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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode antibody directed against TIP5 </strong><br />ChIP assays were performed using the Diagenode antibody against TIP5 (cat. No. CS-090-100). Chromatin from HEK293T and NIH3T3 cells was formaldehyde cross-linked and sheared with the Bioruptor (Diagenode) to yield fragments with an average length of 200 to 400 bp. ChIP was performed overnight at 4°C with 100 μg sheared chromatin and either 5 μl of the TIP5 antibody or 5 μl IgG which was used as negative IP control. The IP’d DNA was analysed by qPCR with primer sets for the promoter and the coding region of the 28s ribosomal RNA gene. Figure 1 shows the recovery by the TIP5 antibody and by IgG (set to 1), normalised to the input DNA. These results show that, both in HEK293T and in NIH3T3 cells, TIP5 is associated with the promoter, but not with the coding region of the 28srRNA gene. </small></p>
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<p><small><strong> Figure 2. Western blot analysis using the Diagenode antibody directed against TIP5 </strong><br />Western blot was performed on 150 μg nuclear extract from either NIH3T3 or HeLa cells with the Diagenode antibody against TIP5 (cat. No. CS-090-100), diluted 1:1,000 in PBS containing 5% milk powder and 0.1% Tween- 20. The molecular weight marker is shown on the left, the location of the protein of interest is indicated on the right. </small></p>
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<p><small><strong> Figure 2. Western blot analysis using the Diagenode antibody directed against TIP5 </strong><br />Western blot was performed on 150 μg nuclear extract from either NIH3T3 or HeLa cells with the Diagenode antibody against TIP5 (cat. No. CS-090-100), diluted 1:1,000 in PBS containing 5% milk powder and 0.1% Tween- 20. The molecular weight marker is shown on the left, the location of the protein of interest is indicated on the right. </small></p>
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<p><small><strong> Figure 2. Western blot analysis using the Diagenode antibody directed against TIP5 </strong><br />Western blot was performed on 150 μg nuclear extract from either NIH3T3 or HeLa cells with the Diagenode antibody against TIP5 (cat. No. CS-090-100), diluted 1:1,000 in PBS containing 5% milk powder and 0.1% Tween- 20. The molecular weight marker is shown on the left, the location of the protein of interest is indicated on the right. </small></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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<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' => 'Prostate cancer is driven by a combination of genetic and/or epigenetic alterations. Epigenetic alterations are frequently observed in all human cancers, yet how aberrant epigenetic signatures are established is poorly understood. Here we show that the gene encoding BAZ2A (TIP5), a factor previously implicated in epigenetic rRNA gene silencing, is overexpressed in prostate cancer and is paradoxically involved in maintaining prostate cancer cell growth, a feature specific to cancer cells. BAZ2A regulates numerous protein-coding genes and directly interacts with EZH2 to maintain epigenetic silencing at genes repressed in metastasis. BAZ2A overexpression is tightly associated with a molecular subtype displaying a CpG island methylator phenotype (CIMP). Finally, high BAZ2A levels serve as an independent predictor of biochemical recurrence in a cohort of 7,682 individuals with prostate cancer. This work identifies a new aberrant role for the epigenetic regulator BAZ2A, which can also serve as a useful marker for metastatic potential in prostate cancer.',
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<p>Learn more about: <a href="https://www.diagenode.com/applications/western-blot">Loading control, MW marker visualization</a><em>. <br /></em></p>
<p><em></em>Check our selection of antibodies validated in Western blot.</p>',
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<p><span style="font-weight: 400;">Diagenode’s highly validated antibodies:</span></p>
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<li>Highly sensitive and specific</li>
<li>Cost-effective (requires less antibody per reaction)</li>
<li>Batch-specific data is available on the website</li>
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'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>
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<div class="small-12 columns"><center></center>
<p><br />Chromatin immunoprecipitation (<b>ChIP</b>) is a technique to study the associations of proteins with the specific genomic regions in intact cells. One of the most important steps of this protocol is the immunoprecipitation of targeted protein using the antibody specifically recognizing it. The quality of antibodies used in ChIP is essential for the success of the experiment. Diagenode offers extensively validated ChIP-grade antibodies, confirmed for their specificity, and high level of performance in ChIP. Each batch is validated, and batch-specific data are available on the website.</p>
<p></p>
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<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
<div class="row">
<div class="small-12 medium-6 large-6 columns"><img src="https://www.diagenode.com/img/product/antibodies/C15410003-fig1-ChIP.jpg" alt="" width="400" height="315" /> </div>
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<p>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' => 'The RNA helicase DHX9 establishes nucleolar heterochromatin, and this activity is required for embryonic stem cell differentiation',
'authors' => 'Leone S. et al.',
