OneDay ChIP kit

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<p><span>For ChIP-qPCR: <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR Kit</a> and <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE Kit</a></span></p>
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<p>For low-input ChIP/ChIP-seq: <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP Kit</a></p>
<p><strong>&nbsp;</strong></p>
<p class="text-right"><a class="tiny alert button" href="https://www.diagenode.com/en/categories/chip-grade-antibodies"> Check out our ChIP-grade antibodies</a></p>',
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<p><span>For ChIP-qPCR: <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR Kit</a> and <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE Kit</a></span></p>
<p><span>For ChIP-seq: <a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq Kit for Histones</a>, <a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a> and <a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></span></p>
<p>For low-input ChIP/ChIP-seq: <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP Kit</a></p>
<p><strong>&nbsp;</strong></p>
<p class="text-right"><a class="tiny alert button" href="https://www.diagenode.com/en/categories/chip-grade-antibodies"> Check out our ChIP-grade antibodies</a></p>',
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<p>For low-input ChIP/ChIP-seq: <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP Kit</a></p>
<p><strong>&nbsp;</strong></p>
<p class="text-right"><a class="tiny alert button" href="https://www.diagenode.com/en/categories/chip-grade-antibodies"> Check out our ChIP-grade antibodies</a></p>',
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<p class="text-justify">Chromatin Immunoprecipitation (ChIP) coupled with quantitative PCR can be used to investigate protein-DNA interaction at known genomic binding sites. if sites are not known, qPCR primers can also be designed against potential regulatory regions such as promoters. ChIP-qPCR is advantageous in studies that focus on specific genes and potential regulatory regions across differing experimental conditions as the cost of performing real-time PCR is minimal. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</p>
<p class="text-justify"><strong>The ChIP-qPCR workflow</strong></p>
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<div class="small-12 medium-12 large-12 columns text-center"><br /> <img src="https://www.diagenode.com/img/chip-qpcr-diagram.png" /></div>
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<li class="large-12 columns"><strong>Chromatin preparation: </strong>cell fixation (cross-linking) of chromatin-bound proteins such as histones or transcription factors to DNA followed by cell lysis.</li>
<li class="large-12 columns"><strong>Chromatin shearing: </strong>fragmentation of chromatin<strong> </strong>by sonication down to desired fragment size (100-500 bp)</li>
<li class="large-12 columns"><strong>Chromatin IP</strong>: protein-DNA complexe capture using<strong> <a href="https://www.diagenode.com/en/categories/chip-grade-antibodies">specific ChIP-grade antibodies</a></strong>&nbsp;against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: chromatin reverse cross-linking and elution followed by purification<strong> </strong></li>
<li class="large-12 columns"><strong>qPCR and analysis</strong>: using previously designed primers to amplify IP'd material at specific loci</li>
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<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
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<p><span>Diagenode provides kits with optimized reagents and simplified protocols for ChIP including the <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR kit</a>, <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE kit</a>,&nbsp; <a href="https://www.diagenode.com/en/categories/chromatin-ip-chip-seq-kits">iDeal ChIP-seq kits</a>, <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a>, <a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit </a>and <a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation">the ChIPmentation for Histones</a>. This protocol describes the use of the OneDay ChIP Kit.</span></p>
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			'name' => 'Transcription of CLDND1 in human brain endothelial cells is regulated bythe myeloid zinc finger 1.',
			'authors' => 'Shima, Akiho and Matsuoka, Hiroshi and Yamaoka, Alice and Michihara,Akihiro',
			'description' => '<p>Increased permeability of endothelial cells lining the blood vessels in the brain leads to vascular oedema and, potentially, to stroke. The tight junctions (TJs), primarily responsible for the regulation of vascular permeability, are multi-protein complexes comprising the claudin family of proteins and occludin. Several studies have reported that downregulation of the claudin domain containing 1 (CLDND1) gene enhances vascular permeability, which consequently increases the risk of stroke. However, the transcriptional regulation of CLDND1 has not been studied extensively. Therefore, this study aimed to identify the transcription factors (TFs) regulating CLDND1 expression. A luciferase reporter assay identified a silencer within the first intron of CLDND1, which was identified as a potential binding site of the myeloid zinc finger 1 (MZF1) through in silico and TFBIND software analyses, and confirmed through a reporter assay using the MZF1 expression vector and chromatin immunoprecipitation (ChIP) assays. Moreover, the transient overexpression of MZF1 significantly increased the mRNA and protein expression levels of CLDND1, conversely, which were suppressed through the siRNA-mediated MZF1 knockdown. Furthermore, the permeability of FITC-dextran was observed to be increased on MZF1 knockdown as compared to that of the siGFP control. Our data revealed the underlying mechanism of the transcriptional regulation of CLDND1 by the MZF1. The findings suggest a potential role of MZF1 in TJ formation, which could be studied further and applied to prevent cerebral haemorrhage.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33037622',
			'doi' => '10.1111/1440-1681.13416',
			'modified' => '2021-02-19 17:48:44',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'id' => '3748',
			'name' => 'Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis.',
			'authors' => 'Vara C, Paytuví-Gallart A, Cuartero Y, Le Dily F, Garcia F, Salvà-Castro J, Gómez-H L, Julià E, Moutinho C, Aiese Cigliano R, Sanseverino W, Fornas O, Pendás AM, Heyn H, Waters PD, Marti-Renom MA, Ruiz-Herrera A',
			'description' => '<p>Mammalian gametogenesis involves dramatic and tightly regulated chromatin remodeling, whose regulatory pathways remain largely unexplored. Here, we generate a comprehensive high-resolution structural and functional atlas of mouse spermatogenesis by combining in situ chromosome conformation capture sequencing (Hi-C), RNA sequencing (RNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) of CCCTC-binding factor (CTCF) and meiotic cohesins, coupled with confocal and super-resolution microscopy. Spermatogonia presents well-defined compartment patterns and topological domains. However, chromosome occupancy and compartmentalization are highly re-arranged during prophase&nbsp;I, with cohesins bound to active promoters in DNA loops out of the chromosomal axes. Compartment patterns re-emerge in round spermatids, where cohesin occupancy correlates with transcriptional activity of key developmental genes. The compact sperm genome contains compartments with actively transcribed genes but no fine-scale topological domains, concomitant with the presence of protamines. Overall, we demonstrate how genome-wide cohesin occupancy and transcriptional activity is associated with three-dimensional (3D) remodeling during spermatogenesis, ultimately reprogramming the genome for the next generation.</p>',
			'date' => '2019-07-09',
			'pmid' => 'http://www.pubmed.gov/31291573',
			'doi' => '10.1016/j.celrep.2019.06.037',
			'modified' => '2019-08-06 16:12:27',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '3739',
			'name' => 'Resveratrol up-regulates ATP2A3 gene expression in breast cancer cell lines through epigenetic mechanisms.',
			'authors' => 'Izquierdo-Torres E, Hernández-Oliveras A, Meneses-Morales I, Rodríguez G, Fuentes-García G, Zarain-Herzberg Á',
			'description' => '<p>Resveratrol (RSV) is a phytoestrogen which has been related to chemoprevention of several types of cancer. In this work, we show up to a 6-fold increased expression of ATP2A3 gene induced by RSV that triggers apoptosis and changes of intracellular Ca management in MCF-7 and MDA-MB-231 breast cancer cell lines. We explored epigenetic mechanisms for that RSV-induced ATP2A3 up-regulation. The results indicate that RSV-induced ATP2A3 up-regulation correlates with about 50% of reduced HDAC activity and reduced nuclear HDAC2 expression and occupancy on ATP2A3 promoter, increasing the global acetylation of histone H3 and the enrichment of histone mark H3K27Ac on the proximal promoter of the ATP2A3 gene in MDA-MB-231 cells. We also quantified HAT activity, finding that it can be boosted with RSV treatment; however, pharmacological inhibition of p300, one of the main HATs, did not have significant effects in RSV-mediated ATP2A3 gene expression. Additionally, DNMT activity was also reduced in cells treated with RSV, as well as the expression of Methyl-DNA binding proteins MeCP2 and MBD2. However, analysis of the methylation pattern of ATP2A3 gene promoter showed un-methylated promoter in both cell lines. Taken together, the results of this work help to explain, at the molecular level, how ATP2A3 gene is regulated in breast cancer cells, and the benefits of RSV intake observed in epidemiological data, studies with animals, and in vitro models.</p>',
			'date' => '2019-06-04',
			'pmid' => 'http://www.pubmed.gov/31173924',
			'doi' => '10.1016/j.biocel.2019.05.020',
			'modified' => '2019-08-06 16:56:19',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'id' => '3660',
			'name' => 'Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia.',
			'authors' => 'Wernig-Zorc S, Yadav MP, Kopparapu PK, Bemark M, Kristjansdottir HL, Andersson PO, Kanduri C, Kanduri M',
			'description' => '<p>BACKGROUND: Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic and diagnostic implications for several cancers. However, there is no global study exploring the role of 5-hydroxymethylcytosine (5-hmC) levels in CLL. Herein, using mass spectrometry and hMeDIP-sequencing, we analysed the dynamics of 5-hmC during B cell maturation and CLL pathogenesis. RESULTS: We show that na&iuml;ve B-cells had higher levels of 5-hmC and 5-mC compared to non-class switched and class-switched memory B-cells. We found a significant decrease in global 5-mC levels in CLL patients (n&thinsp;=&thinsp;15) compared to na&iuml;ve and memory B cells, with no changes detected between the CLL prognostic groups. On the other hand, global 5-hmC levels of CLL patients were similar to memory B cells and reduced compared to na&iuml;ve B cells. Interestingly, 5-hmC levels were increased at regulatory regions such as gene-body, CpG island shores and shelves and 5-hmC distribution over the gene-body positively correlated with degree of transcriptional activity. Importantly, CLL samples showed aberrant 5-hmC and 5-mC pattern over gene-body compared to well-defined patterns in normal B-cells. Integrated analysis of 5-hmC and RNA-sequencing from CLL datasets identified three novel oncogenic drivers that could have potential roles in CLL development and progression. CONCLUSIONS: Thus, our study suggests that the global loss of 5-hmC, accompanied by its significant increase at the gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Our combined analysis of 5-mC and 5-hmC sequencing provided insights into the potential role of 5-hmC in modulating gene expression changes during CLL pathogenesis.</p>',
			'date' => '2019-01-07',
			'pmid' => 'http://www.pubmed.gov/30616658',
			'doi' => '10.1186/s13072‑018‑0252‑7',
			'modified' => '2019-07-01 11:46:16',
			'created' => '2019-06-21 14:55:31',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 4 => array(
			'id' => '3505',
			'name' => 'Genomic Location of PRMT6-Dependent H3R2 Methylation Is Linked to the Transcriptional Outcome of Associated Genes.',
			'authors' => 'Bouchard C, Sahu P, Meixner M, Nötzold RR, Rust MB, Kremmer E, Feederle R, Hart-Smith G, Finkernagel F, Bartkuhn M, Savai Pullamsetti S, Nist A, Stiewe T, Philipsen S, Bauer UM',
			'description' => '<p>Protein arginine methyltransferase 6 (PRMT6) catalyzes asymmetric dimethylation of histone H3 at arginine 2 (H3R2me2a). This mark has been reported to associate with silent genes. Here, we use a cell model&nbsp;of neural differentiation, which upon PRMT6 knockout exhibits proliferation and differentiation defects. Strikingly, we detect PRMT6-dependent H3R2me2a at active genes, both at promoter and enhancer sites. Loss of H3R2me2a from promoter sites leads to enhanced KMT2A binding and H3K4me3 deposition together with increased target gene transcription, supporting a repressive nature of H3R2me2a. At enhancers, H3R2me2a peaks co-localize with the active enhancer marks H3K4me1 and H3K27ac. Here, loss of H3R2me2a results in reduced KMT2D binding and H3K4me1/H3K27ac deposition together with decreased transcription of associated genes, indicating that H3R2me2a also exerts activation functions. Our work suggests that PRMT6 via H3R2me2a interferes with the deposition of adjacent histone marks and modulates the activity of important differentiation-associated genes by opposing transcriptional effects.</p>',
			'date' => '2018-09-18',
			'pmid' => 'http://www.pubmed.gov/30232013',
			'doi' => '10.1016/j.celrep.2018.08.052',
			'modified' => '2019-02-28 10:05:16',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '3443',
			'name' => 'High-fidelity CRISPR/Cas9- based gene-specific hydroxymethylation rescues gene expression and attenuates renal fibrosis.',
			'authors' => 'Xingbo Xu, Xiaoying Tan, Björn Tampe, Tim Wilhelmi, Melanie S. Hulshoff, Shoji Saito, Tobias Moser, Raghu Kalluri, Gerd Hasenfuss, Elisabeth M. Zeisberg & Michael Zeisberg ',
			'description' => '<p>While suppression of specific genes through aberrant promoter methylation contributes to different diseases including organ fibrosis, gene-specific reactivation technology is not yet available for therapy. TET enzymes catalyze hydroxymethylation of methylated DNA, reactivating gene expression. We here report generation of a high-fidelity CRISPR/Cas9-based gene-specific dioxygenase by fusing an endonuclease deactivated high-fidelity Cas9 (dHFCas9) to TET3 catalytic domain (TET3CD), targeted to specific genes by guiding RNAs (sgRNA). We demonstrate use of this technology in four different anti-fibrotic genes in different cell types in vitro, among them RASAL1 and Klotho, both hypermethylated in kidney fibrosis. Furthermore, in vivo lentiviral delivery of the Rasal1-targeted fusion protein to interstitial cells and of the Klotho-targeted fusion protein to tubular epithelial cells each results in specific gene reactivation and attenuation of fibrosis, providing gene-specific demethylating technology in a disease model.</p>',
			'date' => '2018-08-29',
			'pmid' => 'http://www.pubmed.gov/30158531',
			'doi' => '10.1038/s41467-018-05766-5',
			'modified' => '2019-02-28 10:11:31',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '3522',
			'name' => 'Human papillomavirus type 16 antagonizes IRF6 regulation of IL-1β.',
			'authors' => 'Ainouze M, Rochefort P, Parroche P, Roblot G, Tout I, Briat F, Zannetti C, Marotel M, Goutagny N, Auron P, Traverse-Glehen A, Lunel-Potencier A, Golfier F, Masson M, Robitaille A, Tommasino M, Carreira C, Walzer T, Henry T, Zanier K, Trave G, Hasan UA',
			'description' => '<p>Human papillomavirus type 16 (HPV16) and other oncoviruses have been shown to block innate immune responses and to persist in the host. However, to avoid viral persistence, the immune response attempts to clear the infection. IL-1&beta; is a powerful cytokine produced when viral motifs are sensed by innate receptors that are members of the inflammasome family. Whether oncoviruses such as HPV16 can activate the inflammasome pathway remains unknown. Here, we show that infection of human keratinocytes with HPV16 induced the secretion of IL-1&beta;. Yet, upon expression of the viral early genes, IL-1&beta; transcription was blocked. We went on to show that expression of the viral oncoprotein E6 in human keratinocytes inhibited IRF6 transcription which we revealed regulated IL-1&beta; promoter activity. Preventing E6 expression using siRNA, or using E6 mutants that prevented degradation of p53, showed that p53 regulated IRF6 transcription. HPV16 abrogation of p53 binding to the IRF6 promoter was shown by ChIP in tissues from patients with cervical cancer. Thus E6 inhibition of IRF6 is an escape strategy used by HPV16 to block the production IL-1&beta;. Our findings reveal a struggle between oncoviral persistence and host immunity; which is centered on IL-1&beta; regulation.</p>',
			'date' => '2018-08-08',
			'pmid' => 'http://www.pubmed.gov/30089163',
			'doi' => '10.1371/journal.ppat.1007158',
			'modified' => '2019-02-28 10:14:30',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '3583',
			'name' => 'Human papillomavirus type 16 antagonizes IRF6 regulation of IL-1β.',
			'authors' => 'Ainouze M, Rochefort P, Parroche P, Roblot G, Tout I, Briat F, Zannetti C, Marotel M, Goutagny N, Auron P, Traverse-Glehen A, Lunel-Potencier A, Golfier F, Masson M, Robitaille A, Tommasino M, Carreira C, Walzer T, Henry T, Zanier K, Trave G, Hasan UA',
			'description' => '<p>Human papillomavirus type 16 (HPV16) and other oncoviruses have been shown to block innate immune responses and to persist in the host. However, to avoid viral persistence, the immune response attempts to clear the infection. IL-1&beta; is a powerful cytokine produced when viral motifs are sensed by innate receptors that are members of the inflammasome family. Whether oncoviruses such as HPV16 can activate the inflammasome pathway remains unknown. Here, we show that infection of human keratinocytes with HPV16 induced the secretion of IL-1&beta;. Yet, upon expression of the viral early genes, IL-1&beta; transcription was blocked. We went on to show that expression of the viral oncoprotein E6 in human keratinocytes inhibited IRF6 transcription which we revealed regulated IL-1&beta; promoter activity. Preventing E6 expression using siRNA, or using E6 mutants that prevented degradation of p53, showed that p53 regulated IRF6 transcription. HPV16 abrogation of p53 binding to the IRF6 promoter was shown by ChIP in tissues from patients with cervical cancer. Thus E6 inhibition of IRF6 is an escape strategy used by HPV16 to block the production IL-1&beta;. Our findings reveal a struggle between oncoviral persistence and host immunity; which is centered on IL-1&beta; regulation.</p>',
			'date' => '2018-08-08',
			'pmid' => 'http://www.pubmed.gov/30089163',
			'doi' => '10.1371/journal.ppat.1007158',
			'modified' => '2019-04-17 15:50:02',
			'created' => '2019-04-16 12:25:30',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '3480',
			'name' => 'CTCF-KDM4A complex correlates with histone modifications that negatively regulate  gene expression in cancer cell lines.',
			'authors' => 'Guerra-Calderas L, González-Barrios R, Patiño CC, Alcaraz N, Salgado-Albarrán M, de León DC, Hernández CC, Sánchez-Pérez Y, Maldonado-Martínez HA, De la Rosa-Velazquez IA, Vargas-Romero F, Herrera LA, García-Carrancá A, Soto-Reyes E',
			'description' => '<p>Histone demethylase KDM4A is involved in H3K9me3 and H3K36me3 demethylation, which are epigenetic modifications associated with gene silencing and RNA Polymerase II elongation, respectively. is abnormally expressed in cancer, affecting the expression of multiple targets, such as the gene. This enzyme localizes at the first intron of , and the dissociation of KDM4A increases gene expression. assays showed that KDM4A-mediated demethylation is enhanced in the presence of CTCF, suggesting that CTCF could increase its enzymatic activity however the specific mechanism by which and might be involved in the gene repression is poorly understood. Here, we show that CTCF and KDM4A form a protein complex, which is recruited into the first intron of . This is related to a decrease in H3K36me3/2 histone marks and is associated with its transcriptional downregulation. Depletion of or KDM4A by siRNA, triggered the reactivation of expression, suggesting that both proteins are involved in the negative regulation of this gene. Furthermore, the knockout of restored the expression and H3K36me3 and H3K36me2 histone marks. Such mechanism acts independently of promoter DNA methylation. Our findings support a novel mechanism of epigenetic repression at the gene body that does not involve promoter silencing.</p>',
			'date' => '2018-03-30',
			'pmid' => 'http://www.pubmed.gov/29682202',
			'doi' => '10.18632/oncotarget.24798',
			'modified' => '2019-02-14 17:12:34',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '3390',
			'name' => 'The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes.',
			'authors' => 'Ding D, Bergmaier P, Sachs P, Klangwart M, Rückert T, Bartels N, Demmers J, Dekker M, Poot RA, Mermoud JE',
			'description' => '<p>Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has been shown to affect stem cell state, but the mechanistic explanation for this effect is unknown. Here, we set out to gain further insights into the function of SMARCAD1 in mouse ESCs. We identified KRAB-associated protein 1 (KAP1) as the stoichiometric binding partner of SMARCAD1 in ESCs. We found that this interaction occurs on chromatin and that SMARCAD1 binds to different classes of KAP1 target genes, including zinc finger protein (ZFP) and imprinted genes. We also found that the RING B-box coiled-coil (RBCC) domain in KAP1 and the proximal coupling of ubiquitin conjugation to ER degradation (CUE) domain in SMARCAD1 mediate their direct interaction. Of note, retention of SMARCAD1 in the nucleus depended on KAP1 in both mouse ESCs and human somatic cells. Mutations in the CUE1 domain of SMARCAD1 perturbed the binding to KAP1 and Accordingly, an intact CUE1 domain was required for tethering this remodeler to the nucleus. Moreover, mutation of the CUE1 domain compromised SMARCAD1 binding to KAP1 target genes. Taken together, our results reveal a mechanism that localizes SMARCAD1 to genomic sites through the interaction of SMARCAD1's CUE1 motif with KAP1.</p>',
			'date' => '2018-02-23',
			'pmid' => 'http://www.pubmed.gov/29284678',
			'doi' => '10.1074/jbc.RA117.000959',
