsix repression is accompanied by deposition of H3K27me3 at its promoter during differentiation of both female and male cells. However, only in female cells does an active epigenetic landscape emerge at the Xist locus, concomitant with high Xist expression. Several regions within and around the Xic show unsuspected chromatin changes, and we define a series of unusual loci containing highly enriched H3K27me3. Genome-wide ChIP-seq analyses show a female-specific quantitative increase of H3K27me3 across the X chromosome as XCI proceeds in differentiating female ES cells. Using female ES cells with nonrandom XCI and polymorphic X chromosomes, we demonstrate that this increase is specific to the Xi by allele-specific SNP mapping of the ChIP-seq tags. H3K27me3 becomes evenly associated with the Xi in a chromosome-wide fashion. A selective and robust increase of H3K27me3 and concomitant decrease in H3K4me3 is observed over active genes. This indicates that deposition of H3K27me3 during XCI is tightly associated with the act of silencing of individual genes across the Xi.',
'date' => '2009-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19581487',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 14 => array(
'id' => '89',
'name' => 'TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation.',
'authors' => 'Pitulescu ME, Teichmann M, Luo L, Kessel M',
'description' => 'BACKGROUND: The re-replication inhibitor Geminin binds to several transcription factors including homeodomain proteins, and to members of the polycomb and the SWI/SNF complexes. RESULTS: Here we describe the TATA-binding protein-like factor-interacting protein (TIPT) isoform 2, as a strong binding partner of Geminin. TIPT2 is widely expressed in mouse embryonic and adult tissues, residing both in cyto- and nucleoplasma, and enriched in the nucleolus. Like Geminin, also TIPT2 interacts with several polycomb factors, with the general transcription factor TBP (TATA box binding protein), and with the related protein TBPL1 (TRF2). TIPT2 synergizes with geminin and TBP in the activation of TATA box-containing promoters, and with TBPL1 and geminin in the activation of the TATA-less NF1 promoter. Geminin and TIPT2 were detected in the chromatin near TBP/TBPL1 binding sites. CONCLUSION: Together, our study introduces a novel transcriptional regulator and its function in cooperation with chromatin associated factors and the basal transcription machinery.',
'date' => '2009-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19515240',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 15 => array(
'id' => '844',
'name' => 'Identification of novel functional TBP-binding sites and general factor repertoires',
'authors' => 'Denissov S, van Driel M, Voit R, Hekkelman M, Hulsen T, Hernandez N, Grummt I, Wehrens R, Stunnenberg H.',
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<p><small><strong>Figure 1 ChIP-seq results obtained with the Diagenode monoclonal antibody directed against TBP </strong><br />ChIP was performed with 5 μg of the Diagenode antibody against TBP (Cat. No. C15200002) on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022) on the IP-Star automated system. The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoters of the active GAPDH and c-fos genes, used as positive control targets, and for a region 1 kb upstream of the GAPDH promoter and the coding region of the inactive MB gene, used as negative control targets (figure 2A). The IP’d DNA was subsequently analysed with an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2 shows the peak distribution in 50 kb regions surrounding the GAPDH, c-fos, ACTB and MCL1 genes (figure 2B, C, D and E, respectively). These results clearly show a localisation of TBP at the promoters of actively transcribed genes.</small></p>
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<p><small><strong>Figure 2 ChIP results obtained with the Diagenode monoclonal antibody against TBP </strong><br />ChIP assays were performed using U2OS cells, the Diagenode antibody directed against TBP (Cat. No. C15200002) and optimized primer sets for qPCR. Sheared chromatin from 1x10e6 cells and 4 μg of antibody were used per ChIP experiment. QPCR was performed with primers for the promoter of the c-fos and GAPDH genes (Cat. No. C17011004 and C17011001), a region 0.5 and 1 kb upstream of the GAPDH promoter (Cat. No. C17011002 and C17011003), respectively, and for exon 2 of the myoglobin gene (cat. No. C17011006) as a negative control. Figure 1 shows the recovery (the relative amount of immunoprecipitated DNA compared to input DNA) and the occupancy (ratio +/- control target). These results demonstrate the occupancy of both promoters by TBP.</small></p>
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<p><small><strong> Figure 3. Western blot analysis using the Diagenode monoclonal antibody directed against TBP</strong><br />Whole cell extracts (40 μg) from HeLa cells transfected with TBP siRNA (lane 2) and from an untransfected control (lane 1) were analysed by Western blot using the Diagenode antibody against TBP (Cat. No. C15200002) diluted 1:500 in TBSTween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<p>Learn more about: <a href="https://www.diagenode.com/applications/western-blot">Loading control, MW marker visualization</a><em>. <br /></em></p>
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<h3>Epigenetic antibodies you can trust!</h3>
<p>Antibody quality is essential for assay success. Diagenode offers antibodies that are actually validated and have been widely used and published by the scientific community. Now we are adding a new level of siRNA knockdown validation to assure the specificity of our non-histone antibodies.</p>
<p><strong>Short interfering RNA (siRNA)</strong> degrades target mRNA, followed by the knock-down of protein production. If the antibody that recognizes the protein of interest is specific, the Western blot of siRNA-treated cells will show a significant reduction of signal vs. untreated cells.</p>
<center><img src="https://www.diagenode.com/emailing/images/C15100144-wb.png" alt="" /></center>
<p class="text-center"><small>WB results obtained with the HDAC1 pAb (Cat. No. C15100144) <br />on siRNA transfected cells (lane 2) and on untransfected control cells (lane 1).</small></p>
</div>
<div class="small-2 columns">
<p><img src="https://www.diagenode.com/emailing/images/epi-success-guaranteed-icon.png" alt="Epigenetic success guaranteed" /></p>
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<div class="spaced"></div>
<p style="text-align: left;"><span style="font-weight: 400;">The below list shows our first siRNA validated antibodies. More results - coming soon</span>.</p>',
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'description' => '<p><span style="font-weight: 400;">The list of Diagenode’s highly specific antibodies for transcription studies includes the antibodies against many transcription factors and nuclear receptors. Check the list below to see our targets.</span></p>
<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
<ul>
<li><span style="font-weight: 400;"> Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> Expert technical support</span></li>
<li><span style="font-weight: 400;"> Sample sizes available</span></li>
<li><span style="font-weight: 400;"> 100% satisfaction guarantee</span></li>
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'description' => '<p><b>Unparalleled ChIP-Seq results with the most rigorously validated antibodies</b></p>
<p><span style="font-weight: 400;">Diagenode provides leading solutions for epigenetic research. Because ChIP-seq is a widely-used technique, we validate our antibodies in ChIP and ChIP-seq experiments (in addition to conventional methods like Western blot, Dot blot, ELISA, and immunofluorescence) to provide the highest quality antibody. We standardize our validation and production to guarantee high product quality without technical bias. Diagenode guarantees ChIP-seq grade antibody performance under our suggested conditions.</span></p>
<div class="row">
<div class="small-12 medium-9 large-9 columns">
<p><strong>ChIP-seq profile</strong> of active (H3K4me3 and H3K36me3) and inactive (H3K27me3) marks using Diagenode antibodies.</p>
<img src="https://www.diagenode.com/img/categories/antibodies/chip-seq-grade-antibodies.png" /></div>
<div class="small-12 medium-3 large-3 columns">
<p><small> ChIP was performed on sheared chromatin from 100,000 K562 cells using iDeal ChIP-seq kit for Histones (cat. No. C01010051) with 1 µg of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 µg of the antibody against H3K36me3 (cat. No. C15410192). The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. The figure shows the signal distribution along the complete sequence of human chromosome 3, a zoomin to a 10 Mb region and a further zoomin to a 1.5 Mb region. </small></p>
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<p>Diagenode’s highly validated antibodies:</p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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'description' => '<p><span style="font-weight: 400;">All Diagenode’s antibodies are listed below. Please, use our Quick search field to find the antibody of interest by target name, application, purity.</span></p>
<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
<ul>
<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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'description' => '<div class="row">
<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
<p></p>
</div>
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<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
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<div class="small-12 medium-6 large-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" alt="" width="400" height="315" /> </div>
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<p></p>
<p></p>
<p></p>
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<p></p>
<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
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'name' => 'Enhanced frequency of transcription pre-initiation complexes assemblyafter exposure to UV irradiation results in increased repair activity andreduced probabilities for mutagenesis.',
'authors' => 'Liakos A. et al.',