'description' => '<p>Long non-coding RNAs (lncRNAs) have been implicated in the regulation of chromatin conformation and epigenetic patterns. lncRNA expression levels are widely taken as an indicator for functional properties. However, the role of RNA processing in modulating distinct features of the same lncRNA is less understood. The establishment of heterochromatin at rRNA genes depends on the processing of IGS-rRNA into pRNA, a reaction that is impaired in embryonic stem cells (ESCs) and activated only upon differentiation. The production of mature pRNA is essential since it guides the repressor TIP5 to rRNA genes, and IGS-rRNA abolishes this process. Through screening for IGS-rRNA-binding proteins, we here identify the RNA helicase DHX9 as a regulator of pRNA processing. DHX9 binds to rRNA genes only upon ESC differentiation and its activity guides TIP5 to rRNA genes and establishes heterochromatin. Remarkably, ESCs depleted of DHX9 are unable to differentiate and this phenotype is reverted by the addition of pRNA, whereas providing IGS-rRNA and pRNA mutants deficient for TIP5 binding are not sufficient. Our results reveal insights into lncRNA biogenesis during development and support a model in which the state of rRNA gene chromatin is part of the regulatory network that controls exit from pluripotency and initiation of differentiation pathways.</p>',
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'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28588071',
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'description' => '<p>Epigenetic, transcriptional and signaling processes in the nucleolus regulate rRNA transcription and cell growth. We report here that the tumor suppressor ING1b binds rDNA, regulates rDNA chromatin modifications and affects nucleolar localization of mTOR to modulate rRNA levels. ING1 represses rDNA transcription by recruiting HDAC1 to rDNA loci, increasing its association with the NoRC complex and deacetylating the histone H3K9 and H3K27 marks of active transcription. Loss of ING1 enhances nucleolar localization of phospho-mTOR and its association with Raptor and GβL, even during rapamycin treatment. ING1 inhibits rDNA transcription by inhibiting UBF activity and its interaction with mTOR. Regulation of rDNA heterochromatin and rRNA synthesis by ING1 is also apparent during normal cell growth and during cell stress. Moreover, this function was also important during PMA induced differentiation of THP1 cells, since knocking down ING1 affected the process by inhibiting rRNA transcriptional repression. These observations show that ING1 regulates the nucleolar epigenome and rDNA transcription suggesting that regulation of protein synthesis might serve as the basis for ING1 function as a type II tumor suppressor.</p>',
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'description' => 'Prostate cancer is driven by a combination of genetic and/or epigenetic alterations. Epigenetic alterations are frequently observed in all human cancers, yet how aberrant epigenetic signatures are established is poorly understood. Here we show that the gene encoding BAZ2A (TIP5), a factor previously implicated in epigenetic rRNA gene silencing, is overexpressed in prostate cancer and is paradoxically involved in maintaining prostate cancer cell growth, a feature specific to cancer cells. BAZ2A regulates numerous protein-coding genes and directly interacts with EZH2 to maintain epigenetic silencing at genes repressed in metastasis. BAZ2A overexpression is tightly associated with a molecular subtype displaying a CpG island methylator phenotype (CIMP). Finally, high BAZ2A levels serve as an independent predictor of biochemical recurrence in a cohort of 7,682 individuals with prostate cancer. This work identifies a new aberrant role for the epigenetic regulator BAZ2A, which can also serve as a useful marker for metastatic potential in prostate cancer.',
'date' => '2015-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25485837',
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'name' => 'lncRNA Maturation to Initiate Heterochromatin Formation in the Nucleolus Is Required for Exit from Pluripotency in ESCs.',
'authors' => 'Savić N, Bär D, Leone S, Frommel SC, Weber FA, Vollenweider E, Ferrari E, Ziegler U, Kaech A, Shakhova O, Cinelli P, Santoro R',
'description' => 'The open chromatin of embryonic stem cells (ESCs) condenses into repressive heterochromatin as cells exit the pluripotent state. How the 3D genome organization is orchestrated and implicated in pluripotency and lineage specification is not understood. Here, we find that maturation of the long noncoding RNA (lncRNA) pRNA is required for establishment of heterochromatin at ribosomal RNA genes, the genetic component of nucleoli, and this process is inactivated in pluripotent ESCs. By using mature pRNA to tether heterochromatin at nucleoli of ESCs, we find that localized heterochromatin condensation of ribosomal RNA genes initiates establishment of highly condensed chromatin structures outside of the nucleolus. Moreover, we reveal that formation of such highly condensed, transcriptionally repressed heterochromatin promotes transcriptional activation of differentiation genes and loss of pluripotency. Our findings unravel the nucleolus as an active regulator of chromatin plasticity and pluripotency and challenge current views on heterochromatin regulation and function in ESCs.',
'date' => '2014-12-04',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25479748',
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'name' => 'Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase I transcription.',