			'modified' => '2018-11-09 12:27:47',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '3359',
			'name' => 'Miz1 Controls Schwann Cell Proliferation via H3K36me2 Demethylase Kdm8 to Prevent Peripheral Nerve Demyelination',
			'authors' => 'Fuhrmann D. et al.',
			'description' => '<p>Schwann cell differentiation and myelination depends on chromatin remodeling, histone acetylation, and methylation, which all affect Schwann cell proliferation. We previously reported that the deletion of the POZ (POxvirus and Zinc finger) domain of the transcription factor Miz1 (Myc-interacting zinc finger protein; encoded by <i>Zbtb17</i>) in mouse Schwann cells (<i>Miz1</i>&Delta;<i>POZ</i>) causes a neuropathy at 90 d after birth [postnatal day (P) 90], with a subsequent spontaneous regeneration. Here we show that RNA sequencing from <i>Miz1</i>&Delta;<i>POZ</i> and control animals at P30 revealed a set of upregulated genes with a strong correlation to cell-cycle regulation. Consistently, a subset of Schwann cells did not exit the cell cycle as observed in control animals and the growth fraction increased over time. From the RNAseq gene list, two direct Miz1 target genes were identified, one of which encodes the histone H3K36<sup>me2</sup> demethylase Kdm8. We show that the expression of <i>Kdm8</i> is repressed by Miz1 and that its release in <i>Miz1</i>&Delta;<i>POZ</i> cells induces a decrease of H3K36<sup>me2</sup>, especially in deregulated cell-cycle-related genes. The linkage between elevated <i>Kdm8</i> expression, hypomethylation of H3K36 at cell-cycle-relevant genes, and the subsequent re-entering of adult Schwann cells into the cell cycle suggests that the release of <i>Kdm8</i> repression in the absence of a functional Miz1 is a central issue in the development of the <i>Miz1</i>&Delta;<i>POZ</i> phenotype.<b>SIGNIFICANCE STATEMENT</b> The deletion of the Miz1 (Myc-interacting zinc finger protein 1) POZ (POxvirus and Zinc finger) domain in Schwann cells causes a neuropathy. Here we report sustained Schwann cell proliferation caused by an increased expression of the direct Miz1 target gene <i>Kdm8</i>, encoding a H3K36me2 demethylase. Hence, the demethylation of H3K36 is linked to the pathogenesis of a neuropathy.</p>',
			'date' => '2018-01-24',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29217679',
			'doi' => '',
			'modified' => '2018-04-06 09:51:37',
			'created' => '2018-04-06 09:51:37',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '3318',
			'name' => 'The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes ',
			'authors' => 'Dong Ding et. al.',
			'description' => '<p>Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has been shown to affect stem cell state, but the mechanistic explanation for this effect is unknown. Here, we set out to gain further insights into the function of SMARCAD1 in mouse ESCs. We identified KRAB-associated protein 1 (KAP1) as the stoichiometric binding partner of SMARCAD1 in ESCs. We found that this interaction occurs on chromatin and that SMARCAD1 binds to different classes of KAP1 target genes, including zinc finger protein (ZFP) and imprinted genes. We also found that the RING B-box coiled-coil (RBCC) domain in KAP1 and the proximal coupling of ubiquitin conjugation to ER degradation (CUE) domain in SMARCAD1 mediate their direct interaction. Of note, retention of SMARCAD1 in the nucleus depended on KAP1 in both mouse ESCs and human somatic cells. Mutations in the CUE1 domain of SMARCAD1 perturbed the binding to KAP1 <em>in vitro</em> and <em>in vivo</em>. Accordingly, an intact CUE1 domain was required for tethering this remodeler to the nucleus. Moreover, mutation of the CUE1 domain compromised SMARCAD1 binding to KAP1 target genes. Taken together, our results reveal a mechanism that localizes SMARCAD1 to genomic sites through the interaction of SMARCAD1&rsquo;s CUE1 motif with KAP1.</p>',
			'date' => '2017-12-28',
			'pmid' => 'http://www.jbc.org/content/early/2017/12/28/jbc.RA117.000959',
			'doi' => 'doi: 10.1074/jbc.RA117.000959 ',
			'modified' => '2018-01-14 07:43:01',
			'created' => '2018-01-14 07:43:01',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '3304',
			'name' => 'Individual effects of the copia and gypsy enhancer and insulator on chromatin marks, eRNA synthesis, and binding of insulator proteins in transfected genetic constructs.',
			'authors' => 'Fedoseeva D.M. et al.',
			'description' => '<p>Enhancers and insulators are involved in the regulation of gene expression, but the basic underlying mechanisms of action of these elements are unknown. We analyzed the individual effects of the enhancer and the insulator from Drosophila mobile elements copia [enh(copia)] and gypsy using transfected genetic constructs in S2 cells. This system excludes the influence of genomic cis regulatory elements. The enhancer-induced synthesis of 350-1050-nt-long enhancer RNAs (eRNAs) and H3K4me3 and H3K18ac marks, mainly in the region located about 300bp downstream of the enhancer. Insertion of the insulator between the enhancer and the promoter reduced these effects. We also observed the binding of dCTCF to the enhancer and to gypsy insulator. Our data indicate that a single gypsy insulator interacts with both the enhancer and the promoter, while two copies of the gypsy insulator preferentially interact with each other. Our results suggest the formation of chromatin loops that are shaped by the enhancer and the insulator.</p>',
			'date' => '2017-10-16',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29045822',
			'doi' => '',
			'modified' => '2018-01-03 10:13:37',
			'created' => '2018-01-03 10:13:37',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '3277',
			'name' => 'UV Radiation Activates Toll-Like Receptor 9 Expression in Primary Human Keratinocytes, an Event Inhibited by Human Papillomavirus 38 E6 and E7 Oncoproteins',
			'authors' => 'Pacini L. et al.',
			'description' => '<p>Several lines of evidence indicate that cutaneous human papillomavirus (HPV) types belonging to the beta genus of the HPV phylogenetic tree synergize with UV radiation in the development of skin cancer. Accordingly, the E6 and E7 oncoproteins from some beta HPV types are able to deregulate pathways related to immune response and cellular transformation. Toll-like receptor 9 (TLR9), in addition to playing a role in innate immunity, has been shown to be involved in the cellular stress response. Using primary human keratinocytes as experimental models, we have shown that UV irradiation (and other cellular stresses) activates TLR9 expression. This event is closely linked to p53 activation. Silencing the expression of p53 or deleting its encoding gene affected the activation of TLR9 expression after UV irradiation. Using various strategies, we have also shown that the transcription factors p53 and c-Jun are recruited onto a specific region of the TLR9 promoter after UV irradiation. Importantly, the E6 and E7 oncoproteins from beta HPV38, by inducing the accumulation of the p53 antagonist &Delta;Np73&alpha;, prevent the UV-mediated recruitment of these transcription factors onto the TLR9 promoter, with subsequent impairment of TLR9 gene expression. This study provides new insight into the mechanism that mediates TLR9 upregulation in response to cellular stresses. In addition, we show that HPV38 E6 and E7 are able to interfere with this mechanism, providing another explanation for the possible cooperation of beta HPV types with UV radiation in skin carcinogenesis.<b>IMPORTANCE</b> Beta HPV types have been suggested to act as cofactors in UV-induced skin carcinogenesis by altering several cellular mechanisms activated by UV radiation. We show that the expression of TLR9, a sensor of damage-associated molecular patterns produced during cellular stress, is activated by UV radiation in primary human keratinocytes (PHKs). Two transcription factors known to be activated by UV radiation, p53 and c-Jun, play key roles in UV-activated TLR9 expression. The E6 and E7 oncoproteins from beta HPV38 strongly inhibit UV-activated TLR9 expression by preventing the recruitment of p53 and c-Jun to the TLR9 promoter. Our findings provide additional support for the role that beta HPV types play in skin carcinogenesis by preventing activation of specific pathways upon exposure of PHKs to UV radiation.</p>',
			'date' => '2017-09-12',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28724760',
			'doi' => '',
			'modified' => '2017-10-16 10:19:04',
			'created' => '2017-10-16 10:19:04',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '3249',
			'name' => 'The cardiac calsequestrin gene transcription is modulated at the promoter by NFAT and MEF-2 transcription factors',
			'authors' => 'Rafael Estrada-Avilés, Gabriela Rodríguez, Angel Zarain-Herzberg',
			'description' => '<p>Calsequestrin-2 (CASQ2) is the main Ca<sup>2+</sup>-binding protein inside the sarcoplasmic reticulum of cardiomyocytes. Previously, we demonstrated that MEF-2 and SRF binding sites within the human <em>CASQ2</em> gene (<em>hCASQ2</em>) promoter region are functional in neonatal cardiomyocytes. In this work, we investigated if the calcineurin/NFAT pathway regulates <em>hCASQ2</em> expression in neonatal cardiomyocytes. The inhibition of NFAT dephosphorylation with CsA or INCA-6, reduced both the luciferase activity of <em>hCASQ2</em> promoter constructs (-3102/+176 bp and -288/+176 bp) and the CASQ2 mRNA levels in neonatal rat cardiomyocytes. Additionally, NFATc1 and NFATc3 over-expressing neonatal cardiomyocytes showed a 2-3-fold increase in luciferase activity of both <em>hCASQ2</em> promoter constructs, which was prevented by CsA treatment. Site-directed mutagenesis of the -133 bp MEF-2 binding site prevented trans-activation of <em>hCASQ2</em> promoter constructs induced by NFAT overexpression. Chromatin Immunoprecipitation (ChIP) assays revealed NFAT and MEF-2 enrichment within the -288 bp to +76 bp of the <em>hCASQ2</em> gene promoter. Besides, a direct interaction between NFAT and MEF-2 proteins was demonstrated by protein co-immunoprecipitation experiments. Taken together, these data demonstrate that NFAT interacts with MEF-2 bound to the -133 bp binding site at the <em>hCASQ2</em> gene promoter. In conclusion, in this work, we demonstrate that the Ca<sup>2+</sup>-calcineurin/NFAT pathway modulates the transcription of the <em>hCASQ2</em> gene in neonatal cardiomyocytes.</p>',
			'date' => '2017-09-08',
			'pmid' => 'http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0184724',
			'doi' => 'https://doi.org/10.1371/journal.pone.0184724 ',
			'modified' => '2017-09-26 07:16:08',
			'created' => '2017-09-26 07:16:08',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '3300',
			'name' => 'The cardiac calsequestrin gene transcription is modulated at the promoter by NFAT and MEF-2 transcription factors.',
			'authors' => 'Estrada-Avilés R. et al.',
			'description' => '<p>Calsequestrin-2 (CASQ2) is the main Ca2+-binding protein inside the sarcoplasmic reticulum of cardiomyocytes. Previously, we demonstrated that MEF-2 and SRF binding sites within the human CASQ2 gene (hCASQ2) promoter region are functional in neonatal cardiomyocytes. In this work, we investigated if the calcineurin/NFAT pathway regulates hCASQ2 expression in neonatal cardiomyocytes. The inhibition of NFAT dephosphorylation with CsA or INCA-6, reduced both the luciferase activity of hCASQ2 promoter constructs (-3102/+176 bp and -288/+176 bp) and the CASQ2 mRNA levels in neonatal rat cardiomyocytes. Additionally, NFATc1 and NFATc3 over-expressing neonatal cardiomyocytes showed a 2-3-fold increase in luciferase activity of both hCASQ2 promoter constructs, which was prevented by CsA treatment. Site-directed mutagenesis of the -133 bp MEF-2 binding site prevented trans-activation of hCASQ2 promoter constructs induced by NFAT overexpression. Chromatin Immunoprecipitation (ChIP) assays revealed NFAT and MEF-2 enrichment within the -288 bp to +76 bp of the hCASQ2 gene promoter. Besides, a direct interaction between NFAT and MEF-2 proteins was demonstrated by protein co-immunoprecipitation experiments. Taken together, these data demonstrate that NFAT interacts with MEF-2 bound to the -133 bp binding site at the hCASQ2 gene promoter. In conclusion, in this work, we demonstrate that the Ca2+-calcineurin/NFAT pathway modulates the transcription of the hCASQ2 gene in neonatal cardiomyocytes.</p>',
			'date' => '2017-09-08',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28886186',
			'doi' => '',
			'modified' => '2017-12-05 10:13:23',
			'created' => '2017-12-05 10:13:23',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '3264',
			'name' => 'Viral driven epigenetic events alter the expression of cancer-related genes in Epstein-Barr-virus naturally infected Burkitt lymphoma cell lines',
			'authors' => 'Hernandez-Vargas H. et al.',
			'description' => '<p>Epstein-Barr virus (EBV) was identified as the first human virus to be associated with a human malignancy, Burkitt&rsquo;s lymphoma (BL), a pediatric cancer endemic in sub-Saharan Africa. The exact mechanism of how EBV contributes to the process of lymphomagenesis is not fully understood. Recent studies have highlighted a genetic difference between endemic (EBV+) and sporadic (EBV&minus;) BL, with the endemic variant showing a lower somatic mutation load, which suggests the involvement of an alternative virally-driven process of transformation in the pathogenesis of endemic BL. We tested the hypothesis that a global change in DNA methylation may be induced by infection with EBV, possibly thereby accounting for the lower mutation load observed in endemic BL. Our comparative analysis of the methylation profiles of a panel of BL derived cell lines, naturally infected or not with EBV, revealed that the presence of the virus is associated with a specific pattern of DNA methylation resulting in altered expression of cellular genes with a known or potential role in lymphomagenesis. These included ID3, a gene often found to be mutated in sporadic BL. In summary this study provides evidence that EBV may contribute to the pathogenesis of BL through an epigenetic mechanism.</p>',
			'date' => '2017-07-19',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517637/',
			'doi' => '',
			'modified' => '2017-10-09 16:04:14',
			'created' => '2017-10-09 16:04:14',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '3255',
			'name' => 'SOX2 as a New Regulator of HPV16 Transcription',
			'authors' => 'Martínez-Ramírez I. et al.',
			'description' => '<p>Persistent infections with high-risk human papillomavirus (HPV) constitute the main risk factor for cervical cancer development. HPV16 is the most frequent type associated to squamous cell carcinomas (SCC), followed by HPV18. The long control region (LCR) in the HPV genome contains the replication origin and sequences recognized by cellular transcription factors (TFs) controlling viral transcription. Altered expression of <i>E6</i> and <i>E7</i> viral oncogenes, modulated by the LCR, causes modifications in cellular pathways such as proliferation, leading to malignant transformation. The aim of this study was to identify specific TFs that could contribute to the modulation of high-risk HPV transcriptional activity, related to the cellular histological origin. We identified sex determining region Y (SRY)-box 2 (SOX2) response elements present in HPV16-LCR. SOX2 binding to the LCR was demonstrated by in vivo and in vitro assays. The overexpression of this TF repressed HPV16-LCR transcriptional activity, as shown through reporter plasmid assays and by the down-regulation of endogenous HPV oncogenes. Site-directed mutagenesis revealed that three putative SOX2 binding sites are involved in the repression of the LCR activity. We propose that SOX2 acts as a transcriptional repressor of HPV16-LCR, decreasing the expression of <i>E6</i> and <i>E7</i> oncogenes in a SCC context.</p>',
			'date' => '2017-07-05',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28678184',
			'doi' => '',
			'modified' => '2017-10-02 15:11:26',
			'created' => '2017-10-02 15:11:26',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '3079',
			'name' => 'Biphasic regulation of chondrocytes by Rela through induction of anti-apoptotic and catabolic target genes',
			'authors' => 'Kobayashi H. et al.',
			'description' => '<p>In vitro studies have shown that Rela/p65, a key subunit mediating NF-&kappa;B signalling, is involved in chondrogenic differentiation, cell survival and catabolic enzyme production. Here, we analyse in vivo functions of Rela in embryonic limbs and adult articular cartilage, and find that Rela protects chondrocytes from apoptosis through induction of anti-apoptotic genes including Pik3r1. During skeletal development, homozygous knockout of Rela leads to impaired growth through enhanced chondrocyte apoptosis, whereas heterozygous knockout of Rela does not alter growth. In articular cartilage, homozygous knockout of Rela at 7 weeks leads to marked acceleration of osteoarthritis through enhanced chondrocyte apoptosis, whereas heterozygous knockout of Rela results in suppression of osteoarthritis development through inhibition of catabolic gene expression. Haploinsufficiency or a low dose of an IKK inhibitor suppresses catabolic gene expression, but does not alter anti-apoptotic gene expression. The biphasic regulation of chondrocytes by Rela contributes to understanding the pathophysiology of osteoarthritis.</p>',
			'date' => '2016-11-10',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27830706',
			'doi' => '',
			'modified' => '2016-12-12 16:46:36',
			'created' => '2016-12-12 16:46:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '3053',
			'name' => 'Esrrb directly binds to Gata6 promoter and regulates its expression with Dax1 and Ncoa3',
			'authors' => 'Uranishi K et al.',
			'description' => '<p>Estrogen-related receptor beta (Esrrb) is expressed in embryonic stem (ES) cells and is involved in self-renewal ability and pluripotency. Previously, we found that Dax1 is associated with Esrrb and represses its transcriptional activity. Further, the disruption of the Dax1-Esrrb interaction increases the expression of the extra-embryonic endoderm marker Gata6 in ES cells. Here, we investigated the influences of Esrrb and Dax1 on Gata6 expression. Esrrb overexpression in ES cells induced endogenous Gata6 mRNA and Gata6 promoter activity. In addition, the Gata6 promoter was found to contain the Esrrb recognition motifs ERRE1 and ERRE2, and the latter was the responsive element of Esrrb. Associations between ERRE2 and Esrrb were then confirmed by biotin DNA pulldown and chromatin immunoprecipitation assays. Subsequently, we showed that Esrrb activity at the Gata6 promoter was repressed by Dax1, and although Dax1 did not bind to ERRE2, it was associated with Esrrb, which directly binds to ERRE2. In addition, the transcriptional activity of Esrrb was enhanced by nuclear receptor co-activator 3 (Ncoa3), which has recently been shown to be a binding partner of Esrrb. Finally, we showed that Dax1 was associated with Ncoa3 and repressed its transcriptional activity. Taken together, the present study indicates that the Gata6 promoter is activated by Esrrb in association with Ncoa3, and Dax1 inhibited activities of Esrrb and Ncoa3, resulting maintenance of the undifferentiated status of ES cells.</p>',
			'date' => '2016-09-04',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27601327',
			'doi' => '',
			'modified' => '2016-10-24 14:26:35',
			'created' => '2016-10-24 14:26:35',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => array(
			'id' => '3048',
			'name' => 'Chromatin remodeling regulates catalase expression during cancer cells adaptation to chronic oxidative stress.',
			'authors' => 'Glorieux C. et al.',
			'description' => '<p>Regulation of ROS metabolism plays a major role in cellular adaptation to oxidative stress in cancer cells, but the molecular mechanism that regulates catalase, a key antioxidant enzyme responsible for conversion of hydrogen peroxide to water and oxygen, remains to be elucidated. Therefore, we investigated the transcriptional regulatory mechanism controlling catalase expression in three human mammary cell lines: the normal mammary epithelial 250MK primary cells, the breast adenocarcinoma MCF-7 cells and an experimental model of MCF-7 cells resistant against oxidative stress resulting from chronic exposure to H<sub>2</sub>O<sub>2</sub> (Resox), in which catalase was overexpressed. Here we identify a novel promoter region responsible for the regulation of catalase expression at -1518/-1226 locus and the key molecules that interact with this promoter and affect catalase transcription. We show that the AP-1 family member JunB and retinoic acid receptor alpha (RAR&alpha;) mediate catalase transcriptional activation and repression, respectively, by controlling chromatin remodeling through a histone deacetylases-dependent mechanism. This regulatory mechanism plays an important role in redox adaptation to chronic exposure to H<sub>2</sub>O<sub>2</sub> in breast cancer cells. Our study suggests that cancer adaptation to oxidative stress may be regulated by transcriptional factors through chromatin remodeling, and reveals a potential new mechanism to target cancer cells.</p>',
			'date' => '2016-08-31',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27591797',
			'doi' => '',
			'modified' => '2016-10-10 11:15:35',
			'created' => '2016-10-10 11:15:35',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 21 => array(
			'id' => '2996',
			'name' => 'Induction of cell differentiation activates transcription of the Sarco/Endoplasmic Reticulum calcium-ATPase 3 gene (ATP2A3) in gastric and colon cancer cells',
			'authors' => 'Flores-Peredo L et al.',
			'description' => '<p>The Sarco/Endoplasmic Reticulum Ca<sup>2+</sup> -ATPases (SERCAs), pump Ca<sup>2+</sup> into the endoplasmic reticulum lumen modulating cytosolic Ca<sup>2+</sup> concentrations to regulate various cellular processes including cell growth. Previous studies have reported a downregulation of SERCA3 protein expression in gastric and colon cancer cell lines and showed that in vitro cell differentiation increases its expression. However, little is known about the transcriptional mechanisms and transcription factors that regulate SERCA3 expression in epithelial cancer cells. In this work, we demonstrate that SERCA3 mRNA is upregulated up to 45-fold in two epithelial cancer cell lines, KATO-III and Caco-2, induced to differentiate with histone deacetylase inhibitors (HDACi) and by cell confluence, respectively. To evaluate the transcriptional elements responding to the differentiation stimuli, we cloned the human ATP2A3 promoter, generated deletion constructs and transfected them into KATO-III cells. Basal and differentiation responsive DNA elements were located by functional analysis within the first -135&thinsp;bp of the promoter region. Using site-directed mutagenesis and DNA-protein binding assays we found that Sp1, Sp3, and Klf-4 transcription factors bind to ATP2A3 proximal promoter elements and regulate basal gene expression. We showed that these factors participated in the increase of ATP2A3 expression during cancer cell differentiation. This study provides evidence for the first time that Sp1, Sp3, and Klf-4 transcriptionally modulate the expression of SERCA3 during induction of epithelial cancer cell differentiation.</p>',