'description' => '<p>In addition to being essential for gene expression, transcription is crucial for the maintenance of genome integrity. Here, we undertook a systematic approach, to monitor the assembly kinetics of the pre-initiating RNA Polymerase (Pol) II at promoters at steady state and different stages during recovery from UV irradiation-stress, when pre-initiation and initiation steps have been suggested to be transiently shut down. Taking advantage of the reversible dissociation of pre-initiating Pol II after high salt treatment, we found that de novo recruitment of the available Pol II molecules at active promoters not only persists upon UV at all times tested but occurs significantly faster in the early phase of recovery (2 h) than in unexposed human fibroblasts at the majority of active genes. Our method unveiled groups of genes with significantly different pre-initiation complex (PIC) assembly dynamics after UV that present distinct rates of UV-related mutational signatures in melanoma tumours, providing functional relevance to the importance of keeping transcription initiation active during UV recovery. Our findings uncover novel mechanistic insights further detailing the multilayered transcriptional response to genotoxic stress and link PIC assembly dynamics after exposure to genotoxins with cancer mutational landscapes.</p>',
'date' => '2023-07-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/37470822',
'doi' => '10.1093/nar/gkad593',
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'name' => 'A leukemia-protective germline variant mediates chromatin moduleformation via transcription factor nucleation.',
'authors' => 'Llimos G. et al.',
'description' => '<p>Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named "variable chromatin modules" (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect a VCM-modulating noncoding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a large change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with subtle, long-range chromatin compaction and robust AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology.</p>',
'date' => '2022-04-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35440565',
'doi' => '10.1038/s41467-022-29625-6',
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'name' => 'R-Loops Promote Antisense Transcription across the Mammalian Genome',
'authors' => 'Tan-Wong Sue Mei, Dhir Somdutta, Proudfoot Nick J.',
'description' => '<p>Widespread antisense long noncoding RNA (lncRNA) overlap with many protein-coding genes in mammals and emanate from gene promoter, enhancer, and termination regions. However, their origin and biological purpose remain unclear. We show that these antisense lncRNA can be generated by R-loops that form when nascent transcript invades the DNA duplex behind elongating RNA polymerase II (Pol II). Biochemically, R-loops act as intrinsic Pol II promoters to induce de novo RNA synthesis. Furthermore, their removal across the human genome by RNase H1 overexpression causes the selective reduction of antisense transcription. Consequently, we predict that R-loops act to facilitate the synthesis of many gene proximal antisense lncRNA. Not only are R-loops widely associated with DNA damage and repair, but we now show that they have the capacity to promote de novo transcript synthesis that may have aided the evolution of gene regulation.</p>',
'date' => '2019-11-21',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/31679819',
'doi' => '10.1016/j.molcel.2019.10.002',
'modified' => '2019-12-05 11:23:13',
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'name' => 'Adenovirus E1A Activation Domain Regulates H3 Acetylation Affecting Varied Steps in Transcription at Different Viral Promoters.',
'authors' => 'Hsu E, Pennella MA, Zemke NR, Eng C, Berk AJ',
'description' => '<p>How histone acetylation promotes transcription is not clearly understood. Here, we confirm an interaction between p300 and the adenovirus 2 large E1A activation domain (AD) and map the interacting regions in E1A by observing colocalization at an integrated array of fusions of LacI-mCherry to E1A fragments with YFP-p300. Viruses with mutations in E1A subdomains were constructed and analyzed for kinetics of early viral RNA expression and association of acetylated H3K9, K18, K27, TBP, and RNA polymerase II (Pol II) across the viral genome. The results indicate that this E1A interaction with p300 is required for H3K18 and H3K27 acetylation at the E2early, E3, and E4 promoters and is required for TBP and Pol II association with the E2early promoter. In contrast, H3K18/27 acetylation was not required for TBP and Pol II association with the E3 and E4 promoters but was required for E4 transcription at a step subsequent to Pol II preinitiation complex assembly. Despite a wealth of data associating promoter and enhancer region histone N-terminal tail lysine acetylation with transcriptional activity, there are relatively few examples of studies that establish causation between these histone posttranslational modifications and transcription. While hypoacetylation of histone H3 lysines 18 and 27 is associated with repression, the step(s) in the overall process of transcription that is blocked at a hypoacetylated promoter is not clearly established in most instances. Studies presented here confirm that the adenovirus 2 large E1A protein activation domain interacts with p300, as reported previously (P. Pelka, J. N. G. Ablack, J. Torchia, A. S. Turnell, R. J. A. Grand, J. S. Mymryk, Nucleic Acids Res 1095-1106, 2009, https://doi.org/10.1093/nar/gkn1057), and that the resulting acetylation of H3K18/27 affects varied steps in transcription at different viral promoters.</p>',
'date' => '2018-09-15',
'pmid' => 'http://www.pubmed.gov/29976669 ',
'doi' => '10.1093/nar/gkn1057),',
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'name' => 'Condensin targets and reduces unwound DNA structures associated with transcription in mitotic chromosome condensation',
'authors' => 'Sutani T, Sakata T, Nakato R, Masuda K, Ishibashi M, Yamashita D, Suzuki Y, Hirano T, Bando M, Shirahige K',
'description' => '<p>Chromosome condensation is a hallmark of mitosis in eukaryotes and is a prerequisite for faithful segregation of genetic material to daughter cells. Here we show that condensin, which is essential for assembling condensed chromosomes, helps to preclude the detrimental effects of gene transcription on mitotic condensation. ChIP-seq profiling reveals that the fission yeast condensin preferentially binds to active protein-coding genes in a transcription-dependent manner during mitosis. Pharmacological and genetic attenuation of transcription largely rescue bulk chromosome segregation defects observed in condensin mutants. We also demonstrate that condensin is associated with and reduces unwound DNA segments generated by transcription, providing a direct link between an in vitro activity of condensin and its in vivo function. The human condensin isoform condensin I also binds to unwound DNA regions at the transcription start sites of active genes, implying that our findings uncover a fundamental feature of condensin complexes.</p>',
'date' => '2015-07-23',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/26204128',
'doi' => '10.1038/ncomms8815',
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'name' => 'A pro-apoptotic function of iASPP by stabilizing p300 and CBP through inhibition of BRMS1 E3 ubiquitin ligase activity.',
'authors' => 'Kramer D, Schön M, Bayerlová M, Bleckmann A, Schön MP, Zörnig M, Dobbelstein M',
'description' => 'The p53 family and its cofactors are potent inducers of apoptosis and form a barrier to cancer. Here, we investigated the impact of the supposedly inhibitory member of the apoptosis-stimulating protein of p53, iASPP, on the activity of the p53 homolog TAp73, and its cofactors p300 and CBP. We found that iASPP interacted with and stabilized the histone acetyltransferase p300 and its homolog CBP upon cisplatin treatment. Vice versa, iASPP depletion by shRNA resulted in decreased amounts of p300 and CBP, impaired binding of p300 and TAp73 to target site promoters, reduced induction of pro-apoptotic TAp73 target genes, and impaired apoptosis. Mechanistically, we observed that the p300-regulatory E3 ubiquitin ligase BRMS1 could rescue the degradation of p300 and CBP in cisplatin-treated, iASPP-depleted cells. This argues that iASPP stabilizes p300 and CBP by interfering with their BRMS1-mediated ubiquitination, thereby contributing to apoptotic susceptibility. In line, iASPP overexpression partially abolished the interaction of BRMS1 and CBP upon DNA damage. Reduced levels of iASPP mRNA and protein as well as CBP protein were observed in human melanoma compared with normal skin tissue and benign melanocytic nevi. In line with our findings, iASPP overexpression or knockdown of BRMS1 each augmented p300/CBP levels in melanoma cell lines, thereby enhancing apoptosis upon DNA damage. Taken together, destabilization of p300/CBP by downregulation of iASPP expression levels appears to represent a molecular mechanism that contributes to chemoresistance in melanoma cells.',
'date' => '2015-02-12',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25675294',
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'name' => 'The unfolded protein response and the phosphorylations of activating transcription factor 2 in the trans-activation of il23a promoter produced by β-glucans.',
'authors' => 'Rodríguez M, Domingo E, Alonso S, Frade JG, Eiros J, Crespo MS, Fernández N',
'description' => 'Current views on the control of IL-23 production focus on the regulation of il23a, the gene encoding IL-23 p19, by NF-κB in combination with other transcription factors. C/EBP homologous protein (CHOP), X2-Box-binding protein 1 (XBP1), activator protein 1 (AP1), SMAD, CCAAT/enhancer-binding protein (C/EBPβ), and cAMP-response element-binding protein (CREB) have been involved in response to LPS, but no data are available regarding the mechanism triggered by the fungal mimic and β-glucan-containing stimulus zymosan, which produces IL-23 and to a low extent the related cytokine IL-12 p70. Zymosan induced the mobilization of CHOP from the nuclear fractions to phagocytic vesicles. Hypha-forming Candida also induced the nuclear disappearance of CHOP. Assay of transcription factor binding to the il23a promoter showed an increase of Thr(P)-71-Thr(P)-69-activating transcription factor 2 (ATF2) binding in response to zymosan. PKC and PKA/mitogen- and stress-activated kinase inhibitors down-regulated Thr(P)-71-ATF2 binding to the il23a promoter and il23a mRNA expression. Consistent with the current concept of complementary phosphorylations on N-terminal Thr-71 and Thr-69 of ATF2 by ERK and p38 MAPK, MEK, and p38 MAPK inhibitors blunted Thr(P)-69-ATF2 binding. Knockdown of atf2 mRNA with siRNA correlated with inhibition of il23a mRNA, but it did not affect the expression of il12/23b and il10 mRNA. These data indicate the following: (i) zymosan decreases nuclear proapoptotic CHOP, most likely by promoting its accumulation in phagocytic vesicles; (ii) zymosan-induced il23a mRNA expression is best explained through coordinated κB- and ATF2-dependent transcription; and (iii) il23a expression relies on complementary phosphorylation of ATF2 on Thr-69 and Thr-71 dependent on PKC and MAPK activities.',