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'description' => 'Nucleolin is a multi-functional nucleolar protein that is required for ribosomal RNA gene (rRNA) transcription in vivo, but the mechanism by which nucleolin modulates RNA polymerase I (RNAPI) transcription is not well understood. Nucleolin depletion results in an increase in the heterochromatin mark H3K9me2 and a decrease in H4K12Ac and H3K4me3 euchromatin histone marks in rRNA genes. ChIP-seq experiments identified an enrichment of nucleolin in the ribosomal DNA (rDNA) coding and promoter region. Nucleolin is preferentially associated with unmethylated rRNA genes and its depletion leads to the accumulation of RNAPI at the beginning of the transcription unit and a decrease in UBF along the coding and promoter regions. Nucleolin is able to affect the binding of transcription termination factor-1 on the promoter-proximal terminator T0, thus inhibiting the recruitment of TIP5 and HDAC1 and the establishment of a repressive heterochromatin state. These results reveal the importance of nucleolin for the maintenance of the euchromatin state and transcription elongation of rDNA.',
'date' => '2012-08-02',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22859736',
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'description' => 'Maintenance of specific heterochromatic domains is crucial for genome stability. In eukaryotic cells, a fraction of the tandem-repeated ribosomal RNA (rRNA) genes is organized in the heterochromatic structures. The principal determinant of rDNA silencing is the nucleolar remodelling complex, NoRC, that consists of TIP5 (TTF-1-interacting protein-5) and the ATPase SNF2h. Here we showed that TIP5 not only mediates the establishment of rDNA silencing but also the formation of perinucleolar heterochromatin that contains centric and pericentric repeats. Our data indicated that the TIP5-mediated heterochromatin is indispensable for stability of silent rRNA genes and of major and minor satellite repeats. Moreover, depletion of TIP5 impairs rDNA silencing, upregulates rDNA transcription levels and induces cell transformation. These findings point to a role of TIP5 in protecting genome stability and suggest that it can play a role in the cellular transformation process.',
'date' => '2010-07-07',
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'description' => 'ATP-dependent chromatin remodeling complexes rearrange nucleosomes by altering the position of DNA around the histone octamer. Although chromatin remodelers and the histone variant H2A.Z colocalize on transcriptional control regions, whether H2A.Z directly affects remodeler association or activity is unclear. We determined the relative association of remodelers with H2A.Z chromatin and tested whether replacement of H2A.Z in a nucleosome altered the activity of remodeling enzymes. Many families of remodelers showed increased association with H2A.Z chromatin, but only the ISWI family of chromatin remodelers showed stimulated activity in vitro. An acidic patch on the nucleosome surface, extended by inclusion of H2A.Z in nucleosomes and essential for viability, is required for ISWI stimulation. We conclude that H2A.Z incorporation increases nucleosome remodeling activity of the largest class of mammalian remodelers (ISWI) and that it correlates with increased association of other remodelers to chromatin. This reveals two possible modes for regulation of a remodeler by a histone variant.',
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'description' => 'Selection of mammalian high-producer cell lines remains a major challenge for the biopharmaceutical manufacturing industry. Ribosomal RNA (rRNA) genes encode the major component of the ribosome but many rRNA gene copies are not transcribed due to epigenetic silencing by the nucleolar remodelling complex (NoRC) [6], which may limit the cell's full production capacity. Here we show that the knockdown of TIP5, a subunit of NoRC, decreases the number of silent rRNA genes, upregulates rRNA transcription, enhances ribosome synthesis and increases production of recombinant proteins. However, general enhancement of rRNA transcription rate did not stimulate protein synthesis. Our data demonstrates that the number of transcriptionally competent rRNA genes limits efficient ribosome synthesis. Epigenetic engineering of ribosomal RNA genes offers new possibilities for improving biopharmaceutical manufacturing and provides novel insights into the complex regulatory network which governs the translation machinery in normal cellular processes as well as in pathological conditions like cancer.',
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<p><small><sup>*</sup> Please note that of the optimal antibody amount per IP should be determined by the end-user. We recommend testing 1-10 μl per IP.</small></p>',
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'description' => '<p><span>Alternative names: <strong>BAZ2A</strong>, <strong>WALp3</strong></span></p>
<p><span>Polyclonal antibody raised in rabbit against <strong>TIP5 (Transcription termination factor I-interacting protein 5)</strong>, using the recombinant protein.</span></p>',
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<div class="small-4 columns">
<p><img src="https://www.diagenode.com/img/product/antibodies/C15310090_fig2.png" alt="TIP5 Antibody ChIP Grade" style="display: block; margin-left: auto; margin-right: auto;" /></p>
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode antibody directed against TIP5 </strong><br />ChIP assays were performed using the Diagenode antibody against TIP5 (cat. No. CS-090-100). Chromatin from HEK293T and NIH3T3 cells was formaldehyde cross-linked and sheared with the Bioruptor (Diagenode) to yield fragments with an average length of 200 to 400 bp. ChIP was performed overnight at 4°C with 100 μg sheared chromatin and either 5 μl of the TIP5 antibody or 5 μl IgG which was used as negative IP control. The IP’d DNA was analysed by qPCR with primer sets for the promoter and the coding region of the 28s ribosomal RNA gene. Figure 1 shows the recovery by the TIP5 antibody and by IgG (set to 1), normalised to the input DNA. These results show that, both in HEK293T and in NIH3T3 cells, TIP5 is associated with the promoter, but not with the coding region of the 28srRNA gene. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15310090_fig1.png" alt="TIP5 Antibody validated in Western Blot" style="display: block; margin-left: auto; margin-right: auto;" /></p>