			'date' => '2016-07-19',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27433831',
			'doi' => '10.1002/mc.22529',
			'modified' => '2016-08-23 16:57:48',
			'created' => '2016-08-23 16:57:48',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '3027',
			'name' => 'Regulatory Interaction between the Cellular Restriction Factor IFI16 and Viral pp65 (pUL83) Modulates Viral Gene Expression and IFI16 Protein Stability',
			'authors' => 'Biolatti M et al.',
			'description' => '<p>A key player in the intrinsic resistance against human cytomegalovirus (HCMV) is the interferon-&gamma;-inducible protein 16 (IFI16), which behaves as a viral DNA sensor in the first hours post infection and as a repressor of viral gene transcription in the later stages. Previous studies on HCMV replication demonstrated that IFI16 binds to the viral protein kinase pUL97, undergoes phosphorylation and relocalizes to the cytoplasm of infected cells. In this study, we demonstrate that the tegument protein pp65 (pUL83) recruits IFI16 to the promoter of the UL54 gene and downregulates viral replication as shown by use of the HCMV mutant v65Stop, which lacks pp65 expression. Interestingly, at late time-points of HCMV infection, IFI16 is stabilized by its interaction with pp65, which stood in contrast to IFI16 degradation, observed in herpes simplex virus (HSV-1)-infected cells. Moreover, we found that its translocation to the cytoplasm, in addition to pUL97, strictly depends on pp65, as demonstrated with the HCMV mutant RV-VM1, which expresses a form of pp65 unable to translocate into the cytoplasm. Thus, these data reveal a dual role for pp65: during early infection, it modulates IFI16 activity at the promoter of immediate-early and early genes; subsequently, it delocalizes IFI16 from the nucleus into the cytoplasm, thereby stabilizing and protecting it from degradation. Overall, these data identify a novel activity of the pp65/IFI16 interactome involved in the regulation of UL54 gene expression and IFI16 stability during early and late phases of HCMV replication.</p>',
			'date' => '2016-07-06',
			'pmid' => 'http://jvi.asm.org/content/early/2016/06/30/JVI.00923-16.abstract',
			'doi' => '',
			'modified' => '2016-09-07 10:42:20',
			'created' => '2016-09-07 10:42:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '2985',
			'name' => 'miR-125b-1 is repressed by histone modifications in breast cancer cell lines',
			'authors' => 'Cisneros-Soberanis F et al.',
			'description' => '<div class="">
<h4>PURPOSE:</h4>
<p><abstracttext label="PURPOSE" nlmcategory="OBJECTIVE">Downregulation of miR-125b-1 is associated with poor prognosis in breast cancer patients. In this work we investigated the effect of histone modifications on the regulation of this gene promoter.</abstracttext></p>
<h4>METHODS AND RESULTS:</h4>
<p><abstracttext label="METHODS AND RESULTS" nlmcategory="RESULTS">We evaluated the enrichment of two histone modifications involved in gene repression, H3K9me3 and H3K27me3, on the miR-125b-1 promoter in two breast cancer cell lines, MCF7 (luminal A subtype) and MDA-MB-231 (triple-negative subtype), compared to the non-transformed breast cell line MCF10A. H3K27me3 and H3K9me3 were enriched in MCF7 and MDA-MB-231 cells, respectively. Next, we used an EZH2 inhibitor to examine the reactivation of miR-125b-1 in MCF7 cells and evaluated the transcriptional levels of pri-miR-125b-1 and mature miR-125b by qRT-PCR. pri-miRNA and mature miRNA transcripts were both increased after treatment of MCF7 cells with the EZH2 inhibitor, whereas no effect on miR-125b-1 expression levels was observed in MDA-MB-231 and MCF10A cells. We subsequently evaluated the effect of miR-125b-1 reactivation on the expression and protein levels of BAK1, a target of miR-125b. We observed 60 and 70&nbsp;% decreases in the expression and protein levels of BAK1, respectively, compared to cells that were not treated with the EZH2 inhibitor. We over-expressed KDM4B/JMJD2B to reactivate this miRNA, resulting in a three-fold increase in miR-125b expression compared with the same cell line without KDM4B/JMJD2B over-expression.</abstracttext></p>
<h4>CONCLUSION:</h4>
<p><abstracttext label="CONCLUSION" nlmcategory="CONCLUSIONS">The miR-125b-1 is repressed by different epigenetic mechanisms depending on the breast cancer subtype and that miR-125b-1 reactivation specifically eliminates the effect of repressive histone modifications on the expression of an pro-apoptotic target.</abstracttext></p>
</div>',
			'date' => '2016-07-02',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27386402',
			'doi' => ' 10.1186/s40064-016-2475-z',
			'modified' => '2016-07-26 09:50:18',
			'created' => '2016-07-26 09:50:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => array(
			'id' => '2913',
			'name' => 'Osterix and RUNX2 are Transcriptional Regulators of Sclerostin in Human Bone',
			'authors' => 'Flor M. Pérez-Campo, Ana Santurtún, Carmen García-Ibarbia, María A. Pascual, Carmen Valero, Carlos Garcés, Carolina Sañudo, María T. Zarrabeitia, José A. Riancho',
			'description' => '<p><span>Sclerostin, encoded by the </span><em class="EmphasisTypeItalic ">SOST</em><span> gene, works as an inhibitor of the Wnt pathway and therefore is an important regulator of bone homeostasis. Due to its potent action as an inhibitor of bone formation, blocking sclerostin activity is the purpose of recently developed anti-osteoporotic treatments. Two bone-specific transcription factors, RUNX2 and OSX, have been shown to interact and co-ordinately regulate the expression of bone-specific genes. Although it has been recently shown that sclerostin is targeted by OSX in mice, there is currently no information of whether this is also the case in human cells. We have identified SP-protein family and AML1 consensus binding sequences at the human </span><em class="EmphasisTypeItalic ">SOST</em><span> promoter and have shown that OSX, together with RUNX2, binds to a specific region close to the transcription start site. Furthermore, we show that OSX and RUNX2 activate </span><em class="EmphasisTypeItalic ">SOST</em><span> expression in a co-ordinated manner in vitro and that </span><em class="EmphasisTypeItalic ">SOST</em><span> expression levels show a significant positive correlation with </span><em class="EmphasisTypeItalic ">OSX/RUNX2</em><span> expression levels in human bone. We also confirmed previous results showing an association of several SOST/RUNX2 polymorphisms with bone mineral density.</span></p>',
			'date' => '2016-05-06',
			'pmid' => 'http://link.springer.com/article/10.1007/s00223-016-0144-4',
			'doi' => '10.1007/s00223-016-0144-4',
			'modified' => '2016-05-11 17:34:19',
			'created' => '2016-05-11 17:34:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 25 => array(
			'id' => '3036',
			'name' => 'DNMT1 and HDAC2 Cooperate to Facilitate Aberrant Promoter Methylation in Inorganic Phosphate-Induced Endothelial-Mesenchymal Transition',
			'authors' => 'Tan X et al.',
			'description' => '<p>While phosphorus in the form of inorganic or organic phosphate is critically involved in most cellular functions, high plasma levels of inorganic phosphate levels have emerged as independent risk factor for cardiac fibrosis, cardiovascular morbidity and decreased life-expectancy. While the link of high phosphate and cardiovascular disease is commonly explained by direct cellular effects of phospho-regulatory hormones, we here explored the possibility of inorganic phosphate directly eliciting biological responses in cells. We demonstrate that human coronary endothelial cells (HCAEC) undergo an endothelial-mesenchymal transition (EndMT) when exposed to high phosphate. We further demonstrate that such EndMT is initiated by recruitment of aberrantly phosphorylated DNMT1 to the RASAL1 CpG island promoter by HDAC2, causing aberrant promoter methylation and transcriptional suppression, ultimately leading to increased Ras-GTP activity and activation of common EndMT regulators Twist and Snail. Our studies provide a novel aspect for known adverse effects of high phosphate levels, as eukaryotic cells are commonly believed to have lost phosphate-sensing mechanisms of prokaryotes during evolution, rendering them insensitive to extracellular inorganic orthophosphate. In addition, our studies provide novel insights into the mechanisms underlying specific targeting of select genes in context of fibrogenesis.</p>',
			'date' => '2016-01-27',
			'pmid' => 'http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147816',
			'doi' => '',
			'modified' => '2016-09-23 16:44:11',
			'created' => '2016-09-23 16:44:11',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		)
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	'Testimonial' => array(),
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			'countries' => 'GB',
			'modified' => '2020-06-30 18:30:26',
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			'language' => 'en',
			'url' => 'files/SDS/OneDay-ChIP-Kit/SDS-C01010080-OneDay_ChIP_kit-US-en-1_0.pdf',
			'countries' => 'US',
			'modified' => '2020-06-30 18:31:15',
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			'language' => 'nl',
			'url' => 'files/SDS/OneDay-ChIP-Kit/SDS-C01010080-OneDay_ChIP_kit-BE-nl-1_0.pdf',
			'countries' => 'BE',
			'modified' => '2020-06-30 18:28:54',
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<div class="small-12 medium-12 large-12 columns text-justify">
<p class="text-justify">Chromatin Immunoprecipitation (ChIP) coupled with quantitative PCR can be used to investigate protein-DNA interaction at known genomic binding sites. if sites are not known, qPCR primers can also be designed against potential regulatory regions such as promoters. ChIP-qPCR is advantageous in studies that focus on specific genes and potential regulatory regions across differing experimental conditions as the cost of performing real-time PCR is minimal. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</p>
<p class="text-justify"><strong>The ChIP-qPCR workflow</strong></p>
</div>
<div class="small-12 medium-12 large-12 columns text-center"><br /> <img src="https://www.diagenode.com/img/chip-qpcr-diagram.png" /></div>
<div class="small-12 medium-12 large-12 columns"><br />
<ol>
<li class="large-12 columns"><strong>Chromatin preparation: </strong>cell fixation (cross-linking) of chromatin-bound proteins such as histones or transcription factors to DNA followed by cell lysis.</li>
<li class="large-12 columns"><strong>Chromatin shearing: </strong>fragmentation of chromatin<strong> </strong>by sonication down to desired fragment size (100-500 bp)</li>
<li class="large-12 columns"><strong>Chromatin IP</strong>: protein-DNA complexe capture using<strong> <a href="https://www.diagenode.com/en/categories/chip-grade-antibodies">specific ChIP-grade antibodies</a></strong>&nbsp;against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: chromatin reverse cross-linking and elution followed by purification<strong> </strong></li>
<li class="large-12 columns"><strong>qPCR and analysis</strong>: using previously designed primers to amplify IP'd material at specific loci</li>
</ol>
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<div class="small-12 medium-10 large-9 small-centered columns">
<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
<div class="row">
<div class="small-6 medium-6 large-6 columns"><a href="https://www.diagenode.com/pages/which-kit-to-choose"><img src="https://www.diagenode.com/img/banners/banner-decide.png" alt="" /></a></div>
<div class="small-6 medium-6 large-6 columns"><a href="https://www.diagenode.com/pages/chip-kit-customizer-1"><img src="https://www.diagenode.com/img/banners/banner-customizer.png" alt="" /></a></div>
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			'meta_description' => 'Diagenode's ChIP qPCR kits can be used to quantify enriched DNA after chromatin immunoprecipitation. ChIP-qPCR is advantageous in studies that focus on specific genes and potential regulatory regions across differing experimental conditions as the cost of',
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			'name' => 'OneDay ChIP kit',
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<div class="section">
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<div class="small-8 medium-9 large-9 columns">
<div class="page" title="Page 4">
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<p><span>Diagenode provides kits with optimized reagents and simplified protocols for ChIP including the <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR kit</a>, <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE kit</a>,&nbsp; <a href="https://www.diagenode.com/en/categories/chromatin-ip-chip-seq-kits">iDeal ChIP-seq kits</a>, <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a>, <a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit </a>and <a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation">the ChIPmentation for Histones</a>. This protocol describes the use of the OneDay ChIP Kit.</span></p>
</div>
</div>
</div>
</div>
<p></p>
</div>
</div>
</div>
</div>
</div>',
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			'type' => 'Manual',
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	'Publication' => array(
		(int) 0 => array(
			'id' => '4067',
			'name' => 'Transcription of CLDND1 in human brain endothelial cells is regulated bythe myeloid zinc finger 1.',
			'authors' => 'Shima, Akiho and Matsuoka, Hiroshi and Yamaoka, Alice and Michihara,Akihiro',
			'description' => '<p>Increased permeability of endothelial cells lining the blood vessels in the brain leads to vascular oedema and, potentially, to stroke. The tight junctions (TJs), primarily responsible for the regulation of vascular permeability, are multi-protein complexes comprising the claudin family of proteins and occludin. Several studies have reported that downregulation of the claudin domain containing 1 (CLDND1) gene enhances vascular permeability, which consequently increases the risk of stroke. However, the transcriptional regulation of CLDND1 has not been studied extensively. Therefore, this study aimed to identify the transcription factors (TFs) regulating CLDND1 expression. A luciferase reporter assay identified a silencer within the first intron of CLDND1, which was identified as a potential binding site of the myeloid zinc finger 1 (MZF1) through in silico and TFBIND software analyses, and confirmed through a reporter assay using the MZF1 expression vector and chromatin immunoprecipitation (ChIP) assays. Moreover, the transient overexpression of MZF1 significantly increased the mRNA and protein expression levels of CLDND1, conversely, which were suppressed through the siRNA-mediated MZF1 knockdown. Furthermore, the permeability of FITC-dextran was observed to be increased on MZF1 knockdown as compared to that of the siGFP control. Our data revealed the underlying mechanism of the transcriptional regulation of CLDND1 by the MZF1. The findings suggest a potential role of MZF1 in TJ formation, which could be studied further and applied to prevent cerebral haemorrhage.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33037622',
			'doi' => '10.1111/1440-1681.13416',
			'modified' => '2021-02-19 17:48:44',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
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			)
		),
		(int) 1 => array(
			'id' => '3748',
			'name' => 'Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis.',
			'authors' => 'Vara C, Paytuví-Gallart A, Cuartero Y, Le Dily F, Garcia F, Salvà-Castro J, Gómez-H L, Julià E, Moutinho C, Aiese Cigliano R, Sanseverino W, Fornas O, Pendás AM, Heyn H, Waters PD, Marti-Renom MA, Ruiz-Herrera A',
			'description' => '<p>Mammalian gametogenesis involves dramatic and tightly regulated chromatin remodeling, whose regulatory pathways remain largely unexplored. Here, we generate a comprehensive high-resolution structural and functional atlas of mouse spermatogenesis by combining in situ chromosome conformation capture sequencing (Hi-C), RNA sequencing (RNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) of CCCTC-binding factor (CTCF) and meiotic cohesins, coupled with confocal and super-resolution microscopy. Spermatogonia presents well-defined compartment patterns and topological domains. However, chromosome occupancy and compartmentalization are highly re-arranged during prophase&nbsp;I, with cohesins bound to active promoters in DNA loops out of the chromosomal axes. Compartment patterns re-emerge in round spermatids, where cohesin occupancy correlates with transcriptional activity of key developmental genes. The compact sperm genome contains compartments with actively transcribed genes but no fine-scale topological domains, concomitant with the presence of protamines. Overall, we demonstrate how genome-wide cohesin occupancy and transcriptional activity is associated with three-dimensional (3D) remodeling during spermatogenesis, ultimately reprogramming the genome for the next generation.</p>',
			'date' => '2019-07-09',
			'pmid' => 'http://www.pubmed.gov/31291573',
			'doi' => '10.1016/j.celrep.2019.06.037',
			'modified' => '2019-08-06 16:12:27',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '3739',
			'name' => 'Resveratrol up-regulates ATP2A3 gene expression in breast cancer cell lines through epigenetic mechanisms.',
			'authors' => 'Izquierdo-Torres E, Hernández-Oliveras A, Meneses-Morales I, Rodríguez G, Fuentes-García G, Zarain-Herzberg Á',
			'description' => '<p>Resveratrol (RSV) is a phytoestrogen which has been related to chemoprevention of several types of cancer. In this work, we show up to a 6-fold increased expression of ATP2A3 gene induced by RSV that triggers apoptosis and changes of intracellular Ca management in MCF-7 and MDA-MB-231 breast cancer cell lines. We explored epigenetic mechanisms for that RSV-induced ATP2A3 up-regulation. The results indicate that RSV-induced ATP2A3 up-regulation correlates with about 50% of reduced HDAC activity and reduced nuclear HDAC2 expression and occupancy on ATP2A3 promoter, increasing the global acetylation of histone H3 and the enrichment of histone mark H3K27Ac on the proximal promoter of the ATP2A3 gene in MDA-MB-231 cells. We also quantified HAT activity, finding that it can be boosted with RSV treatment; however, pharmacological inhibition of p300, one of the main HATs, did not have significant effects in RSV-mediated ATP2A3 gene expression. Additionally, DNMT activity was also reduced in cells treated with RSV, as well as the expression of Methyl-DNA binding proteins MeCP2 and MBD2. However, analysis of the methylation pattern of ATP2A3 gene promoter showed un-methylated promoter in both cell lines. Taken together, the results of this work help to explain, at the molecular level, how ATP2A3 gene is regulated in breast cancer cells, and the benefits of RSV intake observed in epidemiological data, studies with animals, and in vitro models.</p>',
			'date' => '2019-06-04',
			'pmid' => 'http://www.pubmed.gov/31173924',
			'doi' => '10.1016/j.biocel.2019.05.020',
			'modified' => '2019-08-06 16:56:19',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'id' => '3660',
			'name' => 'Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia.',
			'authors' => 'Wernig-Zorc S, Yadav MP, Kopparapu PK, Bemark M, Kristjansdottir HL, Andersson PO, Kanduri C, Kanduri M',
			'description' => '<p>BACKGROUND: Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic and diagnostic implications for several cancers. However, there is no global study exploring the role of 5-hydroxymethylcytosine (5-hmC) levels in CLL. Herein, using mass spectrometry and hMeDIP-sequencing, we analysed the dynamics of 5-hmC during B cell maturation and CLL pathogenesis. RESULTS: We show that na&iuml;ve B-cells had higher levels of 5-hmC and 5-mC compared to non-class switched and class-switched memory B-cells. We found a significant decrease in global 5-mC levels in CLL patients (n&thinsp;=&thinsp;15) compared to na&iuml;ve and memory B cells, with no changes detected between the CLL prognostic groups. On the other hand, global 5-hmC levels of CLL patients were similar to memory B cells and reduced compared to na&iuml;ve B cells. Interestingly, 5-hmC levels were increased at regulatory regions such as gene-body, CpG island shores and shelves and 5-hmC distribution over the gene-body positively correlated with degree of transcriptional activity. Importantly, CLL samples showed aberrant 5-hmC and 5-mC pattern over gene-body compared to well-defined patterns in normal B-cells. Integrated analysis of 5-hmC and RNA-sequencing from CLL datasets identified three novel oncogenic drivers that could have potential roles in CLL development and progression. CONCLUSIONS: Thus, our study suggests that the global loss of 5-hmC, accompanied by its significant increase at the gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Our combined analysis of 5-mC and 5-hmC sequencing provided insights into the potential role of 5-hmC in modulating gene expression changes during CLL pathogenesis.</p>',
			'date' => '2019-01-07',
			'pmid' => 'http://www.pubmed.gov/30616658',
			'doi' => '10.1186/s13072‑018‑0252‑7',
			'modified' => '2019-07-01 11:46:16',
			'created' => '2019-06-21 14:55:31',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 4 => array(
			'id' => '3505',
			'name' => 'Genomic Location of PRMT6-Dependent H3R2 Methylation Is Linked to the Transcriptional Outcome of Associated Genes.',
			'authors' => 'Bouchard C, Sahu P, Meixner M, Nötzold RR, Rust MB, Kremmer E, Feederle R, Hart-Smith G, Finkernagel F, Bartkuhn M, Savai Pullamsetti S, Nist A, Stiewe T, Philipsen S, Bauer UM',
			'description' => '<p>Protein arginine methyltransferase 6 (PRMT6) catalyzes asymmetric dimethylation of histone H3 at arginine 2 (H3R2me2a). This mark has been reported to associate with silent genes. Here, we use a cell model&nbsp;of neural differentiation, which upon PRMT6 knockout exhibits proliferation and differentiation defects. Strikingly, we detect PRMT6-dependent H3R2me2a at active genes, both at promoter and enhancer sites. Loss of H3R2me2a from promoter sites leads to enhanced KMT2A binding and H3K4me3 deposition together with increased target gene transcription, supporting a repressive nature of H3R2me2a. At enhancers, H3R2me2a peaks co-localize with the active enhancer marks H3K4me1 and H3K27ac. Here, loss of H3R2me2a results in reduced KMT2D binding and H3K4me1/H3K27ac deposition together with decreased transcription of associated genes, indicating that H3R2me2a also exerts activation functions. Our work suggests that PRMT6 via H3R2me2a interferes with the deposition of adjacent histone marks and modulates the activity of important differentiation-associated genes by opposing transcriptional effects.</p>',