'date' => '2014-08-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24982422',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
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'id' => '997',
'name' => 'ERG and FLI1 binding sites demarcate targets for aberrant epigenetic regulation by AML1-ETO in acute myeloid leukemia.',
'authors' => 'Martens JH, Mandoli A, Simmer F, Wierenga BJ, Saeed S, Singh AA, Altucci L, Vellenga E, Stunnenberg HG',
'description' => '<p>ERG and FLI1 are closely related members of the ETS family of transcription factors and have been identified as essential factors for the function and maintenance of normal hematopoietic stem cells. Here, genome-wide analysis revealed that both ERG and FLI1 occupy similar genomic regions as AML1-ETO in t(8;21) AMLs and identified ERG/FLI1 as proteins that facilitate binding of oncofusion protein complexes. In addition, we demonstrate that ERG and FLI1 bind the RUNX1 promoter and that shRNA mediated silencing of ERG leads to reduced expression of RUNX1 and AML1-ETO, consistent with a role of ERG in transcriptional activation of these proteins. Finally, we identify H3 acetylation as the epigenetic mark preferentially associated with ETS factor binding. This intimate connection between ERG/FLI1 binding and H3 acetylation implies that one of the molecular strategies of oncofusion proteins such as AML1-ETO and PML-RARα involves the targeting of histone deacetylase activities to ERG/FLI1 bound hematopoietic regulatory sites. Together these results highlight the dual importance of ETS factors in t(8;21) leukemogenesis, both as transcriptional regulators of the oncofusion protein itself as well as proteins that facilitate AML1-ETO binding.</p>',
'date' => '2012-09-14',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22983443',
'doi' => '',
'modified' => '2016-05-03 12:14:08',
'created' => '2015-07-24 15:38:59',
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(int) 8 => array(
'id' => '795',
'name' => 'Recruitment of histone deacetylase 3 to the interferon-a gene promoters attenuates interferon expression.',
'authors' => 'Génin P, Lin R, Hiscott J, Civas A',
'description' => 'BACKGROUND: Induction of Type I Interferon (IFN) genes constitutes an essential step leading to innate immune responses during virus infection. Sendai virus (SeV) infection of B lymphoid Namalwa cells transiently induces the transcriptional expression of multiple IFN-A genes. Although transcriptional activation of IFN-A genes has been extensively studied, the mechanism responsible for the attenuation of their expression remains to be determined. PRINCIPAL FINDINGS: In this study, we demonstrate that virus infection of Namalwa cells induces transient recruitment of HDAC3 (histone deacetylase 3) to IFN-A promoters. Analysis of chromatin-protein association by Chip-QPCR demonstrated that recruitment of interferon regulatory factor (IRF)3 and IRF7, as well as TBP correlated with enhanced histone H3K9 and H3K14 acetylation, whereas recruitment of HDAC3 correlated with inhibition of histone H3K9/K14 acetylation, removal of IRF7 and TATA-binding protein (TBP) from IFN-A promoters and inhibition of virus-induced IFN-A gene transcription. Additionally, HDAC3 overexpression reduced, and HDAC3 depletion by siRNA enhanced IFN-A gene expression. Furthermore, activation of IRF7 enhanced histone H3K9/K14 acetylation and IFN-A gene expression, whereas activation of both IRF7 and IRF3 led to recruitment of HDAC3 to the IFN-A gene promoters, resulting in impaired histone H3K9 acetylation and attenuation of IFN-A gene transcription. CONCLUSION: Altogether these data indicate that reversal of histone H3K9/K14 acetylation by HDAC3 is required for attenuation of IFN-A gene transcription during viral infection.',
'date' => '2012-06-07',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22685561',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
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[maximum depth reached]
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(int) 9 => array(
'id' => '253',
'name' => 'Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes.',
'authors' => 'Rao NA, McCalman MT, Moulos P, Francoijs KJ, Chatziioannou A, Kolisis FN, Alexis MN, Mitsiou DJ, Stunnenberg HG',
'description' => 'Glucocorticoid receptor (GR) exerts anti-inflammatory action in part by antagonizing proinflammatory transcription factors such as the nuclear factor kappa-b (NFKB). Here, we assess the crosstalk of activated GR and RELA (p65, major NFKB component) by global identification of their binding sites and target genes. We show that coactivation of GR and p65 alters the repertoire of regulated genes and results in their association with novel sites in a mutually dependent manner. These novel sites predominantly cluster with p65 target genes that are antagonized by activated GR and vice versa. Our data show that coactivation of GR and NFKB alters signaling pathways that are regulated by each factor separately and provide insight into the networks underlying the GR and NFKB crosstalk.',
'date' => '2011-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21750107',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
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[maximum depth reached]
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'id' => '680',
'name' => 'Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters.',
'authors' => 'Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C, Eick D, Gut I, Ferrier P, Andrau JC',
'description' => 'Recent work has shown that RNA polymerase (Pol) II can be recruited to and transcribe distal regulatory regions. Here we analyzed transcription initiation and elongation through genome-wide localization of Pol II, general transcription factors (GTFs) and active chromatin in developing T cells. We show that Pol II and GTFs are recruited to known T cell-specific enhancers. We extend this observation to many new putative enhancers, a majority of which can be transcribed with or without polyadenylation. Importantly, we also identify genomic features called transcriptional initiation platforms (TIPs) that are characterized by large areas of Pol II and GTF recruitment at promoters, intergenic and intragenic regions. TIPs show variable widths (0.4-10 kb) and correlate with high CpG content and increased tissue specificity at promoters. Finally, we also report differential recruitment of TFIID and other GTFs at promoters and enhancers. Overall, we propose that TIPs represent important new regulatory hallmarks of the genome.',
'date' => '2011-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21765417',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
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(int) 11 => array(
'id' => '290',
'name' => 'Role of p53 serine 46 in p53 target gene regulation.',
'authors' => 'Smeenk L, van Heeringen SJ, Koeppel M, Gilbert B, Janssen-Megens E, Stunnenberg HG, Lohrum M',
'description' => 'The tumor suppressor p53 plays a crucial role in cellular growth control inducing a plethora of different response pathways. The molecular mechanisms that discriminate between the distinct p53-responses have remained largely elusive. Here, we have analyzed the p53-regulated pathways induced by Actinomycin D and Etoposide treatment resulting in more growth arrested versus apoptotic cells respectively. We found that the genome-wide p53 DNA-binding patterns are almost identical upon both treatments notwithstanding transcriptional differences that we observed in global transcriptome analysis. To assess the role of post-translational modifications in target gene choice and activation we investigated the genome-wide level of phosphorylation of Serine 46 of p53 bound to DNA (p53-pS46) and of Serine 15 (p53-pS15). Interestingly, the extent of S46 phosphorylation of p53 bound to DNA is considerably higher in cells directed towards apoptosis while the degree of phosphorylation at S15 remains highly similar. Moreover, our data suggest that following different chemotherapeutical treatments, the amount of chromatin-associated p53 phosphorylated at S46 but not at pS15 is higher on certain apoptosis related target genes. Our data provide evidence that cell fate decisions are not made primarily on the level of general p53 DNA-binding and that post-translationally modified p53 can have distinct DNA-binding characteristics.',
'date' => '2011-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21394211',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
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[maximum depth reached]
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'id' => '512',
'name' => 'Control of the differentiation of regulatory T cells and T(H)17 cells by the DNA-binding inhibitor Id3.',
'authors' => 'Maruyama T, Li J, Vaque JP, Konkel JE, Wang W, Zhang B, Zhang P, Zamarron BF, Yu D, Wu Y, Zhuang Y, Gutkind JS, Chen W',
'description' => 'The molecular mechanisms that direct transcription of the gene encoding the transcription factor Foxp3 in CD4(+) T cells remain ill-defined. We show here that deletion of the DNA-binding inhibitor Id3 resulted in the defective generation of Foxp3(+) regulatory T cells (T(reg) cells). We identify two transforming growth factor-β1 (TGF-β1)-dependent mechanisms that were vital for activation of Foxp3 transcription and were defective in Id3(-/-) CD4(+) T cells. Enhanced binding of the transcription factor E2A to the Foxp3 promoter promoted Foxp3 transcription. Id3 was required for relief of inhibition by the transcription factor GATA-3 at the Foxp3 promoter. Furthermore, Id3(-/-) T cells showed greater differentiation into the T(H)17 subset of helper T cells in vitro and in a mouse asthma model. Therefore, a network of factors acts in a TGF-β-dependent manner to control Foxp3 expression and inhibit the development of T(H)17 cells.',
'date' => '2010-12-05',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21131965',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
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'id' => '117',
'name' => 'High-resolution analysis of epigenetic changes associated with X inactivation.',
'authors' => 'Marks H, Chow JC, Denissov S, Françoijs KJ, Brockdorff N, Heard E, Stunnenberg HG',