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<div class="small-8 columns">
<p><small><strong> Figure 2. Western blot analysis using the Diagenode antibody directed against TIP5 </strong><br />Western blot was performed on 150 μg nuclear extract from either NIH3T3 or HeLa cells with the Diagenode antibody against TIP5 (cat. No. CS-090-100), diluted 1:1,000 in PBS containing 5% milk powder and 0.1% Tween- 20. The molecular weight marker is shown on the left, the location of the protein of interest is indicated on the right. </small></p>
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<p>Learn more about: <a href="https://www.diagenode.com/applications/western-blot">Loading control, MW marker visualization</a><em>. <br /></em></p>
<p><em></em>Check our selection of antibodies validated in Western blot.</p>',
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<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>
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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>
<p></p>
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<p><strong>ChIP results</strong> obtained with the antibody directed against H3K4me3 (Cat. No. <a href="../p/h3k4me3-polyclonal-antibody-premium-50-ug-50-ul">C15410003</a>). </p>
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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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'name' => 'The RNA helicase DHX9 establishes nucleolar heterochromatin, and this activity is required for embryonic stem cell differentiation',
'authors' => 'Leone S. et al.',
'description' => '<p>Long non-coding RNAs (lncRNAs) have been implicated in the regulation of chromatin conformation and epigenetic patterns. lncRNA expression levels are widely taken as an indicator for functional properties. However, the role of RNA processing in modulating distinct features of the same lncRNA is less understood. The establishment of heterochromatin at rRNA genes depends on the processing of IGS-rRNA into pRNA, a reaction that is impaired in embryonic stem cells (ESCs) and activated only upon differentiation. The production of mature pRNA is essential since it guides the repressor TIP5 to rRNA genes, and IGS-rRNA abolishes this process. Through screening for IGS-rRNA-binding proteins, we here identify the RNA helicase DHX9 as a regulator of pRNA processing. DHX9 binds to rRNA genes only upon ESC differentiation and its activity guides TIP5 to rRNA genes and establishes heterochromatin. Remarkably, ESCs depleted of DHX9 are unable to differentiate and this phenotype is reverted by the addition of pRNA, whereas providing IGS-rRNA and pRNA mutants deficient for TIP5 binding are not sufficient. Our results reveal insights into lncRNA biogenesis during development and support a model in which the state of rRNA gene chromatin is part of the regulatory network that controls exit from pluripotency and initiation of differentiation pathways.</p>',
'date' => '2017-07-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28588071',
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'name' => 'ING1 regulates rRNA levels by altering nucleolar chromatin structure and mTOR localization',
'authors' => 'Rajarajacholan U.K. et al.',
'description' => '<p>Epigenetic, transcriptional and signaling processes in the nucleolus regulate rRNA transcription and cell growth. We report here that the tumor suppressor ING1b binds rDNA, regulates rDNA chromatin modifications and affects nucleolar localization of mTOR to modulate rRNA levels. ING1 represses rDNA transcription by recruiting HDAC1 to rDNA loci, increasing its association with the NoRC complex and deacetylating the histone H3K9 and H3K27 marks of active transcription. Loss of ING1 enhances nucleolar localization of phospho-mTOR and its association with Raptor and GβL, even during rapamycin treatment. ING1 inhibits rDNA transcription by inhibiting UBF activity and its interaction with mTOR. Regulation of rDNA heterochromatin and rRNA synthesis by ING1 is also apparent during normal cell growth and during cell stress. Moreover, this function was also important during PMA induced differentiation of THP1 cells, since knocking down ING1 affected the process by inhibiting rRNA transcriptional repression. These observations show that ING1 regulates the nucleolar epigenome and rDNA transcription suggesting that regulation of protein synthesis might serve as the basis for ING1 function as a type II tumor suppressor.</p>',
'date' => '2016-11-29',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27903908',
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'name' => 'BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence.',
'authors' => 'Gu L, Frommel SC, Oakes CC, Simon R, Grupp K, Gerig CY, Bär D, Robinson MD, Baer C, Weiss M, Gu Z, Schapira M, Kuner R, Sültmann H, Provenzano M, , Yaspo ML, Brors B, Korbel J, Schlomm T, Sauter G, Eils R, Plass C, Santoro R',