			'date' => '2018-09-18',
			'pmid' => 'http://www.pubmed.gov/30232013',
			'doi' => '10.1016/j.celrep.2018.08.052',
			'modified' => '2019-02-28 10:05:16',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
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			)
		),
		(int) 5 => array(
			'id' => '3443',
			'name' => 'High-fidelity CRISPR/Cas9- based gene-specific hydroxymethylation rescues gene expression and attenuates renal fibrosis.',
			'authors' => 'Xingbo Xu, Xiaoying Tan, Björn Tampe, Tim Wilhelmi, Melanie S. Hulshoff, Shoji Saito, Tobias Moser, Raghu Kalluri, Gerd Hasenfuss, Elisabeth M. Zeisberg & Michael Zeisberg ',
			'description' => '<p>While suppression of specific genes through aberrant promoter methylation contributes to different diseases including organ fibrosis, gene-specific reactivation technology is not yet available for therapy. TET enzymes catalyze hydroxymethylation of methylated DNA, reactivating gene expression. We here report generation of a high-fidelity CRISPR/Cas9-based gene-specific dioxygenase by fusing an endonuclease deactivated high-fidelity Cas9 (dHFCas9) to TET3 catalytic domain (TET3CD), targeted to specific genes by guiding RNAs (sgRNA). We demonstrate use of this technology in four different anti-fibrotic genes in different cell types in vitro, among them RASAL1 and Klotho, both hypermethylated in kidney fibrosis. Furthermore, in vivo lentiviral delivery of the Rasal1-targeted fusion protein to interstitial cells and of the Klotho-targeted fusion protein to tubular epithelial cells each results in specific gene reactivation and attenuation of fibrosis, providing gene-specific demethylating technology in a disease model.</p>',
			'date' => '2018-08-29',
			'pmid' => 'http://www.pubmed.gov/30158531',
			'doi' => '10.1038/s41467-018-05766-5',
			'modified' => '2019-02-28 10:11:31',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
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			)
		),
		(int) 6 => array(
			'id' => '3522',
			'name' => 'Human papillomavirus type 16 antagonizes IRF6 regulation of IL-1β.',
			'authors' => 'Ainouze M, Rochefort P, Parroche P, Roblot G, Tout I, Briat F, Zannetti C, Marotel M, Goutagny N, Auron P, Traverse-Glehen A, Lunel-Potencier A, Golfier F, Masson M, Robitaille A, Tommasino M, Carreira C, Walzer T, Henry T, Zanier K, Trave G, Hasan UA',
			'description' => '<p>Human papillomavirus type 16 (HPV16) and other oncoviruses have been shown to block innate immune responses and to persist in the host. However, to avoid viral persistence, the immune response attempts to clear the infection. IL-1&beta; is a powerful cytokine produced when viral motifs are sensed by innate receptors that are members of the inflammasome family. Whether oncoviruses such as HPV16 can activate the inflammasome pathway remains unknown. Here, we show that infection of human keratinocytes with HPV16 induced the secretion of IL-1&beta;. Yet, upon expression of the viral early genes, IL-1&beta; transcription was blocked. We went on to show that expression of the viral oncoprotein E6 in human keratinocytes inhibited IRF6 transcription which we revealed regulated IL-1&beta; promoter activity. Preventing E6 expression using siRNA, or using E6 mutants that prevented degradation of p53, showed that p53 regulated IRF6 transcription. HPV16 abrogation of p53 binding to the IRF6 promoter was shown by ChIP in tissues from patients with cervical cancer. Thus E6 inhibition of IRF6 is an escape strategy used by HPV16 to block the production IL-1&beta;. Our findings reveal a struggle between oncoviral persistence and host immunity; which is centered on IL-1&beta; regulation.</p>',
			'date' => '2018-08-08',
			'pmid' => 'http://www.pubmed.gov/30089163',
			'doi' => '10.1371/journal.ppat.1007158',
			'modified' => '2019-02-28 10:14:30',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '3583',
			'name' => 'Human papillomavirus type 16 antagonizes IRF6 regulation of IL-1β.',
			'authors' => 'Ainouze M, Rochefort P, Parroche P, Roblot G, Tout I, Briat F, Zannetti C, Marotel M, Goutagny N, Auron P, Traverse-Glehen A, Lunel-Potencier A, Golfier F, Masson M, Robitaille A, Tommasino M, Carreira C, Walzer T, Henry T, Zanier K, Trave G, Hasan UA',
			'description' => '<p>Human papillomavirus type 16 (HPV16) and other oncoviruses have been shown to block innate immune responses and to persist in the host. However, to avoid viral persistence, the immune response attempts to clear the infection. IL-1&beta; is a powerful cytokine produced when viral motifs are sensed by innate receptors that are members of the inflammasome family. Whether oncoviruses such as HPV16 can activate the inflammasome pathway remains unknown. Here, we show that infection of human keratinocytes with HPV16 induced the secretion of IL-1&beta;. Yet, upon expression of the viral early genes, IL-1&beta; transcription was blocked. We went on to show that expression of the viral oncoprotein E6 in human keratinocytes inhibited IRF6 transcription which we revealed regulated IL-1&beta; promoter activity. Preventing E6 expression using siRNA, or using E6 mutants that prevented degradation of p53, showed that p53 regulated IRF6 transcription. HPV16 abrogation of p53 binding to the IRF6 promoter was shown by ChIP in tissues from patients with cervical cancer. Thus E6 inhibition of IRF6 is an escape strategy used by HPV16 to block the production IL-1&beta;. Our findings reveal a struggle between oncoviral persistence and host immunity; which is centered on IL-1&beta; regulation.</p>',
			'date' => '2018-08-08',
			'pmid' => 'http://www.pubmed.gov/30089163',
			'doi' => '10.1371/journal.ppat.1007158',
			'modified' => '2019-04-17 15:50:02',
			'created' => '2019-04-16 12:25:30',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '3480',
			'name' => 'CTCF-KDM4A complex correlates with histone modifications that negatively regulate  gene expression in cancer cell lines.',
			'authors' => 'Guerra-Calderas L, González-Barrios R, Patiño CC, Alcaraz N, Salgado-Albarrán M, de León DC, Hernández CC, Sánchez-Pérez Y, Maldonado-Martínez HA, De la Rosa-Velazquez IA, Vargas-Romero F, Herrera LA, García-Carrancá A, Soto-Reyes E',
			'description' => '<p>Histone demethylase KDM4A is involved in H3K9me3 and H3K36me3 demethylation, which are epigenetic modifications associated with gene silencing and RNA Polymerase II elongation, respectively. is abnormally expressed in cancer, affecting the expression of multiple targets, such as the gene. This enzyme localizes at the first intron of , and the dissociation of KDM4A increases gene expression. assays showed that KDM4A-mediated demethylation is enhanced in the presence of CTCF, suggesting that CTCF could increase its enzymatic activity however the specific mechanism by which and might be involved in the gene repression is poorly understood. Here, we show that CTCF and KDM4A form a protein complex, which is recruited into the first intron of . This is related to a decrease in H3K36me3/2 histone marks and is associated with its transcriptional downregulation. Depletion of or KDM4A by siRNA, triggered the reactivation of expression, suggesting that both proteins are involved in the negative regulation of this gene. Furthermore, the knockout of restored the expression and H3K36me3 and H3K36me2 histone marks. Such mechanism acts independently of promoter DNA methylation. Our findings support a novel mechanism of epigenetic repression at the gene body that does not involve promoter silencing.</p>',
			'date' => '2018-03-30',
			'pmid' => 'http://www.pubmed.gov/29682202',
			'doi' => '10.18632/oncotarget.24798',
			'modified' => '2019-02-14 17:12:34',
			'created' => '2019-02-14 15:01:22',
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		(int) 9 => array(
			'id' => '3390',
			'name' => 'The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes.',
			'authors' => 'Ding D, Bergmaier P, Sachs P, Klangwart M, Rückert T, Bartels N, Demmers J, Dekker M, Poot RA, Mermoud JE',
			'description' => '<p>Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has been shown to affect stem cell state, but the mechanistic explanation for this effect is unknown. Here, we set out to gain further insights into the function of SMARCAD1 in mouse ESCs. We identified KRAB-associated protein 1 (KAP1) as the stoichiometric binding partner of SMARCAD1 in ESCs. We found that this interaction occurs on chromatin and that SMARCAD1 binds to different classes of KAP1 target genes, including zinc finger protein (ZFP) and imprinted genes. We also found that the RING B-box coiled-coil (RBCC) domain in KAP1 and the proximal coupling of ubiquitin conjugation to ER degradation (CUE) domain in SMARCAD1 mediate their direct interaction. Of note, retention of SMARCAD1 in the nucleus depended on KAP1 in both mouse ESCs and human somatic cells. Mutations in the CUE1 domain of SMARCAD1 perturbed the binding to KAP1 and Accordingly, an intact CUE1 domain was required for tethering this remodeler to the nucleus. Moreover, mutation of the CUE1 domain compromised SMARCAD1 binding to KAP1 target genes. Taken together, our results reveal a mechanism that localizes SMARCAD1 to genomic sites through the interaction of SMARCAD1's CUE1 motif with KAP1.</p>',
			'date' => '2018-02-23',
			'pmid' => 'http://www.pubmed.gov/29284678',
			'doi' => '10.1074/jbc.RA117.000959',
			'modified' => '2018-11-09 12:27:47',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '3359',
			'name' => 'Miz1 Controls Schwann Cell Proliferation via H3K36me2 Demethylase Kdm8 to Prevent Peripheral Nerve Demyelination',
			'authors' => 'Fuhrmann D. et al.',
			'description' => '<p>Schwann cell differentiation and myelination depends on chromatin remodeling, histone acetylation, and methylation, which all affect Schwann cell proliferation. We previously reported that the deletion of the POZ (POxvirus and Zinc finger) domain of the transcription factor Miz1 (Myc-interacting zinc finger protein; encoded by <i>Zbtb17</i>) in mouse Schwann cells (<i>Miz1</i>&Delta;<i>POZ</i>) causes a neuropathy at 90 d after birth [postnatal day (P) 90], with a subsequent spontaneous regeneration. Here we show that RNA sequencing from <i>Miz1</i>&Delta;<i>POZ</i> and control animals at P30 revealed a set of upregulated genes with a strong correlation to cell-cycle regulation. Consistently, a subset of Schwann cells did not exit the cell cycle as observed in control animals and the growth fraction increased over time. From the RNAseq gene list, two direct Miz1 target genes were identified, one of which encodes the histone H3K36<sup>me2</sup> demethylase Kdm8. We show that the expression of <i>Kdm8</i> is repressed by Miz1 and that its release in <i>Miz1</i>&Delta;<i>POZ</i> cells induces a decrease of H3K36<sup>me2</sup>, especially in deregulated cell-cycle-related genes. The linkage between elevated <i>Kdm8</i> expression, hypomethylation of H3K36 at cell-cycle-relevant genes, and the subsequent re-entering of adult Schwann cells into the cell cycle suggests that the release of <i>Kdm8</i> repression in the absence of a functional Miz1 is a central issue in the development of the <i>Miz1</i>&Delta;<i>POZ</i> phenotype.<b>SIGNIFICANCE STATEMENT</b> The deletion of the Miz1 (Myc-interacting zinc finger protein 1) POZ (POxvirus and Zinc finger) domain in Schwann cells causes a neuropathy. Here we report sustained Schwann cell proliferation caused by an increased expression of the direct Miz1 target gene <i>Kdm8</i>, encoding a H3K36me2 demethylase. Hence, the demethylation of H3K36 is linked to the pathogenesis of a neuropathy.</p>',
			'date' => '2018-01-24',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29217679',
			'doi' => '',
			'modified' => '2018-04-06 09:51:37',
			'created' => '2018-04-06 09:51:37',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '3318',
			'name' => 'The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes ',
			'authors' => 'Dong Ding et. al.',
			'description' => '<p>Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has been shown to affect stem cell state, but the mechanistic explanation for this effect is unknown. Here, we set out to gain further insights into the function of SMARCAD1 in mouse ESCs. We identified KRAB-associated protein 1 (KAP1) as the stoichiometric binding partner of SMARCAD1 in ESCs. We found that this interaction occurs on chromatin and that SMARCAD1 binds to different classes of KAP1 target genes, including zinc finger protein (ZFP) and imprinted genes. We also found that the RING B-box coiled-coil (RBCC) domain in KAP1 and the proximal coupling of ubiquitin conjugation to ER degradation (CUE) domain in SMARCAD1 mediate their direct interaction. Of note, retention of SMARCAD1 in the nucleus depended on KAP1 in both mouse ESCs and human somatic cells. Mutations in the CUE1 domain of SMARCAD1 perturbed the binding to KAP1 <em>in vitro</em> and <em>in vivo</em>. Accordingly, an intact CUE1 domain was required for tethering this remodeler to the nucleus. Moreover, mutation of the CUE1 domain compromised SMARCAD1 binding to KAP1 target genes. Taken together, our results reveal a mechanism that localizes SMARCAD1 to genomic sites through the interaction of SMARCAD1&rsquo;s CUE1 motif with KAP1.</p>',
			'date' => '2017-12-28',
			'pmid' => 'http://www.jbc.org/content/early/2017/12/28/jbc.RA117.000959',
			'doi' => 'doi: 10.1074/jbc.RA117.000959 ',
			'modified' => '2018-01-14 07:43:01',
			'created' => '2018-01-14 07:43:01',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '3304',
			'name' => 'Individual effects of the copia and gypsy enhancer and insulator on chromatin marks, eRNA synthesis, and binding of insulator proteins in transfected genetic constructs.',
			'authors' => 'Fedoseeva D.M. et al.',
			'description' => '<p>Enhancers and insulators are involved in the regulation of gene expression, but the basic underlying mechanisms of action of these elements are unknown. We analyzed the individual effects of the enhancer and the insulator from Drosophila mobile elements copia [enh(copia)] and gypsy using transfected genetic constructs in S2 cells. This system excludes the influence of genomic cis regulatory elements. The enhancer-induced synthesis of 350-1050-nt-long enhancer RNAs (eRNAs) and H3K4me3 and H3K18ac marks, mainly in the region located about 300bp downstream of the enhancer. Insertion of the insulator between the enhancer and the promoter reduced these effects. We also observed the binding of dCTCF to the enhancer and to gypsy insulator. Our data indicate that a single gypsy insulator interacts with both the enhancer and the promoter, while two copies of the gypsy insulator preferentially interact with each other. Our results suggest the formation of chromatin loops that are shaped by the enhancer and the insulator.</p>',
			'date' => '2017-10-16',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29045822',
			'doi' => '',
			'modified' => '2018-01-03 10:13:37',
			'created' => '2018-01-03 10:13:37',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '3277',
			'name' => 'UV Radiation Activates Toll-Like Receptor 9 Expression in Primary Human Keratinocytes, an Event Inhibited by Human Papillomavirus 38 E6 and E7 Oncoproteins',
			'authors' => 'Pacini L. et al.',
			'description' => '<p>Several lines of evidence indicate that cutaneous human papillomavirus (HPV) types belonging to the beta genus of the HPV phylogenetic tree synergize with UV radiation in the development of skin cancer. Accordingly, the E6 and E7 oncoproteins from some beta HPV types are able to deregulate pathways related to immune response and cellular transformation. Toll-like receptor 9 (TLR9), in addition to playing a role in innate immunity, has been shown to be involved in the cellular stress response. Using primary human keratinocytes as experimental models, we have shown that UV irradiation (and other cellular stresses) activates TLR9 expression. This event is closely linked to p53 activation. Silencing the expression of p53 or deleting its encoding gene affected the activation of TLR9 expression after UV irradiation. Using various strategies, we have also shown that the transcription factors p53 and c-Jun are recruited onto a specific region of the TLR9 promoter after UV irradiation. Importantly, the E6 and E7 oncoproteins from beta HPV38, by inducing the accumulation of the p53 antagonist &Delta;Np73&alpha;, prevent the UV-mediated recruitment of these transcription factors onto the TLR9 promoter, with subsequent impairment of TLR9 gene expression. This study provides new insight into the mechanism that mediates TLR9 upregulation in response to cellular stresses. In addition, we show that HPV38 E6 and E7 are able to interfere with this mechanism, providing another explanation for the possible cooperation of beta HPV types with UV radiation in skin carcinogenesis.<b>IMPORTANCE</b> Beta HPV types have been suggested to act as cofactors in UV-induced skin carcinogenesis by altering several cellular mechanisms activated by UV radiation. We show that the expression of TLR9, a sensor of damage-associated molecular patterns produced during cellular stress, is activated by UV radiation in primary human keratinocytes (PHKs). Two transcription factors known to be activated by UV radiation, p53 and c-Jun, play key roles in UV-activated TLR9 expression. The E6 and E7 oncoproteins from beta HPV38 strongly inhibit UV-activated TLR9 expression by preventing the recruitment of p53 and c-Jun to the TLR9 promoter. Our findings provide additional support for the role that beta HPV types play in skin carcinogenesis by preventing activation of specific pathways upon exposure of PHKs to UV radiation.</p>',
			'date' => '2017-09-12',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28724760',
			'doi' => '',
			'modified' => '2017-10-16 10:19:04',
			'created' => '2017-10-16 10:19:04',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '3249',
			'name' => 'The cardiac calsequestrin gene transcription is modulated at the promoter by NFAT and MEF-2 transcription factors',
			'authors' => 'Rafael Estrada-Avilés, Gabriela Rodríguez, Angel Zarain-Herzberg',
			'description' => '<p>Calsequestrin-2 (CASQ2) is the main Ca<sup>2+</sup>-binding protein inside the sarcoplasmic reticulum of cardiomyocytes. Previously, we demonstrated that MEF-2 and SRF binding sites within the human <em>CASQ2</em> gene (<em>hCASQ2</em>) promoter region are functional in neonatal cardiomyocytes. In this work, we investigated if the calcineurin/NFAT pathway regulates <em>hCASQ2</em> expression in neonatal cardiomyocytes. The inhibition of NFAT dephosphorylation with CsA or INCA-6, reduced both the luciferase activity of <em>hCASQ2</em> promoter constructs (-3102/+176 bp and -288/+176 bp) and the CASQ2 mRNA levels in neonatal rat cardiomyocytes. Additionally, NFATc1 and NFATc3 over-expressing neonatal cardiomyocytes showed a 2-3-fold increase in luciferase activity of both <em>hCASQ2</em> promoter constructs, which was prevented by CsA treatment. Site-directed mutagenesis of the -133 bp MEF-2 binding site prevented trans-activation of <em>hCASQ2</em> promoter constructs induced by NFAT overexpression. Chromatin Immunoprecipitation (ChIP) assays revealed NFAT and MEF-2 enrichment within the -288 bp to +76 bp of the <em>hCASQ2</em> gene promoter. Besides, a direct interaction between NFAT and MEF-2 proteins was demonstrated by protein co-immunoprecipitation experiments. Taken together, these data demonstrate that NFAT interacts with MEF-2 bound to the -133 bp binding site at the <em>hCASQ2</em> gene promoter. In conclusion, in this work, we demonstrate that the Ca<sup>2+</sup>-calcineurin/NFAT pathway modulates the transcription of the <em>hCASQ2</em> gene in neonatal cardiomyocytes.</p>',
			'date' => '2017-09-08',
			'pmid' => 'http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0184724',
			'doi' => 'https://doi.org/10.1371/journal.pone.0184724 ',
			'modified' => '2017-09-26 07:16:08',
			'created' => '2017-09-26 07:16:08',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '3300',
			'name' => 'The cardiac calsequestrin gene transcription is modulated at the promoter by NFAT and MEF-2 transcription factors.',
			'authors' => 'Estrada-Avilés R. et al.',
			'description' => '<p>Calsequestrin-2 (CASQ2) is the main Ca2+-binding protein inside the sarcoplasmic reticulum of cardiomyocytes. Previously, we demonstrated that MEF-2 and SRF binding sites within the human CASQ2 gene (hCASQ2) promoter region are functional in neonatal cardiomyocytes. In this work, we investigated if the calcineurin/NFAT pathway regulates hCASQ2 expression in neonatal cardiomyocytes. The inhibition of NFAT dephosphorylation with CsA or INCA-6, reduced both the luciferase activity of hCASQ2 promoter constructs (-3102/+176 bp and -288/+176 bp) and the CASQ2 mRNA levels in neonatal rat cardiomyocytes. Additionally, NFATc1 and NFATc3 over-expressing neonatal cardiomyocytes showed a 2-3-fold increase in luciferase activity of both hCASQ2 promoter constructs, which was prevented by CsA treatment. Site-directed mutagenesis of the -133 bp MEF-2 binding site prevented trans-activation of hCASQ2 promoter constructs induced by NFAT overexpression. Chromatin Immunoprecipitation (ChIP) assays revealed NFAT and MEF-2 enrichment within the -288 bp to +76 bp of the hCASQ2 gene promoter. Besides, a direct interaction between NFAT and MEF-2 proteins was demonstrated by protein co-immunoprecipitation experiments. Taken together, these data demonstrate that NFAT interacts with MEF-2 bound to the -133 bp binding site at the hCASQ2 gene promoter. In conclusion, in this work, we demonstrate that the Ca2+-calcineurin/NFAT pathway modulates the transcription of the hCASQ2 gene in neonatal cardiomyocytes.</p>',
			'date' => '2017-09-08',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28886186',
			'doi' => '',
			'modified' => '2017-12-05 10:13:23',
			'created' => '2017-12-05 10:13:23',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '3264',
			'name' => 'Viral driven epigenetic events alter the expression of cancer-related genes in Epstein-Barr-virus naturally infected Burkitt lymphoma cell lines',
			'authors' => 'Hernandez-Vargas H. et al.',