'description' => 'Differentiation of female murine ES cells triggers silencing of one X chromosome through X-chromosome inactivation (XCI). Immunofluorescence studies showed that soon after Xist RNA coating the inactive X (Xi) undergoes many heterochromatic changes, including the acquisition of H3K27me3. However, the mechanisms that lead to the establishment of heterochromatin remain unclear. We first analyze chromatin changes by ChIP-chip, as well as RNA expression, around the X-inactivation center (Xic) in female and male ES cells, and their day 4 and 10 differentiated derivatives. A dynamic epigenetic landscape is observed within the Xic locus. Tsix repression is accompanied by deposition of H3K27me3 at its promoter during differentiation of both female and male cells. However, only in female cells does an active epigenetic landscape emerge at the Xist locus, concomitant with high Xist expression. Several regions within and around the Xic show unsuspected chromatin changes, and we define a series of unusual loci containing highly enriched H3K27me3. Genome-wide ChIP-seq analyses show a female-specific quantitative increase of H3K27me3 across the X chromosome as XCI proceeds in differentiating female ES cells. Using female ES cells with nonrandom XCI and polymorphic X chromosomes, we demonstrate that this increase is specific to the Xi by allele-specific SNP mapping of the ChIP-seq tags. H3K27me3 becomes evenly associated with the Xi in a chromosome-wide fashion. A selective and robust increase of H3K27me3 and concomitant decrease in H3K4me3 is observed over active genes. This indicates that deposition of H3K27me3 during XCI is tightly associated with the act of silencing of individual genes across the Xi.',
'date' => '2009-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19581487',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
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[maximum depth reached]
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'id' => '89',
'name' => 'TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation.',
'authors' => 'Pitulescu ME, Teichmann M, Luo L, Kessel M',
'description' => 'BACKGROUND: The re-replication inhibitor Geminin binds to several transcription factors including homeodomain proteins, and to members of the polycomb and the SWI/SNF complexes. RESULTS: Here we describe the TATA-binding protein-like factor-interacting protein (TIPT) isoform 2, as a strong binding partner of Geminin. TIPT2 is widely expressed in mouse embryonic and adult tissues, residing both in cyto- and nucleoplasma, and enriched in the nucleolus. Like Geminin, also TIPT2 interacts with several polycomb factors, with the general transcription factor TBP (TATA box binding protein), and with the related protein TBPL1 (TRF2). TIPT2 synergizes with geminin and TBP in the activation of TATA box-containing promoters, and with TBPL1 and geminin in the activation of the TATA-less NF1 promoter. Geminin and TIPT2 were detected in the chromatin near TBP/TBPL1 binding sites. CONCLUSION: Together, our study introduces a novel transcriptional regulator and its function in cooperation with chromatin associated factors and the basal transcription machinery.',
'date' => '2009-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19515240',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
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[maximum depth reached]
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'name' => 'Identification of novel functional TBP-binding sites and general factor repertoires',
'authors' => 'Denissov S, van Driel M, Voit R, Hekkelman M, Hulsen T, Hernandez N, Grummt I, Wehrens R, Stunnenberg H.',
'description' => 'Our current knowledge of the general factor requirement in transcription by the three mammalian RNA polymerases is based on a small number of model promoters. Here, we present a comprehensive chromatin immunoprecipitation (ChIP)-on-chip analysis for 28 transcription factors on a large set of known and novel TATA-binding protein (TBP)-binding sites experimentally identified via ChIP cloning. A large fraction of identified TBP-binding sites is located in introns or lacks a gene/mRNA annotation and is found to direct transcription. Integrated analysis of the ChIP-on-chip data and functional studies revealed that TAF12 hitherto regarded as RNA polymerase II (RNAP II)-specific was found to be also involved in RNAP I transcription. Distinct profiles for general transcription factors and TAF-containing complexes were uncovered for RNAP II promoters located in CpG and non-CpG islands suggesting distinct transcription initiation pathways. Our study broadens the spectrum of general transcription factor function and uncovers a plethora of novel, functional TBP-binding sites in the human genome.',
'date' => '2007-02-21',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/17268553',
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<h3>Epigenetic antibodies you can trust!</h3>
<p>Antibody quality is essential for assay success. Diagenode offers antibodies that are actually validated and have been widely used and published by the scientific community. Now we are adding a new level of siRNA knockdown validation to assure the specificity of our non-histone antibodies.</p>
<p><strong>Short interfering RNA (siRNA)</strong> degrades target mRNA, followed by the knock-down of protein production. If the antibody that recognizes the protein of interest is specific, the Western blot of siRNA-treated cells will show a significant reduction of signal vs. untreated cells.</p>
<center><img src="https://www.diagenode.com/emailing/images/C15100144-wb.png" alt="" /></center>
<p class="text-center"><small>WB results obtained with the HDAC1 pAb (Cat. No. C15100144) <br />on siRNA transfected cells (lane 2) and on untransfected control cells (lane 1).</small></p>
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<p style="text-align: left;"><span style="font-weight: 400;">The below list shows our first siRNA validated antibodies. More results - coming soon</span>.</p>',
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<h3>Epigenetic antibodies you can trust!</h3>
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<p><strong>Short interfering RNA (siRNA)</strong> degrades target mRNA, followed by the knock-down of protein production. If the antibody that recognizes the protein of interest is specific, the Western blot of siRNA-treated cells will show a significant reduction of signal vs. untreated cells.</p>
<center><img src="https://www.diagenode.com/emailing/images/C15100144-wb.png" alt="" /></center>
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<h3>Epigenetic antibodies you can trust!</h3>
<p>Antibody quality is essential for assay success. Diagenode offers antibodies that are actually validated and have been widely used and published by the scientific community. Now we are adding a new level of siRNA knockdown validation to assure the specificity of our non-histone antibodies.</p>
<p><strong>Short interfering RNA (siRNA)</strong> degrades target mRNA, followed by the knock-down of protein production. If the antibody that recognizes the protein of interest is specific, the Western blot of siRNA-treated cells will show a significant reduction of signal vs. untreated cells.</p>
<center><img src="https://www.diagenode.com/emailing/images/C15100144-wb.png" alt="" /></center>
<p class="text-center"><small>WB results obtained with the HDAC1 pAb (Cat. No. C15100144) <br />on siRNA transfected cells (lane 2) and on untransfected control cells (lane 1).</small></p>
</div>
<div class="small-2 columns">
<p><img src="https://www.diagenode.com/emailing/images/epi-success-guaranteed-icon.png" alt="Epigenetic success guaranteed" /></p>
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<div class="spaced"></div>
<p style="text-align: left;"><span style="font-weight: 400;">The below list shows our first siRNA validated antibodies. More results - coming soon</span>.</p>'
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<p><small><strong>Figure 2 ChIP results obtained with the Diagenode monoclonal antibody against TBP </strong><br />ChIP assays were performed using U2OS cells, the Diagenode antibody directed against TBP (Cat. No. C15200002) and optimized primer sets for qPCR. Sheared chromatin from 1x10e6 cells and 4 μg of antibody were used per ChIP experiment. QPCR was performed with primers for the promoter of the c-fos and GAPDH genes (Cat. No. C17011004 and C17011001), a region 0.5 and 1 kb upstream of the GAPDH promoter (Cat. No. C17011002 and C17011003), respectively, and for exon 2 of the myoglobin gene (cat. No. C17011006) as a negative control. Figure 1 shows the recovery (the relative amount of immunoprecipitated DNA compared to input DNA) and the occupancy (ratio +/- control target). These results demonstrate the occupancy of both promoters by TBP.</small></p>
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<p><small><strong> Figure 3. Western blot analysis using the Diagenode monoclonal antibody directed against TBP</strong><br />Whole cell extracts (40 μg) from HeLa cells transfected with TBP siRNA (lane 2) and from an untransfected control (lane 1) were analysed by Western blot using the Diagenode antibody against TBP (Cat. No. C15200002) diluted 1:500 in TBSTween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<p><small><strong>Figure 2 ChIP results obtained with the Diagenode monoclonal antibody against TBP </strong><br />ChIP assays were performed using U2OS cells, the Diagenode antibody directed against TBP (Cat. No. C15200002) and optimized primer sets for qPCR. Sheared chromatin from 1x10e6 cells and 4 μg of antibody were used per ChIP experiment. QPCR was performed with primers for the promoter of the c-fos and GAPDH genes (Cat. No. C17011004 and C17011001), a region 0.5 and 1 kb upstream of the GAPDH promoter (Cat. No. C17011002 and C17011003), respectively, and for exon 2 of the myoglobin gene (cat. No. C17011006) as a negative control. Figure 1 shows the recovery (the relative amount of immunoprecipitated DNA compared to input DNA) and the occupancy (ratio +/- control target). These results demonstrate the occupancy of both promoters by TBP.</small></p>
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'description' => '<p>Alternative names: <strong>GTF2D</strong>, <strong>GTF2D1</strong>, <strong>SCA17</strong>, <strong>TF2D</strong>, <strong>TFIID</strong></p>
<p><span>Monoclonal antibody raised in mouse against the amino-terminal domain of human <strong>TBP (TATA box binding protein).</strong></span></p>',
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<div class="small-4 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-1.png" alt="TBP Antibody ChIP Grade" style="display: block; margin-left: auto; margin-right: auto;" /></div>
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<p><small><strong>Figure 1 ChIP-seq results obtained with the Diagenode monoclonal antibody directed against TBP </strong><br />ChIP was performed with 5 μg of the Diagenode antibody against TBP (Cat. No. C15200002) on sheared chromatin from 1 million HeLaS3 cells using the “Auto Histone ChIP-seq” kit (Cat. No. C01010022) on the IP-Star automated system. The IP’d DNA was analysed by QPCR with optimized PCR primer pairs for the promoters of the active GAPDH and c-fos genes, used as positive control targets, and for a region 1 kb upstream of the GAPDH promoter and the coding region of the inactive MB gene, used as negative control targets (figure 2A). The IP’d DNA was subsequently analysed with an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer’s instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. Figure 2 shows the peak distribution in 50 kb regions surrounding the GAPDH, c-fos, ACTB and MCL1 genes (figure 2B, C, D and E, respectively). These results clearly show a localisation of TBP at the promoters of actively transcribed genes.</small></p>