'description' => 'Prostate cancer is driven by a combination of genetic and/or epigenetic alterations. Epigenetic alterations are frequently observed in all human cancers, yet how aberrant epigenetic signatures are established is poorly understood. Here we show that the gene encoding BAZ2A (TIP5), a factor previously implicated in epigenetic rRNA gene silencing, is overexpressed in prostate cancer and is paradoxically involved in maintaining prostate cancer cell growth, a feature specific to cancer cells. BAZ2A regulates numerous protein-coding genes and directly interacts with EZH2 to maintain epigenetic silencing at genes repressed in metastasis. BAZ2A overexpression is tightly associated with a molecular subtype displaying a CpG island methylator phenotype (CIMP). Finally, high BAZ2A levels serve as an independent predictor of biochemical recurrence in a cohort of 7,682 individuals with prostate cancer. This work identifies a new aberrant role for the epigenetic regulator BAZ2A, which can also serve as a useful marker for metastatic potential in prostate cancer.',
'date' => '2015-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25485837',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
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'id' => '2485',
'name' => 'lncRNA Maturation to Initiate Heterochromatin Formation in the Nucleolus Is Required for Exit from Pluripotency in ESCs.',
'authors' => 'Savić N, Bär D, Leone S, Frommel SC, Weber FA, Vollenweider E, Ferrari E, Ziegler U, Kaech A, Shakhova O, Cinelli P, Santoro R',
'description' => 'The open chromatin of embryonic stem cells (ESCs) condenses into repressive heterochromatin as cells exit the pluripotent state. How the 3D genome organization is orchestrated and implicated in pluripotency and lineage specification is not understood. Here, we find that maturation of the long noncoding RNA (lncRNA) pRNA is required for establishment of heterochromatin at ribosomal RNA genes, the genetic component of nucleoli, and this process is inactivated in pluripotent ESCs. By using mature pRNA to tether heterochromatin at nucleoli of ESCs, we find that localized heterochromatin condensation of ribosomal RNA genes initiates establishment of highly condensed chromatin structures outside of the nucleolus. Moreover, we reveal that formation of such highly condensed, transcriptionally repressed heterochromatin promotes transcriptional activation of differentiation genes and loss of pluripotency. Our findings unravel the nucleolus as an active regulator of chromatin plasticity and pluripotency and challenge current views on heterochromatin regulation and function in ESCs.',
'date' => '2014-12-04',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25479748',
'doi' => '',
'modified' => '2015-07-24 15:39:04',
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'name' => 'Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase I transcription.',
'authors' => 'Cong R, Das S, Ugrinova I, Kumar S, Mongelard F, Wong J, Bouvet P',
'description' => 'Nucleolin is a multi-functional nucleolar protein that is required for ribosomal RNA gene (rRNA) transcription in vivo, but the mechanism by which nucleolin modulates RNA polymerase I (RNAPI) transcription is not well understood. Nucleolin depletion results in an increase in the heterochromatin mark H3K9me2 and a decrease in H4K12Ac and H3K4me3 euchromatin histone marks in rRNA genes. ChIP-seq experiments identified an enrichment of nucleolin in the ribosomal DNA (rDNA) coding and promoter region. Nucleolin is preferentially associated with unmethylated rRNA genes and its depletion leads to the accumulation of RNAPI at the beginning of the transcription unit and a decrease in UBF along the coding and promoter regions. Nucleolin is able to affect the binding of transcription termination factor-1 on the promoter-proximal terminator T0, thus inhibiting the recruitment of TIP5 and HDAC1 and the establishment of a repressive heterochromatin state. These results reveal the importance of nucleolin for the maintenance of the euchromatin state and transcription elongation of rDNA.',
'date' => '2012-08-02',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22859736',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
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(int) 5 => array(
'id' => '557',
'name' => 'The NoRC complex mediates the heterochromatin formation and stability of silent rRNA genes and centromeric repeats',
'authors' => 'Guetg C, Lienemann P, Sirri V, Grummt I, Hernandez-Verdun D, Hottiger MO, Fussenegger M, Santoro R',
'description' => 'Maintenance of specific heterochromatic domains is crucial for genome stability. In eukaryotic cells, a fraction of the tandem-repeated ribosomal RNA (rRNA) genes is organized in the heterochromatic structures. The principal determinant of rDNA silencing is the nucleolar remodelling complex, NoRC, that consists of TIP5 (TTF-1-interacting protein-5) and the ATPase SNF2h. Here we showed that TIP5 not only mediates the establishment of rDNA silencing but also the formation of perinucleolar heterochromatin that contains centric and pericentric repeats. Our data indicated that the TIP5-mediated heterochromatin is indispensable for stability of silent rRNA genes and of major and minor satellite repeats. Moreover, depletion of TIP5 impairs rDNA silencing, upregulates rDNA transcription levels and induces cell transformation. These findings point to a role of TIP5 in protecting genome stability and suggest that it can play a role in the cellular transformation process.',
'date' => '2010-07-07',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/20168299',
'doi' => '',
'modified' => '2015-07-24 15:38:58',
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'name' => 'Chromatin remodeling by imitation switch (ISWI) class ATP-dependent remodelers is stimulated by histone variant H2A.Z.',
'authors' => 'Goldman JA, Garlick JD, Kingston RE',