			'description' => '<p>Epstein-Barr virus (EBV) was identified as the first human virus to be associated with a human malignancy, Burkitt&rsquo;s lymphoma (BL), a pediatric cancer endemic in sub-Saharan Africa. The exact mechanism of how EBV contributes to the process of lymphomagenesis is not fully understood. Recent studies have highlighted a genetic difference between endemic (EBV+) and sporadic (EBV&minus;) BL, with the endemic variant showing a lower somatic mutation load, which suggests the involvement of an alternative virally-driven process of transformation in the pathogenesis of endemic BL. We tested the hypothesis that a global change in DNA methylation may be induced by infection with EBV, possibly thereby accounting for the lower mutation load observed in endemic BL. Our comparative analysis of the methylation profiles of a panel of BL derived cell lines, naturally infected or not with EBV, revealed that the presence of the virus is associated with a specific pattern of DNA methylation resulting in altered expression of cellular genes with a known or potential role in lymphomagenesis. These included ID3, a gene often found to be mutated in sporadic BL. In summary this study provides evidence that EBV may contribute to the pathogenesis of BL through an epigenetic mechanism.</p>',
			'date' => '2017-07-19',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517637/',
			'doi' => '',
			'modified' => '2017-10-09 16:04:14',
			'created' => '2017-10-09 16:04:14',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '3255',
			'name' => 'SOX2 as a New Regulator of HPV16 Transcription',
			'authors' => 'Martínez-Ramírez I. et al.',
			'description' => '<p>Persistent infections with high-risk human papillomavirus (HPV) constitute the main risk factor for cervical cancer development. HPV16 is the most frequent type associated to squamous cell carcinomas (SCC), followed by HPV18. The long control region (LCR) in the HPV genome contains the replication origin and sequences recognized by cellular transcription factors (TFs) controlling viral transcription. Altered expression of <i>E6</i> and <i>E7</i> viral oncogenes, modulated by the LCR, causes modifications in cellular pathways such as proliferation, leading to malignant transformation. The aim of this study was to identify specific TFs that could contribute to the modulation of high-risk HPV transcriptional activity, related to the cellular histological origin. We identified sex determining region Y (SRY)-box 2 (SOX2) response elements present in HPV16-LCR. SOX2 binding to the LCR was demonstrated by in vivo and in vitro assays. The overexpression of this TF repressed HPV16-LCR transcriptional activity, as shown through reporter plasmid assays and by the down-regulation of endogenous HPV oncogenes. Site-directed mutagenesis revealed that three putative SOX2 binding sites are involved in the repression of the LCR activity. We propose that SOX2 acts as a transcriptional repressor of HPV16-LCR, decreasing the expression of <i>E6</i> and <i>E7</i> oncogenes in a SCC context.</p>',
			'date' => '2017-07-05',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28678184',
			'doi' => '',
			'modified' => '2017-10-02 15:11:26',
			'created' => '2017-10-02 15:11:26',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '3079',
			'name' => 'Biphasic regulation of chondrocytes by Rela through induction of anti-apoptotic and catabolic target genes',
			'authors' => 'Kobayashi H. et al.',
			'description' => '<p>In vitro studies have shown that Rela/p65, a key subunit mediating NF-&kappa;B signalling, is involved in chondrogenic differentiation, cell survival and catabolic enzyme production. Here, we analyse in vivo functions of Rela in embryonic limbs and adult articular cartilage, and find that Rela protects chondrocytes from apoptosis through induction of anti-apoptotic genes including Pik3r1. During skeletal development, homozygous knockout of Rela leads to impaired growth through enhanced chondrocyte apoptosis, whereas heterozygous knockout of Rela does not alter growth. In articular cartilage, homozygous knockout of Rela at 7 weeks leads to marked acceleration of osteoarthritis through enhanced chondrocyte apoptosis, whereas heterozygous knockout of Rela results in suppression of osteoarthritis development through inhibition of catabolic gene expression. Haploinsufficiency or a low dose of an IKK inhibitor suppresses catabolic gene expression, but does not alter anti-apoptotic gene expression. The biphasic regulation of chondrocytes by Rela contributes to understanding the pathophysiology of osteoarthritis.</p>',
			'date' => '2016-11-10',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27830706',
			'doi' => '',
			'modified' => '2016-12-12 16:46:36',
			'created' => '2016-12-12 16:46:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '3053',
			'name' => 'Esrrb directly binds to Gata6 promoter and regulates its expression with Dax1 and Ncoa3',
			'authors' => 'Uranishi K et al.',
			'description' => '<p>Estrogen-related receptor beta (Esrrb) is expressed in embryonic stem (ES) cells and is involved in self-renewal ability and pluripotency. Previously, we found that Dax1 is associated with Esrrb and represses its transcriptional activity. Further, the disruption of the Dax1-Esrrb interaction increases the expression of the extra-embryonic endoderm marker Gata6 in ES cells. Here, we investigated the influences of Esrrb and Dax1 on Gata6 expression. Esrrb overexpression in ES cells induced endogenous Gata6 mRNA and Gata6 promoter activity. In addition, the Gata6 promoter was found to contain the Esrrb recognition motifs ERRE1 and ERRE2, and the latter was the responsive element of Esrrb. Associations between ERRE2 and Esrrb were then confirmed by biotin DNA pulldown and chromatin immunoprecipitation assays. Subsequently, we showed that Esrrb activity at the Gata6 promoter was repressed by Dax1, and although Dax1 did not bind to ERRE2, it was associated with Esrrb, which directly binds to ERRE2. In addition, the transcriptional activity of Esrrb was enhanced by nuclear receptor co-activator 3 (Ncoa3), which has recently been shown to be a binding partner of Esrrb. Finally, we showed that Dax1 was associated with Ncoa3 and repressed its transcriptional activity. Taken together, the present study indicates that the Gata6 promoter is activated by Esrrb in association with Ncoa3, and Dax1 inhibited activities of Esrrb and Ncoa3, resulting maintenance of the undifferentiated status of ES cells.</p>',
			'date' => '2016-09-04',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27601327',
			'doi' => '',
			'modified' => '2016-10-24 14:26:35',
			'created' => '2016-10-24 14:26:35',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => array(
			'id' => '3048',
			'name' => 'Chromatin remodeling regulates catalase expression during cancer cells adaptation to chronic oxidative stress.',
			'authors' => 'Glorieux C. et al.',
			'description' => '<p>Regulation of ROS metabolism plays a major role in cellular adaptation to oxidative stress in cancer cells, but the molecular mechanism that regulates catalase, a key antioxidant enzyme responsible for conversion of hydrogen peroxide to water and oxygen, remains to be elucidated. Therefore, we investigated the transcriptional regulatory mechanism controlling catalase expression in three human mammary cell lines: the normal mammary epithelial 250MK primary cells, the breast adenocarcinoma MCF-7 cells and an experimental model of MCF-7 cells resistant against oxidative stress resulting from chronic exposure to H<sub>2</sub>O<sub>2</sub> (Resox), in which catalase was overexpressed. Here we identify a novel promoter region responsible for the regulation of catalase expression at -1518/-1226 locus and the key molecules that interact with this promoter and affect catalase transcription. We show that the AP-1 family member JunB and retinoic acid receptor alpha (RAR&alpha;) mediate catalase transcriptional activation and repression, respectively, by controlling chromatin remodeling through a histone deacetylases-dependent mechanism. This regulatory mechanism plays an important role in redox adaptation to chronic exposure to H<sub>2</sub>O<sub>2</sub> in breast cancer cells. Our study suggests that cancer adaptation to oxidative stress may be regulated by transcriptional factors through chromatin remodeling, and reveals a potential new mechanism to target cancer cells.</p>',
			'date' => '2016-08-31',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27591797',
			'doi' => '',
			'modified' => '2016-10-10 11:15:35',
			'created' => '2016-10-10 11:15:35',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 21 => array(
			'id' => '2996',
			'name' => 'Induction of cell differentiation activates transcription of the Sarco/Endoplasmic Reticulum calcium-ATPase 3 gene (ATP2A3) in gastric and colon cancer cells',
			'authors' => 'Flores-Peredo L et al.',
			'description' => '<p>The Sarco/Endoplasmic Reticulum Ca<sup>2+</sup> -ATPases (SERCAs), pump Ca<sup>2+</sup> into the endoplasmic reticulum lumen modulating cytosolic Ca<sup>2+</sup> concentrations to regulate various cellular processes including cell growth. Previous studies have reported a downregulation of SERCA3 protein expression in gastric and colon cancer cell lines and showed that in vitro cell differentiation increases its expression. However, little is known about the transcriptional mechanisms and transcription factors that regulate SERCA3 expression in epithelial cancer cells. In this work, we demonstrate that SERCA3 mRNA is upregulated up to 45-fold in two epithelial cancer cell lines, KATO-III and Caco-2, induced to differentiate with histone deacetylase inhibitors (HDACi) and by cell confluence, respectively. To evaluate the transcriptional elements responding to the differentiation stimuli, we cloned the human ATP2A3 promoter, generated deletion constructs and transfected them into KATO-III cells. Basal and differentiation responsive DNA elements were located by functional analysis within the first -135&thinsp;bp of the promoter region. Using site-directed mutagenesis and DNA-protein binding assays we found that Sp1, Sp3, and Klf-4 transcription factors bind to ATP2A3 proximal promoter elements and regulate basal gene expression. We showed that these factors participated in the increase of ATP2A3 expression during cancer cell differentiation. This study provides evidence for the first time that Sp1, Sp3, and Klf-4 transcriptionally modulate the expression of SERCA3 during induction of epithelial cancer cell differentiation.</p>',
			'date' => '2016-07-19',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27433831',
			'doi' => '10.1002/mc.22529',
			'modified' => '2016-08-23 16:57:48',
			'created' => '2016-08-23 16:57:48',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '3027',
			'name' => 'Regulatory Interaction between the Cellular Restriction Factor IFI16 and Viral pp65 (pUL83) Modulates Viral Gene Expression and IFI16 Protein Stability',
			'authors' => 'Biolatti M et al.',
			'description' => '<p>A key player in the intrinsic resistance against human cytomegalovirus (HCMV) is the interferon-&gamma;-inducible protein 16 (IFI16), which behaves as a viral DNA sensor in the first hours post infection and as a repressor of viral gene transcription in the later stages. Previous studies on HCMV replication demonstrated that IFI16 binds to the viral protein kinase pUL97, undergoes phosphorylation and relocalizes to the cytoplasm of infected cells. In this study, we demonstrate that the tegument protein pp65 (pUL83) recruits IFI16 to the promoter of the UL54 gene and downregulates viral replication as shown by use of the HCMV mutant v65Stop, which lacks pp65 expression. Interestingly, at late time-points of HCMV infection, IFI16 is stabilized by its interaction with pp65, which stood in contrast to IFI16 degradation, observed in herpes simplex virus (HSV-1)-infected cells. Moreover, we found that its translocation to the cytoplasm, in addition to pUL97, strictly depends on pp65, as demonstrated with the HCMV mutant RV-VM1, which expresses a form of pp65 unable to translocate into the cytoplasm. Thus, these data reveal a dual role for pp65: during early infection, it modulates IFI16 activity at the promoter of immediate-early and early genes; subsequently, it delocalizes IFI16 from the nucleus into the cytoplasm, thereby stabilizing and protecting it from degradation. Overall, these data identify a novel activity of the pp65/IFI16 interactome involved in the regulation of UL54 gene expression and IFI16 stability during early and late phases of HCMV replication.</p>',
			'date' => '2016-07-06',
			'pmid' => 'http://jvi.asm.org/content/early/2016/06/30/JVI.00923-16.abstract',
			'doi' => '',
			'modified' => '2016-09-07 10:42:20',
			'created' => '2016-09-07 10:42:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '2985',
			'name' => 'miR-125b-1 is repressed by histone modifications in breast cancer cell lines',
			'authors' => 'Cisneros-Soberanis F et al.',
			'description' => '<div class="">
<h4>PURPOSE:</h4>
<p><abstracttext label="PURPOSE" nlmcategory="OBJECTIVE">Downregulation of miR-125b-1 is associated with poor prognosis in breast cancer patients. In this work we investigated the effect of histone modifications on the regulation of this gene promoter.</abstracttext></p>
<h4>METHODS AND RESULTS:</h4>
<p><abstracttext label="METHODS AND RESULTS" nlmcategory="RESULTS">We evaluated the enrichment of two histone modifications involved in gene repression, H3K9me3 and H3K27me3, on the miR-125b-1 promoter in two breast cancer cell lines, MCF7 (luminal A subtype) and MDA-MB-231 (triple-negative subtype), compared to the non-transformed breast cell line MCF10A. H3K27me3 and H3K9me3 were enriched in MCF7 and MDA-MB-231 cells, respectively. Next, we used an EZH2 inhibitor to examine the reactivation of miR-125b-1 in MCF7 cells and evaluated the transcriptional levels of pri-miR-125b-1 and mature miR-125b by qRT-PCR. pri-miRNA and mature miRNA transcripts were both increased after treatment of MCF7 cells with the EZH2 inhibitor, whereas no effect on miR-125b-1 expression levels was observed in MDA-MB-231 and MCF10A cells. We subsequently evaluated the effect of miR-125b-1 reactivation on the expression and protein levels of BAK1, a target of miR-125b. We observed 60 and 70&nbsp;% decreases in the expression and protein levels of BAK1, respectively, compared to cells that were not treated with the EZH2 inhibitor. We over-expressed KDM4B/JMJD2B to reactivate this miRNA, resulting in a three-fold increase in miR-125b expression compared with the same cell line without KDM4B/JMJD2B over-expression.</abstracttext></p>
<h4>CONCLUSION:</h4>
<p><abstracttext label="CONCLUSION" nlmcategory="CONCLUSIONS">The miR-125b-1 is repressed by different epigenetic mechanisms depending on the breast cancer subtype and that miR-125b-1 reactivation specifically eliminates the effect of repressive histone modifications on the expression of an pro-apoptotic target.</abstracttext></p>
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<p><span>Diagenode provides kits with optimized reagents and simplified protocols for ChIP including the <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR kit</a>, <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE kit</a>,&nbsp; <a href="https://www.diagenode.com/en/categories/chromatin-ip-chip-seq-kits">iDeal ChIP-seq kits</a>, <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a>, <a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit </a>and <a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation">the ChIPmentation for Histones</a>. This protocol describes the use of the OneDay ChIP Kit.</span></p>
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<p><span>At present we highly recommend our new generation kits with optimized reagents and improved protocols:<br /></span></p>
<p><span>For ChIP-qPCR: <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR Kit</a> and <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE Kit</a></span></p>
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<p>For low-input ChIP/ChIP-seq: <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP Kit</a></p>
<p><strong>&nbsp;</strong></p>
<p class="text-right"><a class="tiny alert button" href="https://www.diagenode.com/en/categories/chip-grade-antibodies"> Check out our ChIP-grade antibodies</a></p>',
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		'description' => '<p>The OneDay ChIP kit is one of Diagenode old generation ChIP kits, still present in the catalogue.</p>
<p><span>At present we highly recommend our new generation kits with optimized reagents and improved protocols:<br /></span></p>
<p><span>For ChIP-qPCR: <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR Kit</a> and <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE Kit</a></span></p>
<p><span>For ChIP-seq: <a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq Kit for Histones</a>, <a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a> and <a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></span></p>
<p>For low-input ChIP/ChIP-seq: <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP Kit</a></p>
<p><strong>&nbsp;</strong></p>
<p class="text-right"><a class="tiny alert button" href="https://www.diagenode.com/en/categories/chip-grade-antibodies"> Check out our ChIP-grade antibodies</a></p>',
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<p><span>At present we highly recommend our new generation kits with optimized reagents and improved protocols:<br /></span></p>
<p><span>For ChIP-qPCR: <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR Kit</a> and <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE Kit</a></span></p>
<p><span>For ChIP-seq: <a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq Kit for Histones</a>, <a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a> and <a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></span></p>
<p>For low-input ChIP/ChIP-seq: <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP Kit</a></p>
<p><strong>&nbsp;</strong></p>
<p class="text-right"><a class="tiny alert button" href="https://www.diagenode.com/en/categories/chip-grade-antibodies"> Check out our ChIP-grade antibodies</a></p>',
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<p class="text-justify">Chromatin Immunoprecipitation (ChIP) coupled with quantitative PCR can be used to investigate protein-DNA interaction at known genomic binding sites. if sites are not known, qPCR primers can also be designed against potential regulatory regions such as promoters. ChIP-qPCR is advantageous in studies that focus on specific genes and potential regulatory regions across differing experimental conditions as the cost of performing real-time PCR is minimal. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</p>
<p class="text-justify"><strong>The ChIP-qPCR workflow</strong></p>
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<div class="small-12 medium-12 large-12 columns text-center"><br /> <img src="https://www.diagenode.com/img/chip-qpcr-diagram.png" /></div>
<div class="small-12 medium-12 large-12 columns"><br />
<ol>
<li class="large-12 columns"><strong>Chromatin preparation: </strong>cell fixation (cross-linking) of chromatin-bound proteins such as histones or transcription factors to DNA followed by cell lysis.</li>
<li class="large-12 columns"><strong>Chromatin shearing: </strong>fragmentation of chromatin<strong> </strong>by sonication down to desired fragment size (100-500 bp)</li>
<li class="large-12 columns"><strong>Chromatin IP</strong>: protein-DNA complexe capture using<strong> <a href="https://www.diagenode.com/en/categories/chip-grade-antibodies">specific ChIP-grade antibodies</a></strong>&nbsp;against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: chromatin reverse cross-linking and elution followed by purification<strong> </strong></li>
<li class="large-12 columns"><strong>qPCR and analysis</strong>: using previously designed primers to amplify IP'd material at specific loci</li>
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<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
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<p><span>Diagenode provides kits with optimized reagents and simplified protocols for ChIP including the <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR kit</a>, <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE kit</a>,&nbsp; <a href="https://www.diagenode.com/en/categories/chromatin-ip-chip-seq-kits">iDeal ChIP-seq kits</a>, <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a>, <a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit </a>and <a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation">the ChIPmentation for Histones</a>. This protocol describes the use of the OneDay ChIP Kit.</span></p>
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<p></p>
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			'id' => '4067',
			'name' => 'Transcription of CLDND1 in human brain endothelial cells is regulated bythe myeloid zinc finger 1.',
			'authors' => 'Shima, Akiho and Matsuoka, Hiroshi and Yamaoka, Alice and Michihara,Akihiro',
			'description' => '<p>Increased permeability of endothelial cells lining the blood vessels in the brain leads to vascular oedema and, potentially, to stroke. The tight junctions (TJs), primarily responsible for the regulation of vascular permeability, are multi-protein complexes comprising the claudin family of proteins and occludin. Several studies have reported that downregulation of the claudin domain containing 1 (CLDND1) gene enhances vascular permeability, which consequently increases the risk of stroke. However, the transcriptional regulation of CLDND1 has not been studied extensively. Therefore, this study aimed to identify the transcription factors (TFs) regulating CLDND1 expression. A luciferase reporter assay identified a silencer within the first intron of CLDND1, which was identified as a potential binding site of the myeloid zinc finger 1 (MZF1) through in silico and TFBIND software analyses, and confirmed through a reporter assay using the MZF1 expression vector and chromatin immunoprecipitation (ChIP) assays. Moreover, the transient overexpression of MZF1 significantly increased the mRNA and protein expression levels of CLDND1, conversely, which were suppressed through the siRNA-mediated MZF1 knockdown. Furthermore, the permeability of FITC-dextran was observed to be increased on MZF1 knockdown as compared to that of the siGFP control. Our data revealed the underlying mechanism of the transcriptional regulation of CLDND1 by the MZF1. The findings suggest a potential role of MZF1 in TJ formation, which could be studied further and applied to prevent cerebral haemorrhage.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33037622',
			'doi' => '10.1111/1440-1681.13416',
			'modified' => '2021-02-19 17:48:44',
			'created' => '2021-02-18 10:21:53',