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<div class="small-12 columns">A. <img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-2.png" alt="TBP Antibody - ChIP-seq Grade" style="display: block; margin-left: auto; margin-right: auto;" /><br /> B. <img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-3.png" alt="TBP Antibody for ChIP-seq" style="display: block; margin-left: auto; margin-right: auto;" /><br /> C. <img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-4.png" alt="TBP Antibody for ChIP-seq assay" style="display: block; margin-left: auto; margin-right: auto;" /><br /> D. <img src="https://www.diagenode.com/img/product/antibodies/C15200002-chipseq-5.png" alt="TBP Antibody validated in ChIP-seq" style="display: block; margin-left: auto; margin-right: auto;" /></div>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15200002-chip.png" alt="TBP Antibody for ChIP assay" width="269" height="340" caption="false" /></p>
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<div class="small-8 columns">
<p><small><strong>Figure 2 ChIP results obtained with the Diagenode monoclonal antibody against TBP </strong><br />ChIP assays were performed using U2OS cells, the Diagenode antibody directed against TBP (Cat. No. C15200002) and optimized primer sets for qPCR. Sheared chromatin from 1x10e6 cells and 4 μg of antibody were used per ChIP experiment. QPCR was performed with primers for the promoter of the c-fos and GAPDH genes (Cat. No. C17011004 and C17011001), a region 0.5 and 1 kb upstream of the GAPDH promoter (Cat. No. C17011002 and C17011003), respectively, and for exon 2 of the myoglobin gene (cat. No. C17011006) as a negative control. Figure 1 shows the recovery (the relative amount of immunoprecipitated DNA compared to input DNA) and the occupancy (ratio +/- control target). These results demonstrate the occupancy of both promoters by TBP.</small></p>
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<div class="small-3 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15200002-wb.png" alt="TBP Antibody validated in Western Blot" style="display: block; margin-left: auto; margin-right: auto;" /></p>
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<div class="small-9 columns">
<p><small><strong> Figure 3. Western blot analysis using the Diagenode monoclonal antibody directed against TBP</strong><br />Whole cell extracts (40 μg) from HeLa cells transfected with TBP siRNA (lane 2) and from an untransfected control (lane 1) were analysed by Western blot using the Diagenode antibody against TBP (Cat. No. C15200002) diluted 1:500 in TBSTween containing 5% skimmed milk. The position of the protein of interest is indicated on the right; the marker (in kDa) is shown on the left.</small></p>
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<p>Learn more about: <a href="https://www.diagenode.com/applications/western-blot">Loading control, MW marker visualization</a><em>. <br /></em></p>
<p><em></em>Check our selection of antibodies validated in Western blot.</p>',
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<h3>Epigenetic antibodies you can trust!</h3>
<p>Antibody quality is essential for assay success. Diagenode offers antibodies that are actually validated and have been widely used and published by the scientific community. Now we are adding a new level of siRNA knockdown validation to assure the specificity of our non-histone antibodies.</p>
<p><strong>Short interfering RNA (siRNA)</strong> degrades target mRNA, followed by the knock-down of protein production. If the antibody that recognizes the protein of interest is specific, the Western blot of siRNA-treated cells will show a significant reduction of signal vs. untreated cells.</p>
<center><img src="https://www.diagenode.com/emailing/images/C15100144-wb.png" alt="" /></center>
<p class="text-center"><small>WB results obtained with the HDAC1 pAb (Cat. No. C15100144) <br />on siRNA transfected cells (lane 2) and on untransfected control cells (lane 1).</small></p>
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<div class="small-2 columns">
<p><img src="https://www.diagenode.com/emailing/images/epi-success-guaranteed-icon.png" alt="Epigenetic success guaranteed" /></p>
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<p style="text-align: left;"><span style="font-weight: 400;">The below list shows our first siRNA validated antibodies. More results - coming soon</span>.</p>',
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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
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<li><span style="font-weight: 400;"> Highly sensitive and specific</span></li>
<li><span style="font-weight: 400;"> Cost-effective (requires less antibody per reaction)</span></li>
<li><span style="font-weight: 400;"> Batch-specific data is available on the website</span></li>
<li><span style="font-weight: 400;"> Expert technical support</span></li>
<li><span style="font-weight: 400;"> Sample sizes available</span></li>
<li><span style="font-weight: 400;"> 100% satisfaction guarantee</span></li>
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'description' => '<p><b>Unparalleled ChIP-Seq results with the most rigorously validated antibodies</b></p>
<p><span style="font-weight: 400;">Diagenode provides leading solutions for epigenetic research. Because ChIP-seq is a widely-used technique, we validate our antibodies in ChIP and ChIP-seq experiments (in addition to conventional methods like Western blot, Dot blot, ELISA, and immunofluorescence) to provide the highest quality antibody. We standardize our validation and production to guarantee high product quality without technical bias. Diagenode guarantees ChIP-seq grade antibody performance under our suggested conditions.</span></p>
<div class="row">
<div class="small-12 medium-9 large-9 columns">
<p><strong>ChIP-seq profile</strong> of active (H3K4me3 and H3K36me3) and inactive (H3K27me3) marks using Diagenode antibodies.</p>
<img src="https://www.diagenode.com/img/categories/antibodies/chip-seq-grade-antibodies.png" /></div>
<div class="small-12 medium-3 large-3 columns">
<p><small> ChIP was performed on sheared chromatin from 100,000 K562 cells using iDeal ChIP-seq kit for Histones (cat. No. C01010051) with 1 µg of the Diagenode antibodies against H3K27me3 (cat. No. C15410195) and H3K4me3 (cat. No. C15410003), and 0.5 µg of the antibody against H3K36me3 (cat. No. C15410192). The IP'd DNA was subsequently analysed on an Illumina Genome Analyzer. Library preparation, cluster generation and sequencing were performed according to the manufacturer's instructions. The 36 bp tags were aligned to the human genome using the ELAND algorithm. The figure shows the signal distribution along the complete sequence of human chromosome 3, a zoomin to a 10 Mb region and a further zoomin to a 1.5 Mb region. </small></p>
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<p>Diagenode’s highly validated antibodies:</p>
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<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
<li>Expert technical support</li>
<li>Sample sizes available</li>
<li>100% satisfaction guarantee</li>
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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
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<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
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<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
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<div class="small-12 medium-6 large-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" alt="" width="400" height="315" /> </div>
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<p>Our aim at Diagenode is to offer the largest collection of highly specific <strong>ChIP-grade antibodies</strong>. We add new antibodies monthly. Find your ChIP-grade antibody in the list below and check more information about tested applications, extensive validation data, and product information.</p>',
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'description' => '<p style="text-align: justify;"><span>Epigenetic research tools have evolved over time from endpoint PCR to qPCR to the analyses of large sets of genome-wide sequencing data. ChIP sequencing (ChIP-seq) has now become the gold standard method for chromatin studies, given the accuracy and coverage scale of the approach over other methods. Successful ChIP-seq, however, requires a higher level of experimental accuracy and consistency in all steps of ChIP than ever before. Particularly crucial is the quality of ChIP antibodies. </span></p>',
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'name' => 'Enhanced frequency of transcription pre-initiation complexes assemblyafter exposure to UV irradiation results in increased repair activity andreduced probabilities for mutagenesis.',
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'description' => '<p>In addition to being essential for gene expression, transcription is crucial for the maintenance of genome integrity. Here, we undertook a systematic approach, to monitor the assembly kinetics of the pre-initiating RNA Polymerase (Pol) II at promoters at steady state and different stages during recovery from UV irradiation-stress, when pre-initiation and initiation steps have been suggested to be transiently shut down. Taking advantage of the reversible dissociation of pre-initiating Pol II after high salt treatment, we found that de novo recruitment of the available Pol II molecules at active promoters not only persists upon UV at all times tested but occurs significantly faster in the early phase of recovery (2 h) than in unexposed human fibroblasts at the majority of active genes. Our method unveiled groups of genes with significantly different pre-initiation complex (PIC) assembly dynamics after UV that present distinct rates of UV-related mutational signatures in melanoma tumours, providing functional relevance to the importance of keeping transcription initiation active during UV recovery. Our findings uncover novel mechanistic insights further detailing the multilayered transcriptional response to genotoxic stress and link PIC assembly dynamics after exposure to genotoxins with cancer mutational landscapes.</p>',