'description' => 'ATP-dependent chromatin remodeling complexes rearrange nucleosomes by altering the position of DNA around the histone octamer. Although chromatin remodelers and the histone variant H2A.Z colocalize on transcriptional control regions, whether H2A.Z directly affects remodeler association or activity is unclear. We determined the relative association of remodelers with H2A.Z chromatin and tested whether replacement of H2A.Z in a nucleosome altered the activity of remodeling enzymes. Many families of remodelers showed increased association with H2A.Z chromatin, but only the ISWI family of chromatin remodelers showed stimulated activity in vitro. An acidic patch on the nucleosome surface, extended by inclusion of H2A.Z in nucleosomes and essential for viability, is required for ISWI stimulation. We conclude that H2A.Z incorporation increases nucleosome remodeling activity of the largest class of mammalian remodelers (ISWI) and that it correlates with increased association of other remodelers to chromatin. This reveals two possible modes for regulation of a remodeler by a histone variant.',
'date' => '2010-02-12',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19940112',
'doi' => '',
'modified' => '2015-07-24 15:38:57',
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'id' => '90',
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode antibody directed against TIP5 </strong><br />ChIP assays were performed using the Diagenode antibody against TIP5 (cat. No. CS-090-100). Chromatin from HEK293T and NIH3T3 cells was formaldehyde cross-linked and sheared with the Bioruptor (Diagenode) to yield fragments with an average length of 200 to 400 bp. ChIP was performed overnight at 4°C with 100 μg sheared chromatin and either 5 μl of the TIP5 antibody or 5 μl IgG which was used as negative IP control. The IP’d DNA was analysed by qPCR with primer sets for the promoter and the coding region of the 28s ribosomal RNA gene. Figure 1 shows the recovery by the TIP5 antibody and by IgG (set to 1), normalised to the input DNA. These results show that, both in HEK293T and in NIH3T3 cells, TIP5 is associated with the promoter, but not with the coding region of the 28srRNA gene. </small></p>
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<p><small><strong> Figure 2. Western blot analysis using the Diagenode antibody directed against TIP5 </strong><br />Western blot was performed on 150 μg nuclear extract from either NIH3T3 or HeLa cells with the Diagenode antibody against TIP5 (cat. No. CS-090-100), diluted 1:1,000 in PBS containing 5% milk powder and 0.1% Tween- 20. The molecular weight marker is shown on the left, the location of the protein of interest is indicated on the right. </small></p>
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode antibody directed against TIP5 </strong><br />ChIP assays were performed using the Diagenode antibody against TIP5 (cat. No. CS-090-100). Chromatin from HEK293T and NIH3T3 cells was formaldehyde cross-linked and sheared with the Bioruptor (Diagenode) to yield fragments with an average length of 200 to 400 bp. ChIP was performed overnight at 4°C with 100 μg sheared chromatin and either 5 μl of the TIP5 antibody or 5 μl IgG which was used as negative IP control. The IP’d DNA was analysed by qPCR with primer sets for the promoter and the coding region of the 28s ribosomal RNA gene. Figure 1 shows the recovery by the TIP5 antibody and by IgG (set to 1), normalised to the input DNA. These results show that, both in HEK293T and in NIH3T3 cells, TIP5 is associated with the promoter, but not with the coding region of the 28srRNA gene. </small></p>
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<p><small><strong> Figure 2. Western blot analysis using the Diagenode antibody directed against TIP5 </strong><br />Western blot was performed on 150 μg nuclear extract from either NIH3T3 or HeLa cells with the Diagenode antibody against TIP5 (cat. No. CS-090-100), diluted 1:1,000 in PBS containing 5% milk powder and 0.1% Tween- 20. The molecular weight marker is shown on the left, the location of the protein of interest is indicated on the right. </small></p>
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<p><small><strong> Figure 1. ChIP results obtained with the Diagenode antibody directed against TIP5 </strong><br />ChIP assays were performed using the Diagenode antibody against TIP5 (cat. No. CS-090-100). Chromatin from HEK293T and NIH3T3 cells was formaldehyde cross-linked and sheared with the Bioruptor (Diagenode) to yield fragments with an average length of 200 to 400 bp. ChIP was performed overnight at 4°C with 100 μg sheared chromatin and either 5 μl of the TIP5 antibody or 5 μl IgG which was used as negative IP control. The IP’d DNA was analysed by qPCR with primer sets for the promoter and the coding region of the 28s ribosomal RNA gene. Figure 1 shows the recovery by the TIP5 antibody and by IgG (set to 1), normalised to the input DNA. These results show that, both in HEK293T and in NIH3T3 cells, TIP5 is associated with the promoter, but not with the coding region of the 28srRNA gene. </small></p>
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<p><img src="https://www.diagenode.com/img/product/antibodies/C15310090_fig1.png" alt="TIP5 Antibody validated in Western Blot" style="display: block; margin-left: auto; margin-right: auto;" /></p>
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<p><small><strong> Figure 2. Western blot analysis using the Diagenode antibody directed against TIP5 </strong><br />Western blot was performed on 150 μg nuclear extract from either NIH3T3 or HeLa cells with the Diagenode antibody against TIP5 (cat. No. CS-090-100), diluted 1:1,000 in PBS containing 5% milk powder and 0.1% Tween- 20. The molecular weight marker is shown on the left, the location of the protein of interest is indicated on the right. </small></p>
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<p>Learn more about: <a href="https://www.diagenode.com/applications/western-blot">Loading control, MW marker visualization</a><em>. <br /></em></p>