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			'id' => '3748',
			'name' => 'Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis.',
			'authors' => 'Vara C, Paytuví-Gallart A, Cuartero Y, Le Dily F, Garcia F, Salvà-Castro J, Gómez-H L, Julià E, Moutinho C, Aiese Cigliano R, Sanseverino W, Fornas O, Pendás AM, Heyn H, Waters PD, Marti-Renom MA, Ruiz-Herrera A',
			'description' => '<p>Mammalian gametogenesis involves dramatic and tightly regulated chromatin remodeling, whose regulatory pathways remain largely unexplored. Here, we generate a comprehensive high-resolution structural and functional atlas of mouse spermatogenesis by combining in situ chromosome conformation capture sequencing (Hi-C), RNA sequencing (RNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) of CCCTC-binding factor (CTCF) and meiotic cohesins, coupled with confocal and super-resolution microscopy. Spermatogonia presents well-defined compartment patterns and topological domains. However, chromosome occupancy and compartmentalization are highly re-arranged during prophase&nbsp;I, with cohesins bound to active promoters in DNA loops out of the chromosomal axes. Compartment patterns re-emerge in round spermatids, where cohesin occupancy correlates with transcriptional activity of key developmental genes. The compact sperm genome contains compartments with actively transcribed genes but no fine-scale topological domains, concomitant with the presence of protamines. Overall, we demonstrate how genome-wide cohesin occupancy and transcriptional activity is associated with three-dimensional (3D) remodeling during spermatogenesis, ultimately reprogramming the genome for the next generation.</p>',
			'date' => '2019-07-09',
			'pmid' => 'http://www.pubmed.gov/31291573',
			'doi' => '10.1016/j.celrep.2019.06.037',
			'modified' => '2019-08-06 16:12:27',
			'created' => '2019-07-31 13:35:50',
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		(int) 2 => array(
			'id' => '3739',
			'name' => 'Resveratrol up-regulates ATP2A3 gene expression in breast cancer cell lines through epigenetic mechanisms.',
			'authors' => 'Izquierdo-Torres E, Hernández-Oliveras A, Meneses-Morales I, Rodríguez G, Fuentes-García G, Zarain-Herzberg Á',
			'description' => '<p>Resveratrol (RSV) is a phytoestrogen which has been related to chemoprevention of several types of cancer. In this work, we show up to a 6-fold increased expression of ATP2A3 gene induced by RSV that triggers apoptosis and changes of intracellular Ca management in MCF-7 and MDA-MB-231 breast cancer cell lines. We explored epigenetic mechanisms for that RSV-induced ATP2A3 up-regulation. The results indicate that RSV-induced ATP2A3 up-regulation correlates with about 50% of reduced HDAC activity and reduced nuclear HDAC2 expression and occupancy on ATP2A3 promoter, increasing the global acetylation of histone H3 and the enrichment of histone mark H3K27Ac on the proximal promoter of the ATP2A3 gene in MDA-MB-231 cells. We also quantified HAT activity, finding that it can be boosted with RSV treatment; however, pharmacological inhibition of p300, one of the main HATs, did not have significant effects in RSV-mediated ATP2A3 gene expression. Additionally, DNMT activity was also reduced in cells treated with RSV, as well as the expression of Methyl-DNA binding proteins MeCP2 and MBD2. However, analysis of the methylation pattern of ATP2A3 gene promoter showed un-methylated promoter in both cell lines. Taken together, the results of this work help to explain, at the molecular level, how ATP2A3 gene is regulated in breast cancer cells, and the benefits of RSV intake observed in epidemiological data, studies with animals, and in vitro models.</p>',
			'date' => '2019-06-04',
			'pmid' => 'http://www.pubmed.gov/31173924',
			'doi' => '10.1016/j.biocel.2019.05.020',
			'modified' => '2019-08-06 16:56:19',
			'created' => '2019-07-31 13:35:50',
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			'id' => '3660',
			'name' => 'Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia.',
			'authors' => 'Wernig-Zorc S, Yadav MP, Kopparapu PK, Bemark M, Kristjansdottir HL, Andersson PO, Kanduri C, Kanduri M',
			'description' => '<p>BACKGROUND: Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic and diagnostic implications for several cancers. However, there is no global study exploring the role of 5-hydroxymethylcytosine (5-hmC) levels in CLL. Herein, using mass spectrometry and hMeDIP-sequencing, we analysed the dynamics of 5-hmC during B cell maturation and CLL pathogenesis. RESULTS: We show that na&iuml;ve B-cells had higher levels of 5-hmC and 5-mC compared to non-class switched and class-switched memory B-cells. We found a significant decrease in global 5-mC levels in CLL patients (n&thinsp;=&thinsp;15) compared to na&iuml;ve and memory B cells, with no changes detected between the CLL prognostic groups. On the other hand, global 5-hmC levels of CLL patients were similar to memory B cells and reduced compared to na&iuml;ve B cells. Interestingly, 5-hmC levels were increased at regulatory regions such as gene-body, CpG island shores and shelves and 5-hmC distribution over the gene-body positively correlated with degree of transcriptional activity. Importantly, CLL samples showed aberrant 5-hmC and 5-mC pattern over gene-body compared to well-defined patterns in normal B-cells. Integrated analysis of 5-hmC and RNA-sequencing from CLL datasets identified three novel oncogenic drivers that could have potential roles in CLL development and progression. CONCLUSIONS: Thus, our study suggests that the global loss of 5-hmC, accompanied by its significant increase at the gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Our combined analysis of 5-mC and 5-hmC sequencing provided insights into the potential role of 5-hmC in modulating gene expression changes during CLL pathogenesis.</p>',
			'date' => '2019-01-07',
			'pmid' => 'http://www.pubmed.gov/30616658',
			'doi' => '10.1186/s13072‑018‑0252‑7',
			'modified' => '2019-07-01 11:46:16',
			'created' => '2019-06-21 14:55:31',
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		(int) 4 => array(
			'id' => '3505',
			'name' => 'Genomic Location of PRMT6-Dependent H3R2 Methylation Is Linked to the Transcriptional Outcome of Associated Genes.',
			'authors' => 'Bouchard C, Sahu P, Meixner M, Nötzold RR, Rust MB, Kremmer E, Feederle R, Hart-Smith G, Finkernagel F, Bartkuhn M, Savai Pullamsetti S, Nist A, Stiewe T, Philipsen S, Bauer UM',
			'description' => '<p>Protein arginine methyltransferase 6 (PRMT6) catalyzes asymmetric dimethylation of histone H3 at arginine 2 (H3R2me2a). This mark has been reported to associate with silent genes. Here, we use a cell model&nbsp;of neural differentiation, which upon PRMT6 knockout exhibits proliferation and differentiation defects. Strikingly, we detect PRMT6-dependent H3R2me2a at active genes, both at promoter and enhancer sites. Loss of H3R2me2a from promoter sites leads to enhanced KMT2A binding and H3K4me3 deposition together with increased target gene transcription, supporting a repressive nature of H3R2me2a. At enhancers, H3R2me2a peaks co-localize with the active enhancer marks H3K4me1 and H3K27ac. Here, loss of H3R2me2a results in reduced KMT2D binding and H3K4me1/H3K27ac deposition together with decreased transcription of associated genes, indicating that H3R2me2a also exerts activation functions. Our work suggests that PRMT6 via H3R2me2a interferes with the deposition of adjacent histone marks and modulates the activity of important differentiation-associated genes by opposing transcriptional effects.</p>',
			'date' => '2018-09-18',
			'pmid' => 'http://www.pubmed.gov/30232013',
			'doi' => '10.1016/j.celrep.2018.08.052',
			'modified' => '2019-02-28 10:05:16',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '3443',
			'name' => 'High-fidelity CRISPR/Cas9- based gene-specific hydroxymethylation rescues gene expression and attenuates renal fibrosis.',
			'authors' => 'Xingbo Xu, Xiaoying Tan, Björn Tampe, Tim Wilhelmi, Melanie S. Hulshoff, Shoji Saito, Tobias Moser, Raghu Kalluri, Gerd Hasenfuss, Elisabeth M. Zeisberg & Michael Zeisberg ',
			'description' => '<p>While suppression of specific genes through aberrant promoter methylation contributes to different diseases including organ fibrosis, gene-specific reactivation technology is not yet available for therapy. TET enzymes catalyze hydroxymethylation of methylated DNA, reactivating gene expression. We here report generation of a high-fidelity CRISPR/Cas9-based gene-specific dioxygenase by fusing an endonuclease deactivated high-fidelity Cas9 (dHFCas9) to TET3 catalytic domain (TET3CD), targeted to specific genes by guiding RNAs (sgRNA). We demonstrate use of this technology in four different anti-fibrotic genes in different cell types in vitro, among them RASAL1 and Klotho, both hypermethylated in kidney fibrosis. Furthermore, in vivo lentiviral delivery of the Rasal1-targeted fusion protein to interstitial cells and of the Klotho-targeted fusion protein to tubular epithelial cells each results in specific gene reactivation and attenuation of fibrosis, providing gene-specific demethylating technology in a disease model.</p>',
			'date' => '2018-08-29',
			'pmid' => 'http://www.pubmed.gov/30158531',
			'doi' => '10.1038/s41467-018-05766-5',
			'modified' => '2019-02-28 10:11:31',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '3522',
			'name' => 'Human papillomavirus type 16 antagonizes IRF6 regulation of IL-1β.',
			'authors' => 'Ainouze M, Rochefort P, Parroche P, Roblot G, Tout I, Briat F, Zannetti C, Marotel M, Goutagny N, Auron P, Traverse-Glehen A, Lunel-Potencier A, Golfier F, Masson M, Robitaille A, Tommasino M, Carreira C, Walzer T, Henry T, Zanier K, Trave G, Hasan UA',
			'description' => '<p>Human papillomavirus type 16 (HPV16) and other oncoviruses have been shown to block innate immune responses and to persist in the host. However, to avoid viral persistence, the immune response attempts to clear the infection. IL-1&beta; is a powerful cytokine produced when viral motifs are sensed by innate receptors that are members of the inflammasome family. Whether oncoviruses such as HPV16 can activate the inflammasome pathway remains unknown. Here, we show that infection of human keratinocytes with HPV16 induced the secretion of IL-1&beta;. Yet, upon expression of the viral early genes, IL-1&beta; transcription was blocked. We went on to show that expression of the viral oncoprotein E6 in human keratinocytes inhibited IRF6 transcription which we revealed regulated IL-1&beta; promoter activity. Preventing E6 expression using siRNA, or using E6 mutants that prevented degradation of p53, showed that p53 regulated IRF6 transcription. HPV16 abrogation of p53 binding to the IRF6 promoter was shown by ChIP in tissues from patients with cervical cancer. Thus E6 inhibition of IRF6 is an escape strategy used by HPV16 to block the production IL-1&beta;. Our findings reveal a struggle between oncoviral persistence and host immunity; which is centered on IL-1&beta; regulation.</p>',
			'date' => '2018-08-08',
			'pmid' => 'http://www.pubmed.gov/30089163',
			'doi' => '10.1371/journal.ppat.1007158',
			'modified' => '2019-02-28 10:14:30',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '3583',
			'name' => 'Human papillomavirus type 16 antagonizes IRF6 regulation of IL-1β.',
			'authors' => 'Ainouze M, Rochefort P, Parroche P, Roblot G, Tout I, Briat F, Zannetti C, Marotel M, Goutagny N, Auron P, Traverse-Glehen A, Lunel-Potencier A, Golfier F, Masson M, Robitaille A, Tommasino M, Carreira C, Walzer T, Henry T, Zanier K, Trave G, Hasan UA',
			'description' => '<p>Human papillomavirus type 16 (HPV16) and other oncoviruses have been shown to block innate immune responses and to persist in the host. However, to avoid viral persistence, the immune response attempts to clear the infection. IL-1&beta; is a powerful cytokine produced when viral motifs are sensed by innate receptors that are members of the inflammasome family. Whether oncoviruses such as HPV16 can activate the inflammasome pathway remains unknown. Here, we show that infection of human keratinocytes with HPV16 induced the secretion of IL-1&beta;. Yet, upon expression of the viral early genes, IL-1&beta; transcription was blocked. We went on to show that expression of the viral oncoprotein E6 in human keratinocytes inhibited IRF6 transcription which we revealed regulated IL-1&beta; promoter activity. Preventing E6 expression using siRNA, or using E6 mutants that prevented degradation of p53, showed that p53 regulated IRF6 transcription. HPV16 abrogation of p53 binding to the IRF6 promoter was shown by ChIP in tissues from patients with cervical cancer. Thus E6 inhibition of IRF6 is an escape strategy used by HPV16 to block the production IL-1&beta;. Our findings reveal a struggle between oncoviral persistence and host immunity; which is centered on IL-1&beta; regulation.</p>',
			'date' => '2018-08-08',
			'pmid' => 'http://www.pubmed.gov/30089163',
			'doi' => '10.1371/journal.ppat.1007158',
			'modified' => '2019-04-17 15:50:02',
			'created' => '2019-04-16 12:25:30',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '3480',
			'name' => 'CTCF-KDM4A complex correlates with histone modifications that negatively regulate  gene expression in cancer cell lines.',
			'authors' => 'Guerra-Calderas L, González-Barrios R, Patiño CC, Alcaraz N, Salgado-Albarrán M, de León DC, Hernández CC, Sánchez-Pérez Y, Maldonado-Martínez HA, De la Rosa-Velazquez IA, Vargas-Romero F, Herrera LA, García-Carrancá A, Soto-Reyes E',
			'description' => '<p>Histone demethylase KDM4A is involved in H3K9me3 and H3K36me3 demethylation, which are epigenetic modifications associated with gene silencing and RNA Polymerase II elongation, respectively. is abnormally expressed in cancer, affecting the expression of multiple targets, such as the gene. This enzyme localizes at the first intron of , and the dissociation of KDM4A increases gene expression. assays showed that KDM4A-mediated demethylation is enhanced in the presence of CTCF, suggesting that CTCF could increase its enzymatic activity however the specific mechanism by which and might be involved in the gene repression is poorly understood. Here, we show that CTCF and KDM4A form a protein complex, which is recruited into the first intron of . This is related to a decrease in H3K36me3/2 histone marks and is associated with its transcriptional downregulation. Depletion of or KDM4A by siRNA, triggered the reactivation of expression, suggesting that both proteins are involved in the negative regulation of this gene. Furthermore, the knockout of restored the expression and H3K36me3 and H3K36me2 histone marks. Such mechanism acts independently of promoter DNA methylation. Our findings support a novel mechanism of epigenetic repression at the gene body that does not involve promoter silencing.</p>',
			'date' => '2018-03-30',
			'pmid' => 'http://www.pubmed.gov/29682202',
			'doi' => '10.18632/oncotarget.24798',
			'modified' => '2019-02-14 17:12:34',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '3390',
			'name' => 'The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes.',
			'authors' => 'Ding D, Bergmaier P, Sachs P, Klangwart M, Rückert T, Bartels N, Demmers J, Dekker M, Poot RA, Mermoud JE',
			'description' => '<p>Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has been shown to affect stem cell state, but the mechanistic explanation for this effect is unknown. Here, we set out to gain further insights into the function of SMARCAD1 in mouse ESCs. We identified KRAB-associated protein 1 (KAP1) as the stoichiometric binding partner of SMARCAD1 in ESCs. We found that this interaction occurs on chromatin and that SMARCAD1 binds to different classes of KAP1 target genes, including zinc finger protein (ZFP) and imprinted genes. We also found that the RING B-box coiled-coil (RBCC) domain in KAP1 and the proximal coupling of ubiquitin conjugation to ER degradation (CUE) domain in SMARCAD1 mediate their direct interaction. Of note, retention of SMARCAD1 in the nucleus depended on KAP1 in both mouse ESCs and human somatic cells. Mutations in the CUE1 domain of SMARCAD1 perturbed the binding to KAP1 and Accordingly, an intact CUE1 domain was required for tethering this remodeler to the nucleus. Moreover, mutation of the CUE1 domain compromised SMARCAD1 binding to KAP1 target genes. Taken together, our results reveal a mechanism that localizes SMARCAD1 to genomic sites through the interaction of SMARCAD1's CUE1 motif with KAP1.</p>',
			'date' => '2018-02-23',
			'pmid' => 'http://www.pubmed.gov/29284678',
			'doi' => '10.1074/jbc.RA117.000959',
			'modified' => '2018-11-09 12:27:47',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '3359',
			'name' => 'Miz1 Controls Schwann Cell Proliferation via H3K36me2 Demethylase Kdm8 to Prevent Peripheral Nerve Demyelination',
			'authors' => 'Fuhrmann D. et al.',
			'description' => '<p>Schwann cell differentiation and myelination depends on chromatin remodeling, histone acetylation, and methylation, which all affect Schwann cell proliferation. We previously reported that the deletion of the POZ (POxvirus and Zinc finger) domain of the transcription factor Miz1 (Myc-interacting zinc finger protein; encoded by <i>Zbtb17</i>) in mouse Schwann cells (<i>Miz1</i>&Delta;<i>POZ</i>) causes a neuropathy at 90 d after birth [postnatal day (P) 90], with a subsequent spontaneous regeneration. Here we show that RNA sequencing from <i>Miz1</i>&Delta;<i>POZ</i> and control animals at P30 revealed a set of upregulated genes with a strong correlation to cell-cycle regulation. Consistently, a subset of Schwann cells did not exit the cell cycle as observed in control animals and the growth fraction increased over time. From the RNAseq gene list, two direct Miz1 target genes were identified, one of which encodes the histone H3K36<sup>me2</sup> demethylase Kdm8. We show that the expression of <i>Kdm8</i> is repressed by Miz1 and that its release in <i>Miz1</i>&Delta;<i>POZ</i> cells induces a decrease of H3K36<sup>me2</sup>, especially in deregulated cell-cycle-related genes. The linkage between elevated <i>Kdm8</i> expression, hypomethylation of H3K36 at cell-cycle-relevant genes, and the subsequent re-entering of adult Schwann cells into the cell cycle suggests that the release of <i>Kdm8</i> repression in the absence of a functional Miz1 is a central issue in the development of the <i>Miz1</i>&Delta;<i>POZ</i> phenotype.<b>SIGNIFICANCE STATEMENT</b> The deletion of the Miz1 (Myc-interacting zinc finger protein 1) POZ (POxvirus and Zinc finger) domain in Schwann cells causes a neuropathy. Here we report sustained Schwann cell proliferation caused by an increased expression of the direct Miz1 target gene <i>Kdm8</i>, encoding a H3K36me2 demethylase. Hence, the demethylation of H3K36 is linked to the pathogenesis of a neuropathy.</p>',
			'date' => '2018-01-24',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29217679',
			'doi' => '',
			'modified' => '2018-04-06 09:51:37',
			'created' => '2018-04-06 09:51:37',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '3318',
			'name' => 'The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes ',
			'authors' => 'Dong Ding et. al.',
			'description' => '<p>Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has been shown to affect stem cell state, but the mechanistic explanation for this effect is unknown. Here, we set out to gain further insights into the function of SMARCAD1 in mouse ESCs. We identified KRAB-associated protein 1 (KAP1) as the stoichiometric binding partner of SMARCAD1 in ESCs. We found that this interaction occurs on chromatin and that SMARCAD1 binds to different classes of KAP1 target genes, including zinc finger protein (ZFP) and imprinted genes. We also found that the RING B-box coiled-coil (RBCC) domain in KAP1 and the proximal coupling of ubiquitin conjugation to ER degradation (CUE) domain in SMARCAD1 mediate their direct interaction. Of note, retention of SMARCAD1 in the nucleus depended on KAP1 in both mouse ESCs and human somatic cells. Mutations in the CUE1 domain of SMARCAD1 perturbed the binding to KAP1 <em>in vitro</em> and <em>in vivo</em>. Accordingly, an intact CUE1 domain was required for tethering this remodeler to the nucleus. Moreover, mutation of the CUE1 domain compromised SMARCAD1 binding to KAP1 target genes. Taken together, our results reveal a mechanism that localizes SMARCAD1 to genomic sites through the interaction of SMARCAD1&rsquo;s CUE1 motif with KAP1.</p>',
			'date' => '2017-12-28',
			'pmid' => 'http://www.jbc.org/content/early/2017/12/28/jbc.RA117.000959',
			'doi' => 'doi: 10.1074/jbc.RA117.000959 ',
			'modified' => '2018-01-14 07:43:01',
			'created' => '2018-01-14 07:43:01',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '3304',
			'name' => 'Individual effects of the copia and gypsy enhancer and insulator on chromatin marks, eRNA synthesis, and binding of insulator proteins in transfected genetic constructs.',
			'authors' => 'Fedoseeva D.M. et al.',
			'description' => '<p>Enhancers and insulators are involved in the regulation of gene expression, but the basic underlying mechanisms of action of these elements are unknown. We analyzed the individual effects of the enhancer and the insulator from Drosophila mobile elements copia [enh(copia)] and gypsy using transfected genetic constructs in S2 cells. This system excludes the influence of genomic cis regulatory elements. The enhancer-induced synthesis of 350-1050-nt-long enhancer RNAs (eRNAs) and H3K4me3 and H3K18ac marks, mainly in the region located about 300bp downstream of the enhancer. Insertion of the insulator between the enhancer and the promoter reduced these effects. We also observed the binding of dCTCF to the enhancer and to gypsy insulator. Our data indicate that a single gypsy insulator interacts with both the enhancer and the promoter, while two copies of the gypsy insulator preferentially interact with each other. Our results suggest the formation of chromatin loops that are shaped by the enhancer and the insulator.</p>',
			'date' => '2017-10-16',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29045822',
			'doi' => '',
			'modified' => '2018-01-03 10:13:37',
			'created' => '2018-01-03 10:13:37',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '3277',
			'name' => 'UV Radiation Activates Toll-Like Receptor 9 Expression in Primary Human Keratinocytes, an Event Inhibited by Human Papillomavirus 38 E6 and E7 Oncoproteins',
			'authors' => 'Pacini L. et al.',