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'description' => '<p>Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named "variable chromatin modules" (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect a VCM-modulating noncoding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a large change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with subtle, long-range chromatin compaction and robust AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology.</p>',
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'name' => 'R-Loops Promote Antisense Transcription across the Mammalian Genome',
'authors' => 'Tan-Wong Sue Mei, Dhir Somdutta, Proudfoot Nick J.',
'description' => '<p>Widespread antisense long noncoding RNA (lncRNA) overlap with many protein-coding genes in mammals and emanate from gene promoter, enhancer, and termination regions. However, their origin and biological purpose remain unclear. We show that these antisense lncRNA can be generated by R-loops that form when nascent transcript invades the DNA duplex behind elongating RNA polymerase II (Pol II). Biochemically, R-loops act as intrinsic Pol II promoters to induce de novo RNA synthesis. Furthermore, their removal across the human genome by RNase H1 overexpression causes the selective reduction of antisense transcription. Consequently, we predict that R-loops act to facilitate the synthesis of many gene proximal antisense lncRNA. Not only are R-loops widely associated with DNA damage and repair, but we now show that they have the capacity to promote de novo transcript synthesis that may have aided the evolution of gene regulation.</p>',
'date' => '2019-11-21',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/31679819',
'doi' => '10.1016/j.molcel.2019.10.002',
'modified' => '2019-12-05 11:23:13',
'created' => '2019-12-02 15:25:44',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'id' => '3415',
'name' => 'Adenovirus E1A Activation Domain Regulates H3 Acetylation Affecting Varied Steps in Transcription at Different Viral Promoters.',
'authors' => 'Hsu E, Pennella MA, Zemke NR, Eng C, Berk AJ',
'description' => '<p>How histone acetylation promotes transcription is not clearly understood. Here, we confirm an interaction between p300 and the adenovirus 2 large E1A activation domain (AD) and map the interacting regions in E1A by observing colocalization at an integrated array of fusions of LacI-mCherry to E1A fragments with YFP-p300. Viruses with mutations in E1A subdomains were constructed and analyzed for kinetics of early viral RNA expression and association of acetylated H3K9, K18, K27, TBP, and RNA polymerase II (Pol II) across the viral genome. The results indicate that this E1A interaction with p300 is required for H3K18 and H3K27 acetylation at the E2early, E3, and E4 promoters and is required for TBP and Pol II association with the E2early promoter. In contrast, H3K18/27 acetylation was not required for TBP and Pol II association with the E3 and E4 promoters but was required for E4 transcription at a step subsequent to Pol II preinitiation complex assembly. Despite a wealth of data associating promoter and enhancer region histone N-terminal tail lysine acetylation with transcriptional activity, there are relatively few examples of studies that establish causation between these histone posttranslational modifications and transcription. While hypoacetylation of histone H3 lysines 18 and 27 is associated with repression, the step(s) in the overall process of transcription that is blocked at a hypoacetylated promoter is not clearly established in most instances. Studies presented here confirm that the adenovirus 2 large E1A protein activation domain interacts with p300, as reported previously (P. Pelka, J. N. G. Ablack, J. Torchia, A. S. Turnell, R. J. A. Grand, J. S. Mymryk, Nucleic Acids Res 1095-1106, 2009, https://doi.org/10.1093/nar/gkn1057), and that the resulting acetylation of H3K18/27 affects varied steps in transcription at different viral promoters.</p>',
'date' => '2018-09-15',
'pmid' => 'http://www.pubmed.gov/29976669 ',
'doi' => '10.1093/nar/gkn1057),',
'modified' => '2018-12-31 11:29:42',
'created' => '2018-12-04 09:51:07',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 4 => array(
'id' => '2872',
'name' => 'Condensin targets and reduces unwound DNA structures associated with transcription in mitotic chromosome condensation',
'authors' => 'Sutani T, Sakata T, Nakato R, Masuda K, Ishibashi M, Yamashita D, Suzuki Y, Hirano T, Bando M, Shirahige K',
'description' => '<p>Chromosome condensation is a hallmark of mitosis in eukaryotes and is a prerequisite for faithful segregation of genetic material to daughter cells. Here we show that condensin, which is essential for assembling condensed chromosomes, helps to preclude the detrimental effects of gene transcription on mitotic condensation. ChIP-seq profiling reveals that the fission yeast condensin preferentially binds to active protein-coding genes in a transcription-dependent manner during mitosis. Pharmacological and genetic attenuation of transcription largely rescue bulk chromosome segregation defects observed in condensin mutants. We also demonstrate that condensin is associated with and reduces unwound DNA segments generated by transcription, providing a direct link between an in vitro activity of condensin and its in vivo function. The human condensin isoform condensin I also binds to unwound DNA regions at the transcription start sites of active genes, implying that our findings uncover a fundamental feature of condensin complexes.</p>',
'date' => '2015-07-23',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/26204128',
'doi' => '10.1038/ncomms8815',
'modified' => '2016-03-25 11:03:02',
'created' => '2016-03-25 11:03:02',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 5 => array(
'id' => '2593',
'name' => 'A pro-apoptotic function of iASPP by stabilizing p300 and CBP through inhibition of BRMS1 E3 ubiquitin ligase activity.',
'authors' => 'Kramer D, Schön M, Bayerlová M, Bleckmann A, Schön MP, Zörnig M, Dobbelstein M',
'description' => 'The p53 family and its cofactors are potent inducers of apoptosis and form a barrier to cancer. Here, we investigated the impact of the supposedly inhibitory member of the apoptosis-stimulating protein of p53, iASPP, on the activity of the p53 homolog TAp73, and its cofactors p300 and CBP. We found that iASPP interacted with and stabilized the histone acetyltransferase p300 and its homolog CBP upon cisplatin treatment. Vice versa, iASPP depletion by shRNA resulted in decreased amounts of p300 and CBP, impaired binding of p300 and TAp73 to target site promoters, reduced induction of pro-apoptotic TAp73 target genes, and impaired apoptosis. Mechanistically, we observed that the p300-regulatory E3 ubiquitin ligase BRMS1 could rescue the degradation of p300 and CBP in cisplatin-treated, iASPP-depleted cells. This argues that iASPP stabilizes p300 and CBP by interfering with their BRMS1-mediated ubiquitination, thereby contributing to apoptotic susceptibility. In line, iASPP overexpression partially abolished the interaction of BRMS1 and CBP upon DNA damage. Reduced levels of iASPP mRNA and protein as well as CBP protein were observed in human melanoma compared with normal skin tissue and benign melanocytic nevi. In line with our findings, iASPP overexpression or knockdown of BRMS1 each augmented p300/CBP levels in melanoma cell lines, thereby enhancing apoptosis upon DNA damage. Taken together, destabilization of p300/CBP by downregulation of iASPP expression levels appears to represent a molecular mechanism that contributes to chemoresistance in melanoma cells.',
'date' => '2015-02-12',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25675294',
'doi' => '',
'modified' => '2015-07-24 15:39:05',
'created' => '2015-07-24 15:39:05',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 6 => array(
'id' => '2424',
'name' => 'The unfolded protein response and the phosphorylations of activating transcription factor 2 in the trans-activation of il23a promoter produced by β-glucans.',
'authors' => 'Rodríguez M, Domingo E, Alonso S, Frade JG, Eiros J, Crespo MS, Fernández N',
'description' => 'Current views on the control of IL-23 production focus on the regulation of il23a, the gene encoding IL-23 p19, by NF-κB in combination with other transcription factors. C/EBP homologous protein (CHOP), X2-Box-binding protein 1 (XBP1), activator protein 1 (AP1), SMAD, CCAAT/enhancer-binding protein (C/EBPβ), and cAMP-response element-binding protein (CREB) have been involved in response to LPS, but no data are available regarding the mechanism triggered by the fungal mimic and β-glucan-containing stimulus zymosan, which produces IL-23 and to a low extent the related cytokine IL-12 p70. Zymosan induced the mobilization of CHOP from the nuclear fractions to phagocytic vesicles. Hypha-forming Candida also induced the nuclear disappearance of CHOP. Assay of transcription factor binding to the il23a promoter showed an increase of Thr(P)-71-Thr(P)-69-activating transcription factor 2 (ATF2) binding in response to zymosan. PKC and PKA/mitogen- and stress-activated kinase inhibitors down-regulated Thr(P)-71-ATF2 binding to the il23a promoter and il23a mRNA expression. Consistent with the current concept of complementary phosphorylations on N-terminal Thr-71 and Thr-69 of ATF2 by ERK and p38 MAPK, MEK, and p38 MAPK inhibitors blunted Thr(P)-69-ATF2 binding. Knockdown of atf2 mRNA with siRNA correlated with inhibition of il23a mRNA, but it did not affect the expression of il12/23b and il10 mRNA. These data indicate the following: (i) zymosan decreases nuclear proapoptotic CHOP, most likely by promoting its accumulation in phagocytic vesicles; (ii) zymosan-induced il23a mRNA expression is best explained through coordinated κB- and ATF2-dependent transcription; and (iii) il23a expression relies on complementary phosphorylation of ATF2 on Thr-69 and Thr-71 dependent on PKC and MAPK activities.',
'date' => '2014-08-15',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/24982422',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
'created' => '2015-07-24 15:39:04',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 7 => array(
'id' => '997',
'name' => 'ERG and FLI1 binding sites demarcate targets for aberrant epigenetic regulation by AML1-ETO in acute myeloid leukemia.',
'authors' => 'Martens JH, Mandoli A, Simmer F, Wierenga BJ, Saeed S, Singh AA, Altucci L, Vellenga E, Stunnenberg HG',