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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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'description' => '<p>Long non-coding RNAs (lncRNAs) have been implicated in the regulation of chromatin conformation and epigenetic patterns. lncRNA expression levels are widely taken as an indicator for functional properties. However, the role of RNA processing in modulating distinct features of the same lncRNA is less understood. The establishment of heterochromatin at rRNA genes depends on the processing of IGS-rRNA into pRNA, a reaction that is impaired in embryonic stem cells (ESCs) and activated only upon differentiation. The production of mature pRNA is essential since it guides the repressor TIP5 to rRNA genes, and IGS-rRNA abolishes this process. Through screening for IGS-rRNA-binding proteins, we here identify the RNA helicase DHX9 as a regulator of pRNA processing. DHX9 binds to rRNA genes only upon ESC differentiation and its activity guides TIP5 to rRNA genes and establishes heterochromatin. Remarkably, ESCs depleted of DHX9 are unable to differentiate and this phenotype is reverted by the addition of pRNA, whereas providing IGS-rRNA and pRNA mutants deficient for TIP5 binding are not sufficient. Our results reveal insights into lncRNA biogenesis during development and support a model in which the state of rRNA gene chromatin is part of the regulatory network that controls exit from pluripotency and initiation of differentiation pathways.</p>',
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'description' => 'Prostate cancer is driven by a combination of genetic and/or epigenetic alterations. Epigenetic alterations are frequently observed in all human cancers, yet how aberrant epigenetic signatures are established is poorly understood. Here we show that the gene encoding BAZ2A (TIP5), a factor previously implicated in epigenetic rRNA gene silencing, is overexpressed in prostate cancer and is paradoxically involved in maintaining prostate cancer cell growth, a feature specific to cancer cells. BAZ2A regulates numerous protein-coding genes and directly interacts with EZH2 to maintain epigenetic silencing at genes repressed in metastasis. BAZ2A overexpression is tightly associated with a molecular subtype displaying a CpG island methylator phenotype (CIMP). Finally, high BAZ2A levels serve as an independent predictor of biochemical recurrence in a cohort of 7,682 individuals with prostate cancer. This work identifies a new aberrant role for the epigenetic regulator BAZ2A, which can also serve as a useful marker for metastatic potential in prostate cancer.',
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'id' => '2485',
'name' => 'lncRNA Maturation to Initiate Heterochromatin Formation in the Nucleolus Is Required for Exit from Pluripotency in ESCs.',
'authors' => 'Savić N, Bär D, Leone S, Frommel SC, Weber FA, Vollenweider E, Ferrari E, Ziegler U, Kaech A, Shakhova O, Cinelli P, Santoro R',
'description' => 'The open chromatin of embryonic stem cells (ESCs) condenses into repressive heterochromatin as cells exit the pluripotent state. How the 3D genome organization is orchestrated and implicated in pluripotency and lineage specification is not understood. Here, we find that maturation of the long noncoding RNA (lncRNA) pRNA is required for establishment of heterochromatin at ribosomal RNA genes, the genetic component of nucleoli, and this process is inactivated in pluripotent ESCs. By using mature pRNA to tether heterochromatin at nucleoli of ESCs, we find that localized heterochromatin condensation of ribosomal RNA genes initiates establishment of highly condensed chromatin structures outside of the nucleolus. Moreover, we reveal that formation of such highly condensed, transcriptionally repressed heterochromatin promotes transcriptional activation of differentiation genes and loss of pluripotency. Our findings unravel the nucleolus as an active regulator of chromatin plasticity and pluripotency and challenge current views on heterochromatin regulation and function in ESCs.',
'date' => '2014-12-04',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/25479748',
'doi' => '',
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'created' => '2015-07-24 15:39:04',
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[maximum depth reached]
)
),
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'id' => '941',
'name' => 'Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase I transcription.',
'authors' => 'Cong R, Das S, Ugrinova I, Kumar S, Mongelard F, Wong J, Bouvet P',
'description' => 'Nucleolin is a multi-functional nucleolar protein that is required for ribosomal RNA gene (rRNA) transcription in vivo, but the mechanism by which nucleolin modulates RNA polymerase I (RNAPI) transcription is not well understood. Nucleolin depletion results in an increase in the heterochromatin mark H3K9me2 and a decrease in H4K12Ac and H3K4me3 euchromatin histone marks in rRNA genes. ChIP-seq experiments identified an enrichment of nucleolin in the ribosomal DNA (rDNA) coding and promoter region. Nucleolin is preferentially associated with unmethylated rRNA genes and its depletion leads to the accumulation of RNAPI at the beginning of the transcription unit and a decrease in UBF along the coding and promoter regions. Nucleolin is able to affect the binding of transcription termination factor-1 on the promoter-proximal terminator T0, thus inhibiting the recruitment of TIP5 and HDAC1 and the establishment of a repressive heterochromatin state. These results reveal the importance of nucleolin for the maintenance of the euchromatin state and transcription elongation of rDNA.',
'date' => '2012-08-02',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/22859736',
'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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'id' => '557',