			'description' => '<p>Several lines of evidence indicate that cutaneous human papillomavirus (HPV) types belonging to the beta genus of the HPV phylogenetic tree synergize with UV radiation in the development of skin cancer. Accordingly, the E6 and E7 oncoproteins from some beta HPV types are able to deregulate pathways related to immune response and cellular transformation. Toll-like receptor 9 (TLR9), in addition to playing a role in innate immunity, has been shown to be involved in the cellular stress response. Using primary human keratinocytes as experimental models, we have shown that UV irradiation (and other cellular stresses) activates TLR9 expression. This event is closely linked to p53 activation. Silencing the expression of p53 or deleting its encoding gene affected the activation of TLR9 expression after UV irradiation. Using various strategies, we have also shown that the transcription factors p53 and c-Jun are recruited onto a specific region of the TLR9 promoter after UV irradiation. Importantly, the E6 and E7 oncoproteins from beta HPV38, by inducing the accumulation of the p53 antagonist &Delta;Np73&alpha;, prevent the UV-mediated recruitment of these transcription factors onto the TLR9 promoter, with subsequent impairment of TLR9 gene expression. This study provides new insight into the mechanism that mediates TLR9 upregulation in response to cellular stresses. In addition, we show that HPV38 E6 and E7 are able to interfere with this mechanism, providing another explanation for the possible cooperation of beta HPV types with UV radiation in skin carcinogenesis.<b>IMPORTANCE</b> Beta HPV types have been suggested to act as cofactors in UV-induced skin carcinogenesis by altering several cellular mechanisms activated by UV radiation. We show that the expression of TLR9, a sensor of damage-associated molecular patterns produced during cellular stress, is activated by UV radiation in primary human keratinocytes (PHKs). Two transcription factors known to be activated by UV radiation, p53 and c-Jun, play key roles in UV-activated TLR9 expression. The E6 and E7 oncoproteins from beta HPV38 strongly inhibit UV-activated TLR9 expression by preventing the recruitment of p53 and c-Jun to the TLR9 promoter. Our findings provide additional support for the role that beta HPV types play in skin carcinogenesis by preventing activation of specific pathways upon exposure of PHKs to UV radiation.</p>',
			'date' => '2017-09-12',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28724760',
			'doi' => '',
			'modified' => '2017-10-16 10:19:04',
			'created' => '2017-10-16 10:19:04',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '3249',
			'name' => 'The cardiac calsequestrin gene transcription is modulated at the promoter by NFAT and MEF-2 transcription factors',
			'authors' => 'Rafael Estrada-Avilés, Gabriela Rodríguez, Angel Zarain-Herzberg',
			'description' => '<p>Calsequestrin-2 (CASQ2) is the main Ca<sup>2+</sup>-binding protein inside the sarcoplasmic reticulum of cardiomyocytes. Previously, we demonstrated that MEF-2 and SRF binding sites within the human <em>CASQ2</em> gene (<em>hCASQ2</em>) promoter region are functional in neonatal cardiomyocytes. In this work, we investigated if the calcineurin/NFAT pathway regulates <em>hCASQ2</em> expression in neonatal cardiomyocytes. The inhibition of NFAT dephosphorylation with CsA or INCA-6, reduced both the luciferase activity of <em>hCASQ2</em> promoter constructs (-3102/+176 bp and -288/+176 bp) and the CASQ2 mRNA levels in neonatal rat cardiomyocytes. Additionally, NFATc1 and NFATc3 over-expressing neonatal cardiomyocytes showed a 2-3-fold increase in luciferase activity of both <em>hCASQ2</em> promoter constructs, which was prevented by CsA treatment. Site-directed mutagenesis of the -133 bp MEF-2 binding site prevented trans-activation of <em>hCASQ2</em> promoter constructs induced by NFAT overexpression. Chromatin Immunoprecipitation (ChIP) assays revealed NFAT and MEF-2 enrichment within the -288 bp to +76 bp of the <em>hCASQ2</em> gene promoter. Besides, a direct interaction between NFAT and MEF-2 proteins was demonstrated by protein co-immunoprecipitation experiments. Taken together, these data demonstrate that NFAT interacts with MEF-2 bound to the -133 bp binding site at the <em>hCASQ2</em> gene promoter. In conclusion, in this work, we demonstrate that the Ca<sup>2+</sup>-calcineurin/NFAT pathway modulates the transcription of the <em>hCASQ2</em> gene in neonatal cardiomyocytes.</p>',
			'date' => '2017-09-08',
			'pmid' => 'http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0184724',
			'doi' => 'https://doi.org/10.1371/journal.pone.0184724 ',
			'modified' => '2017-09-26 07:16:08',
			'created' => '2017-09-26 07:16:08',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '3300',
			'name' => 'The cardiac calsequestrin gene transcription is modulated at the promoter by NFAT and MEF-2 transcription factors.',
			'authors' => 'Estrada-Avilés R. et al.',
			'description' => '<p>Calsequestrin-2 (CASQ2) is the main Ca2+-binding protein inside the sarcoplasmic reticulum of cardiomyocytes. Previously, we demonstrated that MEF-2 and SRF binding sites within the human CASQ2 gene (hCASQ2) promoter region are functional in neonatal cardiomyocytes. In this work, we investigated if the calcineurin/NFAT pathway regulates hCASQ2 expression in neonatal cardiomyocytes. The inhibition of NFAT dephosphorylation with CsA or INCA-6, reduced both the luciferase activity of hCASQ2 promoter constructs (-3102/+176 bp and -288/+176 bp) and the CASQ2 mRNA levels in neonatal rat cardiomyocytes. Additionally, NFATc1 and NFATc3 over-expressing neonatal cardiomyocytes showed a 2-3-fold increase in luciferase activity of both hCASQ2 promoter constructs, which was prevented by CsA treatment. Site-directed mutagenesis of the -133 bp MEF-2 binding site prevented trans-activation of hCASQ2 promoter constructs induced by NFAT overexpression. Chromatin Immunoprecipitation (ChIP) assays revealed NFAT and MEF-2 enrichment within the -288 bp to +76 bp of the hCASQ2 gene promoter. Besides, a direct interaction between NFAT and MEF-2 proteins was demonstrated by protein co-immunoprecipitation experiments. Taken together, these data demonstrate that NFAT interacts with MEF-2 bound to the -133 bp binding site at the hCASQ2 gene promoter. In conclusion, in this work, we demonstrate that the Ca2+-calcineurin/NFAT pathway modulates the transcription of the hCASQ2 gene in neonatal cardiomyocytes.</p>',
			'date' => '2017-09-08',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28886186',
			'doi' => '',
			'modified' => '2017-12-05 10:13:23',
			'created' => '2017-12-05 10:13:23',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '3264',
			'name' => 'Viral driven epigenetic events alter the expression of cancer-related genes in Epstein-Barr-virus naturally infected Burkitt lymphoma cell lines',
			'authors' => 'Hernandez-Vargas H. et al.',
			'description' => '<p>Epstein-Barr virus (EBV) was identified as the first human virus to be associated with a human malignancy, Burkitt&rsquo;s lymphoma (BL), a pediatric cancer endemic in sub-Saharan Africa. The exact mechanism of how EBV contributes to the process of lymphomagenesis is not fully understood. Recent studies have highlighted a genetic difference between endemic (EBV+) and sporadic (EBV&minus;) BL, with the endemic variant showing a lower somatic mutation load, which suggests the involvement of an alternative virally-driven process of transformation in the pathogenesis of endemic BL. We tested the hypothesis that a global change in DNA methylation may be induced by infection with EBV, possibly thereby accounting for the lower mutation load observed in endemic BL. Our comparative analysis of the methylation profiles of a panel of BL derived cell lines, naturally infected or not with EBV, revealed that the presence of the virus is associated with a specific pattern of DNA methylation resulting in altered expression of cellular genes with a known or potential role in lymphomagenesis. These included ID3, a gene often found to be mutated in sporadic BL. In summary this study provides evidence that EBV may contribute to the pathogenesis of BL through an epigenetic mechanism.</p>',
			'date' => '2017-07-19',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517637/',
			'doi' => '',
			'modified' => '2017-10-09 16:04:14',
			'created' => '2017-10-09 16:04:14',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '3255',
			'name' => 'SOX2 as a New Regulator of HPV16 Transcription',
			'authors' => 'Martínez-Ramírez I. et al.',
			'description' => '<p>Persistent infections with high-risk human papillomavirus (HPV) constitute the main risk factor for cervical cancer development. HPV16 is the most frequent type associated to squamous cell carcinomas (SCC), followed by HPV18. The long control region (LCR) in the HPV genome contains the replication origin and sequences recognized by cellular transcription factors (TFs) controlling viral transcription. Altered expression of <i>E6</i> and <i>E7</i> viral oncogenes, modulated by the LCR, causes modifications in cellular pathways such as proliferation, leading to malignant transformation. The aim of this study was to identify specific TFs that could contribute to the modulation of high-risk HPV transcriptional activity, related to the cellular histological origin. We identified sex determining region Y (SRY)-box 2 (SOX2) response elements present in HPV16-LCR. SOX2 binding to the LCR was demonstrated by in vivo and in vitro assays. The overexpression of this TF repressed HPV16-LCR transcriptional activity, as shown through reporter plasmid assays and by the down-regulation of endogenous HPV oncogenes. Site-directed mutagenesis revealed that three putative SOX2 binding sites are involved in the repression of the LCR activity. We propose that SOX2 acts as a transcriptional repressor of HPV16-LCR, decreasing the expression of <i>E6</i> and <i>E7</i> oncogenes in a SCC context.</p>',
			'date' => '2017-07-05',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28678184',
			'doi' => '',
			'modified' => '2017-10-02 15:11:26',
			'created' => '2017-10-02 15:11:26',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '3079',
			'name' => 'Biphasic regulation of chondrocytes by Rela through induction of anti-apoptotic and catabolic target genes',
			'authors' => 'Kobayashi H. et al.',
			'description' => '<p>In vitro studies have shown that Rela/p65, a key subunit mediating NF-&kappa;B signalling, is involved in chondrogenic differentiation, cell survival and catabolic enzyme production. Here, we analyse in vivo functions of Rela in embryonic limbs and adult articular cartilage, and find that Rela protects chondrocytes from apoptosis through induction of anti-apoptotic genes including Pik3r1. During skeletal development, homozygous knockout of Rela leads to impaired growth through enhanced chondrocyte apoptosis, whereas heterozygous knockout of Rela does not alter growth. In articular cartilage, homozygous knockout of Rela at 7 weeks leads to marked acceleration of osteoarthritis through enhanced chondrocyte apoptosis, whereas heterozygous knockout of Rela results in suppression of osteoarthritis development through inhibition of catabolic gene expression. Haploinsufficiency or a low dose of an IKK inhibitor suppresses catabolic gene expression, but does not alter anti-apoptotic gene expression. The biphasic regulation of chondrocytes by Rela contributes to understanding the pathophysiology of osteoarthritis.</p>',
			'date' => '2016-11-10',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27830706',
			'doi' => '',
			'modified' => '2016-12-12 16:46:36',
			'created' => '2016-12-12 16:46:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '3053',
			'name' => 'Esrrb directly binds to Gata6 promoter and regulates its expression with Dax1 and Ncoa3',
			'authors' => 'Uranishi K et al.',
			'description' => '<p>Estrogen-related receptor beta (Esrrb) is expressed in embryonic stem (ES) cells and is involved in self-renewal ability and pluripotency. Previously, we found that Dax1 is associated with Esrrb and represses its transcriptional activity. Further, the disruption of the Dax1-Esrrb interaction increases the expression of the extra-embryonic endoderm marker Gata6 in ES cells. Here, we investigated the influences of Esrrb and Dax1 on Gata6 expression. Esrrb overexpression in ES cells induced endogenous Gata6 mRNA and Gata6 promoter activity. In addition, the Gata6 promoter was found to contain the Esrrb recognition motifs ERRE1 and ERRE2, and the latter was the responsive element of Esrrb. Associations between ERRE2 and Esrrb were then confirmed by biotin DNA pulldown and chromatin immunoprecipitation assays. Subsequently, we showed that Esrrb activity at the Gata6 promoter was repressed by Dax1, and although Dax1 did not bind to ERRE2, it was associated with Esrrb, which directly binds to ERRE2. In addition, the transcriptional activity of Esrrb was enhanced by nuclear receptor co-activator 3 (Ncoa3), which has recently been shown to be a binding partner of Esrrb. Finally, we showed that Dax1 was associated with Ncoa3 and repressed its transcriptional activity. Taken together, the present study indicates that the Gata6 promoter is activated by Esrrb in association with Ncoa3, and Dax1 inhibited activities of Esrrb and Ncoa3, resulting maintenance of the undifferentiated status of ES cells.</p>',
			'date' => '2016-09-04',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27601327',
			'doi' => '',
			'modified' => '2016-10-24 14:26:35',
			'created' => '2016-10-24 14:26:35',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => array(
			'id' => '3048',
			'name' => 'Chromatin remodeling regulates catalase expression during cancer cells adaptation to chronic oxidative stress.',
			'authors' => 'Glorieux C. et al.',
			'description' => '<p>Regulation of ROS metabolism plays a major role in cellular adaptation to oxidative stress in cancer cells, but the molecular mechanism that regulates catalase, a key antioxidant enzyme responsible for conversion of hydrogen peroxide to water and oxygen, remains to be elucidated. Therefore, we investigated the transcriptional regulatory mechanism controlling catalase expression in three human mammary cell lines: the normal mammary epithelial 250MK primary cells, the breast adenocarcinoma MCF-7 cells and an experimental model of MCF-7 cells resistant against oxidative stress resulting from chronic exposure to H<sub>2</sub>O<sub>2</sub> (Resox), in which catalase was overexpressed. Here we identify a novel promoter region responsible for the regulation of catalase expression at -1518/-1226 locus and the key molecules that interact with this promoter and affect catalase transcription. We show that the AP-1 family member JunB and retinoic acid receptor alpha (RAR&alpha;) mediate catalase transcriptional activation and repression, respectively, by controlling chromatin remodeling through a histone deacetylases-dependent mechanism. This regulatory mechanism plays an important role in redox adaptation to chronic exposure to H<sub>2</sub>O<sub>2</sub> in breast cancer cells. Our study suggests that cancer adaptation to oxidative stress may be regulated by transcriptional factors through chromatin remodeling, and reveals a potential new mechanism to target cancer cells.</p>',
			'date' => '2016-08-31',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27591797',
			'doi' => '',
			'modified' => '2016-10-10 11:15:35',
			'created' => '2016-10-10 11:15:35',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 21 => array(
			'id' => '2996',
			'name' => 'Induction of cell differentiation activates transcription of the Sarco/Endoplasmic Reticulum calcium-ATPase 3 gene (ATP2A3) in gastric and colon cancer cells',
			'authors' => 'Flores-Peredo L et al.',
			'description' => '<p>The Sarco/Endoplasmic Reticulum Ca<sup>2+</sup> -ATPases (SERCAs), pump Ca<sup>2+</sup> into the endoplasmic reticulum lumen modulating cytosolic Ca<sup>2+</sup> concentrations to regulate various cellular processes including cell growth. Previous studies have reported a downregulation of SERCA3 protein expression in gastric and colon cancer cell lines and showed that in vitro cell differentiation increases its expression. However, little is known about the transcriptional mechanisms and transcription factors that regulate SERCA3 expression in epithelial cancer cells. In this work, we demonstrate that SERCA3 mRNA is upregulated up to 45-fold in two epithelial cancer cell lines, KATO-III and Caco-2, induced to differentiate with histone deacetylase inhibitors (HDACi) and by cell confluence, respectively. To evaluate the transcriptional elements responding to the differentiation stimuli, we cloned the human ATP2A3 promoter, generated deletion constructs and transfected them into KATO-III cells. Basal and differentiation responsive DNA elements were located by functional analysis within the first -135&thinsp;bp of the promoter region. Using site-directed mutagenesis and DNA-protein binding assays we found that Sp1, Sp3, and Klf-4 transcription factors bind to ATP2A3 proximal promoter elements and regulate basal gene expression. We showed that these factors participated in the increase of ATP2A3 expression during cancer cell differentiation. This study provides evidence for the first time that Sp1, Sp3, and Klf-4 transcriptionally modulate the expression of SERCA3 during induction of epithelial cancer cell differentiation.</p>',
			'date' => '2016-07-19',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27433831',
			'doi' => '10.1002/mc.22529',
			'modified' => '2016-08-23 16:57:48',
			'created' => '2016-08-23 16:57:48',
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			'id' => '3027',
			'name' => 'Regulatory Interaction between the Cellular Restriction Factor IFI16 and Viral pp65 (pUL83) Modulates Viral Gene Expression and IFI16 Protein Stability',
			'authors' => 'Biolatti M et al.',
			'description' => '<p>A key player in the intrinsic resistance against human cytomegalovirus (HCMV) is the interferon-&gamma;-inducible protein 16 (IFI16), which behaves as a viral DNA sensor in the first hours post infection and as a repressor of viral gene transcription in the later stages. Previous studies on HCMV replication demonstrated that IFI16 binds to the viral protein kinase pUL97, undergoes phosphorylation and relocalizes to the cytoplasm of infected cells. In this study, we demonstrate that the tegument protein pp65 (pUL83) recruits IFI16 to the promoter of the UL54 gene and downregulates viral replication as shown by use of the HCMV mutant v65Stop, which lacks pp65 expression. Interestingly, at late time-points of HCMV infection, IFI16 is stabilized by its interaction with pp65, which stood in contrast to IFI16 degradation, observed in herpes simplex virus (HSV-1)-infected cells. Moreover, we found that its translocation to the cytoplasm, in addition to pUL97, strictly depends on pp65, as demonstrated with the HCMV mutant RV-VM1, which expresses a form of pp65 unable to translocate into the cytoplasm. Thus, these data reveal a dual role for pp65: during early infection, it modulates IFI16 activity at the promoter of immediate-early and early genes; subsequently, it delocalizes IFI16 from the nucleus into the cytoplasm, thereby stabilizing and protecting it from degradation. Overall, these data identify a novel activity of the pp65/IFI16 interactome involved in the regulation of UL54 gene expression and IFI16 stability during early and late phases of HCMV replication.</p>',
			'date' => '2016-07-06',
			'pmid' => 'http://jvi.asm.org/content/early/2016/06/30/JVI.00923-16.abstract',
			'doi' => '',
			'modified' => '2016-09-07 10:42:20',
			'created' => '2016-09-07 10:42:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '2985',
			'name' => 'miR-125b-1 is repressed by histone modifications in breast cancer cell lines',
			'authors' => 'Cisneros-Soberanis F et al.',
			'description' => '<div class="">
<h4>PURPOSE:</h4>
<p><abstracttext label="PURPOSE" nlmcategory="OBJECTIVE">Downregulation of miR-125b-1 is associated with poor prognosis in breast cancer patients. In this work we investigated the effect of histone modifications on the regulation of this gene promoter.</abstracttext></p>
<h4>METHODS AND RESULTS:</h4>
<p><abstracttext label="METHODS AND RESULTS" nlmcategory="RESULTS">We evaluated the enrichment of two histone modifications involved in gene repression, H3K9me3 and H3K27me3, on the miR-125b-1 promoter in two breast cancer cell lines, MCF7 (luminal A subtype) and MDA-MB-231 (triple-negative subtype), compared to the non-transformed breast cell line MCF10A. H3K27me3 and H3K9me3 were enriched in MCF7 and MDA-MB-231 cells, respectively. Next, we used an EZH2 inhibitor to examine the reactivation of miR-125b-1 in MCF7 cells and evaluated the transcriptional levels of pri-miR-125b-1 and mature miR-125b by qRT-PCR. pri-miRNA and mature miRNA transcripts were both increased after treatment of MCF7 cells with the EZH2 inhibitor, whereas no effect on miR-125b-1 expression levels was observed in MDA-MB-231 and MCF10A cells. We subsequently evaluated the effect of miR-125b-1 reactivation on the expression and protein levels of BAK1, a target of miR-125b. We observed 60 and 70&nbsp;% decreases in the expression and protein levels of BAK1, respectively, compared to cells that were not treated with the EZH2 inhibitor. We over-expressed KDM4B/JMJD2B to reactivate this miRNA, resulting in a three-fold increase in miR-125b expression compared with the same cell line without KDM4B/JMJD2B over-expression.</abstracttext></p>
<h4>CONCLUSION:</h4>
<p><abstracttext label="CONCLUSION" nlmcategory="CONCLUSIONS">The miR-125b-1 is repressed by different epigenetic mechanisms depending on the breast cancer subtype and that miR-125b-1 reactivation specifically eliminates the effect of repressive histone modifications on the expression of an pro-apoptotic target.</abstracttext></p>
</div>',
			'date' => '2016-07-02',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27386402',
			'doi' => ' 10.1186/s40064-016-2475-z',
			'modified' => '2016-07-26 09:50:18',
			'created' => '2016-07-26 09:50:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => array(
			'id' => '2913',
			'name' => 'Osterix and RUNX2 are Transcriptional Regulators of Sclerostin in Human Bone',
			'authors' => 'Flor M. Pérez-Campo, Ana Santurtún, Carmen García-Ibarbia, María A. Pascual, Carmen Valero, Carlos Garcés, Carolina Sañudo, María T. Zarrabeitia, José A. Riancho',