'description' => '<p>ERG and FLI1 are closely related members of the ETS family of transcription factors and have been identified as essential factors for the function and maintenance of normal hematopoietic stem cells. Here, genome-wide analysis revealed that both ERG and FLI1 occupy similar genomic regions as AML1-ETO in t(8;21) AMLs and identified ERG/FLI1 as proteins that facilitate binding of oncofusion protein complexes. In addition, we demonstrate that ERG and FLI1 bind the RUNX1 promoter and that shRNA mediated silencing of ERG leads to reduced expression of RUNX1 and AML1-ETO, consistent with a role of ERG in transcriptional activation of these proteins. Finally, we identify H3 acetylation as the epigenetic mark preferentially associated with ETS factor binding. This intimate connection between ERG/FLI1 binding and H3 acetylation implies that one of the molecular strategies of oncofusion proteins such as AML1-ETO and PML-RARα involves the targeting of histone deacetylase activities to ERG/FLI1 bound hematopoietic regulatory sites. Together these results highlight the dual importance of ETS factors in t(8;21) leukemogenesis, both as transcriptional regulators of the oncofusion protein itself as well as proteins that facilitate AML1-ETO binding.</p>',
'date' => '2012-09-14',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22983443',
'doi' => '',
'modified' => '2016-05-03 12:14:08',
'created' => '2015-07-24 15:38:59',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 8 => array(
'id' => '795',
'name' => 'Recruitment of histone deacetylase 3 to the interferon-a gene promoters attenuates interferon expression.',
'authors' => 'Génin P, Lin R, Hiscott J, Civas A',
'description' => 'BACKGROUND: Induction of Type I Interferon (IFN) genes constitutes an essential step leading to innate immune responses during virus infection. Sendai virus (SeV) infection of B lymphoid Namalwa cells transiently induces the transcriptional expression of multiple IFN-A genes. Although transcriptional activation of IFN-A genes has been extensively studied, the mechanism responsible for the attenuation of their expression remains to be determined. PRINCIPAL FINDINGS: In this study, we demonstrate that virus infection of Namalwa cells induces transient recruitment of HDAC3 (histone deacetylase 3) to IFN-A promoters. Analysis of chromatin-protein association by Chip-QPCR demonstrated that recruitment of interferon regulatory factor (IRF)3 and IRF7, as well as TBP correlated with enhanced histone H3K9 and H3K14 acetylation, whereas recruitment of HDAC3 correlated with inhibition of histone H3K9/K14 acetylation, removal of IRF7 and TATA-binding protein (TBP) from IFN-A promoters and inhibition of virus-induced IFN-A gene transcription. Additionally, HDAC3 overexpression reduced, and HDAC3 depletion by siRNA enhanced IFN-A gene expression. Furthermore, activation of IRF7 enhanced histone H3K9/K14 acetylation and IFN-A gene expression, whereas activation of both IRF7 and IRF3 led to recruitment of HDAC3 to the IFN-A gene promoters, resulting in impaired histone H3K9 acetylation and attenuation of IFN-A gene transcription. CONCLUSION: Altogether these data indicate that reversal of histone H3K9/K14 acetylation by HDAC3 is required for attenuation of IFN-A gene transcription during viral infection.',
'date' => '2012-06-07',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22685561',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 9 => array(
'id' => '253',
'name' => 'Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes.',
'authors' => 'Rao NA, McCalman MT, Moulos P, Francoijs KJ, Chatziioannou A, Kolisis FN, Alexis MN, Mitsiou DJ, Stunnenberg HG',
'description' => 'Glucocorticoid receptor (GR) exerts anti-inflammatory action in part by antagonizing proinflammatory transcription factors such as the nuclear factor kappa-b (NFKB). Here, we assess the crosstalk of activated GR and RELA (p65, major NFKB component) by global identification of their binding sites and target genes. We show that coactivation of GR and p65 alters the repertoire of regulated genes and results in their association with novel sites in a mutually dependent manner. These novel sites predominantly cluster with p65 target genes that are antagonized by activated GR and vice versa. Our data show that coactivation of GR and NFKB alters signaling pathways that are regulated by each factor separately and provide insight into the networks underlying the GR and NFKB crosstalk.',
'date' => '2011-09-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21750107',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 10 => array(
'id' => '680',
'name' => 'Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters.',
'authors' => 'Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C, Eick D, Gut I, Ferrier P, Andrau JC',
'description' => 'Recent work has shown that RNA polymerase (Pol) II can be recruited to and transcribe distal regulatory regions. Here we analyzed transcription initiation and elongation through genome-wide localization of Pol II, general transcription factors (GTFs) and active chromatin in developing T cells. We show that Pol II and GTFs are recruited to known T cell-specific enhancers. We extend this observation to many new putative enhancers, a majority of which can be transcribed with or without polyadenylation. Importantly, we also identify genomic features called transcriptional initiation platforms (TIPs) that are characterized by large areas of Pol II and GTF recruitment at promoters, intergenic and intragenic regions. TIPs show variable widths (0.4-10 kb) and correlate with high CpG content and increased tissue specificity at promoters. Finally, we also report differential recruitment of TFIID and other GTFs at promoters and enhancers. Overall, we propose that TIPs represent important new regulatory hallmarks of the genome.',
'date' => '2011-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21765417',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 11 => array(
'id' => '290',
'name' => 'Role of p53 serine 46 in p53 target gene regulation.',
'authors' => 'Smeenk L, van Heeringen SJ, Koeppel M, Gilbert B, Janssen-Megens E, Stunnenberg HG, Lohrum M',
'description' => 'The tumor suppressor p53 plays a crucial role in cellular growth control inducing a plethora of different response pathways. The molecular mechanisms that discriminate between the distinct p53-responses have remained largely elusive. Here, we have analyzed the p53-regulated pathways induced by Actinomycin D and Etoposide treatment resulting in more growth arrested versus apoptotic cells respectively. We found that the genome-wide p53 DNA-binding patterns are almost identical upon both treatments notwithstanding transcriptional differences that we observed in global transcriptome analysis. To assess the role of post-translational modifications in target gene choice and activation we investigated the genome-wide level of phosphorylation of Serine 46 of p53 bound to DNA (p53-pS46) and of Serine 15 (p53-pS15). Interestingly, the extent of S46 phosphorylation of p53 bound to DNA is considerably higher in cells directed towards apoptosis while the degree of phosphorylation at S15 remains highly similar. Moreover, our data suggest that following different chemotherapeutical treatments, the amount of chromatin-associated p53 phosphorylated at S46 but not at pS15 is higher on certain apoptosis related target genes. Our data provide evidence that cell fate decisions are not made primarily on the level of general p53 DNA-binding and that post-translationally modified p53 can have distinct DNA-binding characteristics.',
'date' => '2011-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21394211',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 12 => array(
'id' => '512',
'name' => 'Control of the differentiation of regulatory T cells and T(H)17 cells by the DNA-binding inhibitor Id3.',
'authors' => 'Maruyama T, Li J, Vaque JP, Konkel JE, Wang W, Zhang B, Zhang P, Zamarron BF, Yu D, Wu Y, Zhuang Y, Gutkind JS, Chen W',
'description' => 'The molecular mechanisms that direct transcription of the gene encoding the transcription factor Foxp3 in CD4(+) T cells remain ill-defined. We show here that deletion of the DNA-binding inhibitor Id3 resulted in the defective generation of Foxp3(+) regulatory T cells (T(reg) cells). We identify two transforming growth factor-β1 (TGF-β1)-dependent mechanisms that were vital for activation of Foxp3 transcription and were defective in Id3(-/-) CD4(+) T cells. Enhanced binding of the transcription factor E2A to the Foxp3 promoter promoted Foxp3 transcription. Id3 was required for relief of inhibition by the transcription factor GATA-3 at the Foxp3 promoter. Furthermore, Id3(-/-) T cells showed greater differentiation into the T(H)17 subset of helper T cells in vitro and in a mouse asthma model. Therefore, a network of factors acts in a TGF-β-dependent manner to control Foxp3 expression and inhibit the development of T(H)17 cells.',
'date' => '2010-12-05',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/21131965',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 13 => array(
'id' => '117',
'name' => 'High-resolution analysis of epigenetic changes associated with X inactivation.',
'authors' => 'Marks H, Chow JC, Denissov S, Françoijs KJ, Brockdorff N, Heard E, Stunnenberg HG',
'description' => 'Differentiation of female murine ES cells triggers silencing of one X chromosome through X-chromosome inactivation (XCI). Immunofluorescence studies showed that soon after Xist RNA coating the inactive X (Xi) undergoes many heterochromatic changes, including the acquisition of H3K27me3. However, the mechanisms that lead to the establishment of heterochromatin remain unclear. We first analyze chromatin changes by ChIP-chip, as well as RNA expression, around the X-inactivation center (Xic) in female and male ES cells, and their day 4 and 10 differentiated derivatives. A dynamic epigenetic landscape is observed within the Xic locus. Tsix repression is accompanied by deposition of H3K27me3 at its promoter during differentiation of both female and male cells. However, only in female cells does an active epigenetic landscape emerge at the Xist locus, concomitant with high Xist expression. Several regions within and around the Xic show unsuspected chromatin changes, and we define a series of unusual loci containing highly enriched H3K27me3. Genome-wide ChIP-seq analyses show a female-specific quantitative increase of H3K27me3 across the X chromosome as XCI proceeds in differentiating female ES cells. Using female ES cells with nonrandom XCI and polymorphic X chromosomes, we demonstrate that this increase is specific to the Xi by allele-specific SNP mapping of the ChIP-seq tags. H3K27me3 becomes evenly associated with the Xi in a chromosome-wide fashion. A selective and robust increase of H3K27me3 and concomitant decrease in H3K4me3 is observed over active genes. This indicates that deposition of H3K27me3 during XCI is tightly associated with the act of silencing of individual genes across the Xi.',
'date' => '2009-08-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19581487',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