'name' => 'The NoRC complex mediates the heterochromatin formation and stability of silent rRNA genes and centromeric repeats',
'authors' => 'Guetg C, Lienemann P, Sirri V, Grummt I, Hernandez-Verdun D, Hottiger MO, Fussenegger M, Santoro R',
'description' => 'Maintenance of specific heterochromatic domains is crucial for genome stability. In eukaryotic cells, a fraction of the tandem-repeated ribosomal RNA (rRNA) genes is organized in the heterochromatic structures. The principal determinant of rDNA silencing is the nucleolar remodelling complex, NoRC, that consists of TIP5 (TTF-1-interacting protein-5) and the ATPase SNF2h. Here we showed that TIP5 not only mediates the establishment of rDNA silencing but also the formation of perinucleolar heterochromatin that contains centric and pericentric repeats. Our data indicated that the TIP5-mediated heterochromatin is indispensable for stability of silent rRNA genes and of major and minor satellite repeats. Moreover, depletion of TIP5 impairs rDNA silencing, upregulates rDNA transcription levels and induces cell transformation. These findings point to a role of TIP5 in protecting genome stability and suggest that it can play a role in the cellular transformation process.',
'date' => '2010-07-07',
'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/20168299',
'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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'id' => '539',
'name' => 'Chromatin remodeling by imitation switch (ISWI) class ATP-dependent remodelers is stimulated by histone variant H2A.Z.',
'authors' => 'Goldman JA, Garlick JD, Kingston RE',
'description' => 'ATP-dependent chromatin remodeling complexes rearrange nucleosomes by altering the position of DNA around the histone octamer. Although chromatin remodelers and the histone variant H2A.Z colocalize on transcriptional control regions, whether H2A.Z directly affects remodeler association or activity is unclear. We determined the relative association of remodelers with H2A.Z chromatin and tested whether replacement of H2A.Z in a nucleosome altered the activity of remodeling enzymes. Many families of remodelers showed increased association with H2A.Z chromatin, but only the ISWI family of chromatin remodelers showed stimulated activity in vitro. An acidic patch on the nucleosome surface, extended by inclusion of H2A.Z in nucleosomes and essential for viability, is required for ISWI stimulation. We conclude that H2A.Z incorporation increases nucleosome remodeling activity of the largest class of mammalian remodelers (ISWI) and that it correlates with increased association of other remodelers to chromatin. This reveals two possible modes for regulation of a remodeler by a histone variant.',
'date' => '2010-02-12',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19940112',
'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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'name' => 'Epigenetic engineering of ribosomal RNA genes enhances protein production.',
'authors' => 'Santoro R, Lienemann P, Fussenegger M',
'description' => 'Selection of mammalian high-producer cell lines remains a major challenge for the biopharmaceutical manufacturing industry. Ribosomal RNA (rRNA) genes encode the major component of the ribosome but many rRNA gene copies are not transcribed due to epigenetic silencing by the nucleolar remodelling complex (NoRC) [6], which may limit the cell's full production capacity. Here we show that the knockdown of TIP5, a subunit of NoRC, decreases the number of silent rRNA genes, upregulates rRNA transcription, enhances ribosome synthesis and increases production of recombinant proteins. However, general enhancement of rRNA transcription rate did not stimulate protein synthesis. Our data demonstrates that the number of transcriptionally competent rRNA genes limits efficient ribosome synthesis. Epigenetic engineering of ribosomal RNA genes offers new possibilities for improving biopharmaceutical manufacturing and provides novel insights into the complex regulatory network which governs the translation machinery in normal cellular processes as well as in pathological conditions like cancer.',
'date' => '2009-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19680546',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
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)
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'description' => 'Selection of mammalian high-producer cell lines remains a major challenge for the biopharmaceutical manufacturing industry. Ribosomal RNA (rRNA) genes encode the major component of the ribosome but many rRNA gene copies are not transcribed due to epigenetic silencing by the nucleolar remodelling complex (NoRC) [6], which may limit the cell's full production capacity. Here we show that the knockdown of TIP5, a subunit of NoRC, decreases the number of silent rRNA genes, upregulates rRNA transcription, enhances ribosome synthesis and increases production of recombinant proteins. However, general enhancement of rRNA transcription rate did not stimulate protein synthesis. Our data demonstrates that the number of transcriptionally competent rRNA genes limits efficient ribosome synthesis. Epigenetic engineering of ribosomal RNA genes offers new possibilities for improving biopharmaceutical manufacturing and provides novel insights into the complex regulatory network which governs the translation machinery in normal cellular processes as well as in pathological conditions like cancer.',
'date' => '2009-01-01',
'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/19680546',
'doi' => '',
'modified' => '2015-07-24 15:38:56',
'created' => '2015-07-24 15:38:56',
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$externalLink = ' <a href="https://www.ncbi.nlm.nih.gov/pubmed/19680546" 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
×