'created' => '2015-07-24 15:38:57',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 14 => array(
'id' => '89',
'name' => 'TIPT2 and geminin interact with basal transcription factors to synergize in transcriptional regulation.',
'authors' => 'Pitulescu ME, Teichmann M, Luo L, Kessel M',
'description' => 'BACKGROUND: The re-replication inhibitor Geminin binds to several transcription factors including homeodomain proteins, and to members of the polycomb and the SWI/SNF complexes. RESULTS: Here we describe the TATA-binding protein-like factor-interacting protein (TIPT) isoform 2, as a strong binding partner of Geminin. TIPT2 is widely expressed in mouse embryonic and adult tissues, residing both in cyto- and nucleoplasma, and enriched in the nucleolus. Like Geminin, also TIPT2 interacts with several polycomb factors, with the general transcription factor TBP (TATA box binding protein), and with the related protein TBPL1 (TRF2). TIPT2 synergizes with geminin and TBP in the activation of TATA box-containing promoters, and with TBPL1 and geminin in the activation of the TATA-less NF1 promoter. Geminin and TIPT2 were detected in the chromatin near TBP/TBPL1 binding sites. CONCLUSION: Together, our study introduces a novel transcriptional regulator and its function in cooperation with chromatin associated factors and the basal transcription machinery.',
'date' => '2009-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19515240',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
'ProductsPublication' => array(
[maximum depth reached]
)
),
(int) 15 => array(
'id' => '844',
'name' => 'Identification of novel functional TBP-binding sites and general factor repertoires',
'authors' => 'Denissov S, van Driel M, Voit R, Hekkelman M, Hulsen T, Hernandez N, Grummt I, Wehrens R, Stunnenberg H.',
'description' => 'Our current knowledge of the general factor requirement in transcription by the three mammalian RNA polymerases is based on a small number of model promoters. Here, we present a comprehensive chromatin immunoprecipitation (ChIP)-on-chip analysis for 28 transcription factors on a large set of known and novel TATA-binding protein (TBP)-binding sites experimentally identified via ChIP cloning. A large fraction of identified TBP-binding sites is located in introns or lacks a gene/mRNA annotation and is found to direct transcription. Integrated analysis of the ChIP-on-chip data and functional studies revealed that TAF12 hitherto regarded as RNA polymerase II (RNAP II)-specific was found to be also involved in RNAP I transcription. Distinct profiles for general transcription factors and TAF-containing complexes were uncovered for RNAP II promoters located in CpG and non-CpG islands suggesting distinct transcription initiation pathways. Our study broadens the spectrum of general transcription factor function and uncovers a plethora of novel, functional TBP-binding sites in the human genome.',
'date' => '2007-02-21',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/17268553',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
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[maximum depth reached]
)
)
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'name' => 'TBP antibody SDS GB en',
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'modified' => '2020-07-01 15:08:26',
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'modified' => '2020-07-01 15:07:36',
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'price_JPY' => '16450',
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'description' => '<div class="row">
<div class="small-10 columns">
<h3>Epigenetic antibodies you can trust!</h3>
<p>Antibody quality is essential for assay success. Diagenode offers antibodies that are actually validated and have been widely used and published by the scientific community. Now we are adding a new level of siRNA knockdown validation to assure the specificity of our non-histone antibodies.</p>
<p><strong>Short interfering RNA (siRNA)</strong> degrades target mRNA, followed by the knock-down of protein production. If the antibody that recognizes the protein of interest is specific, the Western blot of siRNA-treated cells will show a significant reduction of signal vs. untreated cells.</p>
<center><img src="https://www.diagenode.com/emailing/images/C15100144-wb.png" alt="" /></center>
<p class="text-center"><small>WB results obtained with the HDAC1 pAb (Cat. No. C15100144) <br />on siRNA transfected cells (lane 2) and on untransfected control cells (lane 1).</small></p>
</div>
<div class="small-2 columns">
<p><img src="https://www.diagenode.com/emailing/images/epi-success-guaranteed-icon.png" alt="Epigenetic success guaranteed" /></p>
</div>
</div>
<div class="spaced"></div>
<p style="text-align: left;"><span style="font-weight: 400;">The below list shows our first siRNA validated antibodies. More results - coming soon</span>.</p>',
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'description' => '<div class="row">
<div class="small-10 columns">
<h3>Epigenetic antibodies you can trust!</h3>
<p>Antibody quality is essential for assay success. Diagenode offers antibodies that are actually validated and have been widely used and published by the scientific community. Now we are adding a new level of siRNA knockdown validation to assure the specificity of our non-histone antibodies.</p>
<p><strong>Short interfering RNA (siRNA)</strong> degrades target mRNA, followed by the knock-down of protein production. If the antibody that recognizes the protein of interest is specific, the Western blot of siRNA-treated cells will show a significant reduction of signal vs. untreated cells.</p>
<center><img src="https://www.diagenode.com/emailing/images/C15100144-wb.png" alt="" /></center>
<p class="text-center"><small>WB results obtained with the HDAC1 pAb (Cat. No. C15100144) <br />on siRNA transfected cells (lane 2) and on untransfected control cells (lane 1).</small></p>
</div>
<div class="small-2 columns">
<p><img src="https://www.diagenode.com/emailing/images/epi-success-guaranteed-icon.png" alt="Epigenetic success guaranteed" /></p>
</div>
</div>
<div class="spaced"></div>
<p style="text-align: left;"><span style="font-weight: 400;">The below list shows our first siRNA validated antibodies. More results - coming soon</span>.</p>',
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'meta_keywords' => 'siRNA knockdown antibodies',
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$description = '<div class="row">
<div class="small-10 columns">
<h3>Epigenetic antibodies you can trust!</h3>
<p>Antibody quality is essential for assay success. Diagenode offers antibodies that are actually validated and have been widely used and published by the scientific community. Now we are adding a new level of siRNA knockdown validation to assure the specificity of our non-histone antibodies.</p>
<p><strong>Short interfering RNA (siRNA)</strong> degrades target mRNA, followed by the knock-down of protein production. If the antibody that recognizes the protein of interest is specific, the Western blot of siRNA-treated cells will show a significant reduction of signal vs. untreated cells.</p>
<center><img src="https://www.diagenode.com/emailing/images/C15100144-wb.png" alt="" /></center>
<p class="text-center"><small>WB results obtained with the HDAC1 pAb (Cat. No. C15100144) <br />on siRNA transfected cells (lane 2) and on untransfected control cells (lane 1).</small></p>
</div>
<div class="small-2 columns">
<p><img src="https://www.diagenode.com/emailing/images/epi-success-guaranteed-icon.png" alt="Epigenetic success guaranteed" /></p>
</div>
</div>
<div class="spaced"></div>
<p style="text-align: left;"><span style="font-weight: 400;">The below list shows our first siRNA validated antibodies. More results - coming soon</span>.</p>'
$name = 'siRNA Knockdown'
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'id' => '38',
'name' => 'Epigenetic Antibodies Brochure',
'description' => '<p>More than in any other immuoprecipitation assays, quality antibodies are critical tools in many epigenetics experiments. Since 10 years, Diagenode has developed the most stringent quality production available on the market for antibodies exclusively focused on epigenetic uses. All our antibodies have been qualified to work in epigenetic applications.</p>',
'image_id' => null,
'type' => 'Brochure',
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'slug' => 'epigenetic-antibodies-brochure',
'meta_keywords' => '',
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'modified' => '2016-06-15 11:24:06',
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'name' => 'TBP antibody SDS ES es',
'language' => 'es',
'url' => 'files/SDS/TBP/SDS-C15200002-TBP_Antibody-ES-es-GHS_2_0.pdf',
'countries' => 'ES',
'modified' => '2020-07-01 15:07:36',
'created' => '2020-07-01 15:07:36',
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)
)
$publication = array(
'id' => '844',
'name' => 'Identification of novel functional TBP-binding sites and general factor repertoires',
'authors' => 'Denissov S, van Driel M, Voit R, Hekkelman M, Hulsen T, Hernandez N, Grummt I, Wehrens R, Stunnenberg H.',
'description' => 'Our current knowledge of the general factor requirement in transcription by the three mammalian RNA polymerases is based on a small number of model promoters. Here, we present a comprehensive chromatin immunoprecipitation (ChIP)-on-chip analysis for 28 transcription factors on a large set of known and novel TATA-binding protein (TBP)-binding sites experimentally identified via ChIP cloning. A large fraction of identified TBP-binding sites is located in introns or lacks a gene/mRNA annotation and is found to direct transcription. Integrated analysis of the ChIP-on-chip data and functional studies revealed that TAF12 hitherto regarded as RNA polymerase II (RNAP II)-specific was found to be also involved in RNAP I transcription. Distinct profiles for general transcription factors and TAF-containing complexes were uncovered for RNAP II promoters located in CpG and non-CpG islands suggesting distinct transcription initiation pathways. Our study broadens the spectrum of general transcription factor function and uncovers a plethora of novel, functional TBP-binding sites in the human genome.',
'date' => '2007-02-21',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/17268553',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
'created' => '2015-07-24 15:38:58',
'ProductsPublication' => array(
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)
$externalLink = ' <a href="http://www.ncbi.nlm.nih.gov/pubmed/17268553" target="_blank"><i class="fa fa-external-link"></i></a>'include - APP/View/Products/view.ctp, line 755
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 193
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 118
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