			'description' => '<p><span>Sclerostin, encoded by the </span><em class="EmphasisTypeItalic ">SOST</em><span> gene, works as an inhibitor of the Wnt pathway and therefore is an important regulator of bone homeostasis. Due to its potent action as an inhibitor of bone formation, blocking sclerostin activity is the purpose of recently developed anti-osteoporotic treatments. Two bone-specific transcription factors, RUNX2 and OSX, have been shown to interact and co-ordinately regulate the expression of bone-specific genes. Although it has been recently shown that sclerostin is targeted by OSX in mice, there is currently no information of whether this is also the case in human cells. We have identified SP-protein family and AML1 consensus binding sequences at the human </span><em class="EmphasisTypeItalic ">SOST</em><span> promoter and have shown that OSX, together with RUNX2, binds to a specific region close to the transcription start site. Furthermore, we show that OSX and RUNX2 activate </span><em class="EmphasisTypeItalic ">SOST</em><span> expression in a co-ordinated manner in vitro and that </span><em class="EmphasisTypeItalic ">SOST</em><span> expression levels show a significant positive correlation with </span><em class="EmphasisTypeItalic ">OSX/RUNX2</em><span> expression levels in human bone. We also confirmed previous results showing an association of several SOST/RUNX2 polymorphisms with bone mineral density.</span></p>',
			'date' => '2016-05-06',
			'pmid' => 'http://link.springer.com/article/10.1007/s00223-016-0144-4',
			'doi' => '10.1007/s00223-016-0144-4',
			'modified' => '2016-05-11 17:34:19',
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				[maximum depth reached]
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			'id' => '3036',
			'name' => 'DNMT1 and HDAC2 Cooperate to Facilitate Aberrant Promoter Methylation in Inorganic Phosphate-Induced Endothelial-Mesenchymal Transition',
			'authors' => 'Tan X et al.',
			'description' => '<p>While phosphorus in the form of inorganic or organic phosphate is critically involved in most cellular functions, high plasma levels of inorganic phosphate levels have emerged as independent risk factor for cardiac fibrosis, cardiovascular morbidity and decreased life-expectancy. While the link of high phosphate and cardiovascular disease is commonly explained by direct cellular effects of phospho-regulatory hormones, we here explored the possibility of inorganic phosphate directly eliciting biological responses in cells. We demonstrate that human coronary endothelial cells (HCAEC) undergo an endothelial-mesenchymal transition (EndMT) when exposed to high phosphate. We further demonstrate that such EndMT is initiated by recruitment of aberrantly phosphorylated DNMT1 to the RASAL1 CpG island promoter by HDAC2, causing aberrant promoter methylation and transcriptional suppression, ultimately leading to increased Ras-GTP activity and activation of common EndMT regulators Twist and Snail. Our studies provide a novel aspect for known adverse effects of high phosphate levels, as eukaryotic cells are commonly believed to have lost phosphate-sensing mechanisms of prokaryotes during evolution, rendering them insensitive to extracellular inorganic orthophosphate. In addition, our studies provide novel insights into the mechanisms underlying specific targeting of select genes in context of fibrogenesis.</p>',
			'date' => '2016-01-27',
			'pmid' => 'http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147816',
			'doi' => '',
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<div class="page" title="Page 4">
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<p><span>Diagenode provides kits with optimized reagents and simplified protocols for ChIP including the <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR kit</a>, <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE kit</a>,&nbsp; <a href="https://www.diagenode.com/en/categories/chromatin-ip-chip-seq-kits">iDeal ChIP-seq kits</a>, <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a>, <a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit </a>and <a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation">the ChIPmentation for Histones</a>. This protocol describes the use of the OneDay ChIP Kit.</span></p>
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	'name' => 'DNMT1 and HDAC2 Cooperate to Facilitate Aberrant Promoter Methylation in Inorganic Phosphate-Induced Endothelial-Mesenchymal Transition',
	'authors' => 'Tan X et al.',
	'description' => '<p>While phosphorus in the form of inorganic or organic phosphate is critically involved in most cellular functions, high plasma levels of inorganic phosphate levels have emerged as independent risk factor for cardiac fibrosis, cardiovascular morbidity and decreased life-expectancy. While the link of high phosphate and cardiovascular disease is commonly explained by direct cellular effects of phospho-regulatory hormones, we here explored the possibility of inorganic phosphate directly eliciting biological responses in cells. We demonstrate that human coronary endothelial cells (HCAEC) undergo an endothelial-mesenchymal transition (EndMT) when exposed to high phosphate. We further demonstrate that such EndMT is initiated by recruitment of aberrantly phosphorylated DNMT1 to the RASAL1 CpG island promoter by HDAC2, causing aberrant promoter methylation and transcriptional suppression, ultimately leading to increased Ras-GTP activity and activation of common EndMT regulators Twist and Snail. Our studies provide a novel aspect for known adverse effects of high phosphate levels, as eukaryotic cells are commonly believed to have lost phosphate-sensing mechanisms of prokaryotes during evolution, rendering them insensitive to extracellular inorganic orthophosphate. In addition, our studies provide novel insights into the mechanisms underlying specific targeting of select genes in context of fibrogenesis.</p>',
	'date' => '2016-01-27',
	'pmid' => 'http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147816',
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include - APP/View/Products/view.ctp, line 755
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 193
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 118

Notice (8): Undefined variable: campaign_id [APP/View/Products/view.ctp, line 755]
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<p><span>For ChIP-qPCR: <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR Kit</a> and <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE Kit</a></span></p>
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<p><strong>&nbsp;</strong></p>
<p class="text-right"><a class="tiny alert button" href="https://www.diagenode.com/en/categories/chip-grade-antibodies"> Check out our ChIP-grade antibodies</a></p>',
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<p><span>For ChIP-qPCR: <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR Kit</a> and <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE Kit</a></span></p>
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<p><strong>&nbsp;</strong></p>
<p class="text-right"><a class="tiny alert button" href="https://www.diagenode.com/en/categories/chip-grade-antibodies"> Check out our ChIP-grade antibodies</a></p>',
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<p><span>For ChIP-seq: <a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-x24-24-rxns">iDeal ChIP-seq Kit for Histones</a>, <a href="https://www.diagenode.com/en/p/manual-chipmentation-kit-for-histones-24-rxns">ChIPmentation Kit for Histones</a> and <a href="https://www.diagenode.com/en/p/ideal-chip-seq-kit-for-transcription-factors-x24-24-rxns">iDeal ChIP-seq Kit for Transcription Factors</a></span></p>
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<p><strong>&nbsp;</strong></p>
<p class="text-right"><a class="tiny alert button" href="https://www.diagenode.com/en/categories/chip-grade-antibodies"> Check out our ChIP-grade antibodies</a></p>',
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<p class="text-justify">Chromatin Immunoprecipitation (ChIP) coupled with quantitative PCR can be used to investigate protein-DNA interaction at known genomic binding sites. if sites are not known, qPCR primers can also be designed against potential regulatory regions such as promoters. ChIP-qPCR is advantageous in studies that focus on specific genes and potential regulatory regions across differing experimental conditions as the cost of performing real-time PCR is minimal. This technique is now used in a variety of life science disciplines including cellular differentiation, tumor suppressor gene silencing, and the effect of histone modifications on gene expression.</p>
<p class="text-justify"><strong>The ChIP-qPCR workflow</strong></p>
</div>
<div class="small-12 medium-12 large-12 columns text-center"><br /> <img src="https://www.diagenode.com/img/chip-qpcr-diagram.png" /></div>
<div class="small-12 medium-12 large-12 columns"><br />
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<li class="large-12 columns"><strong>Chromatin preparation: </strong>cell fixation (cross-linking) of chromatin-bound proteins such as histones or transcription factors to DNA followed by cell lysis.</li>
<li class="large-12 columns"><strong>Chromatin shearing: </strong>fragmentation of chromatin<strong> </strong>by sonication down to desired fragment size (100-500 bp)</li>
<li class="large-12 columns"><strong>Chromatin IP</strong>: protein-DNA complexe capture using<strong> <a href="https://www.diagenode.com/en/categories/chip-grade-antibodies">specific ChIP-grade antibodies</a></strong>&nbsp;against the histone or transcription factor of interest</li>
<li class="large-12 columns"><strong>DNA purification</strong>: chromatin reverse cross-linking and elution followed by purification<strong> </strong></li>
<li class="large-12 columns"><strong>qPCR and analysis</strong>: using previously designed primers to amplify IP'd material at specific loci</li>
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<div class="radius panel" style="background-color: #fff;">
<h3 class="text-center" style="color: #b21329;">Need guidance?</h3>
<p class="text-justify">Choose our full ChIP kits or simply choose what you need from antibodies, buffers, beads, chromatin shearing and purification reagents. With the ChIP Kit Customizer, you have complete flexibility on which components you want from our validated ChIP kits.</p>
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<div class="small-6 medium-6 large-6 columns"><a href="https://www.diagenode.com/pages/which-kit-to-choose"><img src="https://www.diagenode.com/img/banners/banner-decide.png" alt="" /></a></div>
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<p><span>Diagenode provides kits with optimized reagents and simplified protocols for ChIP including the <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR kit</a>, <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE kit</a>,&nbsp; <a href="https://www.diagenode.com/en/categories/chromatin-ip-chip-seq-kits">iDeal ChIP-seq kits</a>, <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a>, <a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit </a>and <a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation">the ChIPmentation for Histones</a>. This protocol describes the use of the OneDay ChIP Kit.</span></p>
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<p></p>
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			'name' => 'Transcription of CLDND1 in human brain endothelial cells is regulated bythe myeloid zinc finger 1.',
			'authors' => 'Shima, Akiho and Matsuoka, Hiroshi and Yamaoka, Alice and Michihara,Akihiro',
			'description' => '<p>Increased permeability of endothelial cells lining the blood vessels in the brain leads to vascular oedema and, potentially, to stroke. The tight junctions (TJs), primarily responsible for the regulation of vascular permeability, are multi-protein complexes comprising the claudin family of proteins and occludin. Several studies have reported that downregulation of the claudin domain containing 1 (CLDND1) gene enhances vascular permeability, which consequently increases the risk of stroke. However, the transcriptional regulation of CLDND1 has not been studied extensively. Therefore, this study aimed to identify the transcription factors (TFs) regulating CLDND1 expression. A luciferase reporter assay identified a silencer within the first intron of CLDND1, which was identified as a potential binding site of the myeloid zinc finger 1 (MZF1) through in silico and TFBIND software analyses, and confirmed through a reporter assay using the MZF1 expression vector and chromatin immunoprecipitation (ChIP) assays. Moreover, the transient overexpression of MZF1 significantly increased the mRNA and protein expression levels of CLDND1, conversely, which were suppressed through the siRNA-mediated MZF1 knockdown. Furthermore, the permeability of FITC-dextran was observed to be increased on MZF1 knockdown as compared to that of the siGFP control. Our data revealed the underlying mechanism of the transcriptional regulation of CLDND1 by the MZF1. The findings suggest a potential role of MZF1 in TJ formation, which could be studied further and applied to prevent cerebral haemorrhage.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33037622',
			'doi' => '10.1111/1440-1681.13416',
			'modified' => '2021-02-19 17:48:44',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'id' => '3748',
			'name' => 'Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis.',
			'authors' => 'Vara C, Paytuví-Gallart A, Cuartero Y, Le Dily F, Garcia F, Salvà-Castro J, Gómez-H L, Julià E, Moutinho C, Aiese Cigliano R, Sanseverino W, Fornas O, Pendás AM, Heyn H, Waters PD, Marti-Renom MA, Ruiz-Herrera A',
			'description' => '<p>Mammalian gametogenesis involves dramatic and tightly regulated chromatin remodeling, whose regulatory pathways remain largely unexplored. Here, we generate a comprehensive high-resolution structural and functional atlas of mouse spermatogenesis by combining in situ chromosome conformation capture sequencing (Hi-C), RNA sequencing (RNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) of CCCTC-binding factor (CTCF) and meiotic cohesins, coupled with confocal and super-resolution microscopy. Spermatogonia presents well-defined compartment patterns and topological domains. However, chromosome occupancy and compartmentalization are highly re-arranged during prophase&nbsp;I, with cohesins bound to active promoters in DNA loops out of the chromosomal axes. Compartment patterns re-emerge in round spermatids, where cohesin occupancy correlates with transcriptional activity of key developmental genes. The compact sperm genome contains compartments with actively transcribed genes but no fine-scale topological domains, concomitant with the presence of protamines. Overall, we demonstrate how genome-wide cohesin occupancy and transcriptional activity is associated with three-dimensional (3D) remodeling during spermatogenesis, ultimately reprogramming the genome for the next generation.</p>',
			'date' => '2019-07-09',
			'pmid' => 'http://www.pubmed.gov/31291573',
			'doi' => '10.1016/j.celrep.2019.06.037',
			'modified' => '2019-08-06 16:12:27',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '3739',
			'name' => 'Resveratrol up-regulates ATP2A3 gene expression in breast cancer cell lines through epigenetic mechanisms.',
			'authors' => 'Izquierdo-Torres E, Hernández-Oliveras A, Meneses-Morales I, Rodríguez G, Fuentes-García G, Zarain-Herzberg Á',
			'description' => '<p>Resveratrol (RSV) is a phytoestrogen which has been related to chemoprevention of several types of cancer. In this work, we show up to a 6-fold increased expression of ATP2A3 gene induced by RSV that triggers apoptosis and changes of intracellular Ca management in MCF-7 and MDA-MB-231 breast cancer cell lines. We explored epigenetic mechanisms for that RSV-induced ATP2A3 up-regulation. The results indicate that RSV-induced ATP2A3 up-regulation correlates with about 50% of reduced HDAC activity and reduced nuclear HDAC2 expression and occupancy on ATP2A3 promoter, increasing the global acetylation of histone H3 and the enrichment of histone mark H3K27Ac on the proximal promoter of the ATP2A3 gene in MDA-MB-231 cells. We also quantified HAT activity, finding that it can be boosted with RSV treatment; however, pharmacological inhibition of p300, one of the main HATs, did not have significant effects in RSV-mediated ATP2A3 gene expression. Additionally, DNMT activity was also reduced in cells treated with RSV, as well as the expression of Methyl-DNA binding proteins MeCP2 and MBD2. However, analysis of the methylation pattern of ATP2A3 gene promoter showed un-methylated promoter in both cell lines. Taken together, the results of this work help to explain, at the molecular level, how ATP2A3 gene is regulated in breast cancer cells, and the benefits of RSV intake observed in epidemiological data, studies with animals, and in vitro models.</p>',
			'date' => '2019-06-04',
			'pmid' => 'http://www.pubmed.gov/31173924',
			'doi' => '10.1016/j.biocel.2019.05.020',
			'modified' => '2019-08-06 16:56:19',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'id' => '3660',
			'name' => 'Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia.',
			'authors' => 'Wernig-Zorc S, Yadav MP, Kopparapu PK, Bemark M, Kristjansdottir HL, Andersson PO, Kanduri C, Kanduri M',
			'description' => '<p>BACKGROUND: Chronic lymphocytic leukemia (CLL) has been a good model system to understand the functional role of 5-methylcytosine (5-mC) in cancer progression. More recently, an oxidized form of 5-mC, 5-hydroxymethylcytosine (5-hmC) has gained lot of attention as a regulatory epigenetic modification with prognostic and diagnostic implications for several cancers. However, there is no global study exploring the role of 5-hydroxymethylcytosine (5-hmC) levels in CLL. Herein, using mass spectrometry and hMeDIP-sequencing, we analysed the dynamics of 5-hmC during B cell maturation and CLL pathogenesis. RESULTS: We show that na&iuml;ve B-cells had higher levels of 5-hmC and 5-mC compared to non-class switched and class-switched memory B-cells. We found a significant decrease in global 5-mC levels in CLL patients (n&thinsp;=&thinsp;15) compared to na&iuml;ve and memory B cells, with no changes detected between the CLL prognostic groups. On the other hand, global 5-hmC levels of CLL patients were similar to memory B cells and reduced compared to na&iuml;ve B cells. Interestingly, 5-hmC levels were increased at regulatory regions such as gene-body, CpG island shores and shelves and 5-hmC distribution over the gene-body positively correlated with degree of transcriptional activity. Importantly, CLL samples showed aberrant 5-hmC and 5-mC pattern over gene-body compared to well-defined patterns in normal B-cells. Integrated analysis of 5-hmC and RNA-sequencing from CLL datasets identified three novel oncogenic drivers that could have potential roles in CLL development and progression. CONCLUSIONS: Thus, our study suggests that the global loss of 5-hmC, accompanied by its significant increase at the gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Our combined analysis of 5-mC and 5-hmC sequencing provided insights into the potential role of 5-hmC in modulating gene expression changes during CLL pathogenesis.</p>',
			'date' => '2019-01-07',
			'pmid' => 'http://www.pubmed.gov/30616658',
			'doi' => '10.1186/s13072‑018‑0252‑7',
			'modified' => '2019-07-01 11:46:16',
			'created' => '2019-06-21 14:55:31',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 4 => array(
			'id' => '3505',
			'name' => 'Genomic Location of PRMT6-Dependent H3R2 Methylation Is Linked to the Transcriptional Outcome of Associated Genes.',
			'authors' => 'Bouchard C, Sahu P, Meixner M, Nötzold RR, Rust MB, Kremmer E, Feederle R, Hart-Smith G, Finkernagel F, Bartkuhn M, Savai Pullamsetti S, Nist A, Stiewe T, Philipsen S, Bauer UM',
			'description' => '<p>Protein arginine methyltransferase 6 (PRMT6) catalyzes asymmetric dimethylation of histone H3 at arginine 2 (H3R2me2a). This mark has been reported to associate with silent genes. Here, we use a cell model&nbsp;of neural differentiation, which upon PRMT6 knockout exhibits proliferation and differentiation defects. Strikingly, we detect PRMT6-dependent H3R2me2a at active genes, both at promoter and enhancer sites. Loss of H3R2me2a from promoter sites leads to enhanced KMT2A binding and H3K4me3 deposition together with increased target gene transcription, supporting a repressive nature of H3R2me2a. At enhancers, H3R2me2a peaks co-localize with the active enhancer marks H3K4me1 and H3K27ac. Here, loss of H3R2me2a results in reduced KMT2D binding and H3K4me1/H3K27ac deposition together with decreased transcription of associated genes, indicating that H3R2me2a also exerts activation functions. Our work suggests that PRMT6 via H3R2me2a interferes with the deposition of adjacent histone marks and modulates the activity of important differentiation-associated genes by opposing transcriptional effects.</p>',
			'date' => '2018-09-18',
			'pmid' => 'http://www.pubmed.gov/30232013',
			'doi' => '10.1016/j.celrep.2018.08.052',
			'modified' => '2019-02-28 10:05:16',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '3443',
			'name' => 'High-fidelity CRISPR/Cas9- based gene-specific hydroxymethylation rescues gene expression and attenuates renal fibrosis.',
			'authors' => 'Xingbo Xu, Xiaoying Tan, Björn Tampe, Tim Wilhelmi, Melanie S. Hulshoff, Shoji Saito, Tobias Moser, Raghu Kalluri, Gerd Hasenfuss, Elisabeth M. Zeisberg & Michael Zeisberg ',
			'description' => '<p>While suppression of specific genes through aberrant promoter methylation contributes to different diseases including organ fibrosis, gene-specific reactivation technology is not yet available for therapy. TET enzymes catalyze hydroxymethylation of methylated DNA, reactivating gene expression. We here report generation of a high-fidelity CRISPR/Cas9-based gene-specific dioxygenase by fusing an endonuclease deactivated high-fidelity Cas9 (dHFCas9) to TET3 catalytic domain (TET3CD), targeted to specific genes by guiding RNAs (sgRNA). We demonstrate use of this technology in four different anti-fibrotic genes in different cell types in vitro, among them RASAL1 and Klotho, both hypermethylated in kidney fibrosis. Furthermore, in vivo lentiviral delivery of the Rasal1-targeted fusion protein to interstitial cells and of the Klotho-targeted fusion protein to tubular epithelial cells each results in specific gene reactivation and attenuation of fibrosis, providing gene-specific demethylating technology in a disease model.</p>',
			'date' => '2018-08-29',
			'pmid' => 'http://www.pubmed.gov/30158531',
			'doi' => '10.1038/s41467-018-05766-5',
			'modified' => '2019-02-28 10:11:31',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '3522',
			'name' => 'Human papillomavirus type 16 antagonizes IRF6 regulation of IL-1β.',
			'authors' => 'Ainouze M, Rochefort P, Parroche P, Roblot G, Tout I, Briat F, Zannetti C, Marotel M, Goutagny N, Auron P, Traverse-Glehen A, Lunel-Potencier A, Golfier F, Masson M, Robitaille A, Tommasino M, Carreira C, Walzer T, Henry T, Zanier K, Trave G, Hasan UA',
			'description' => '<p>Human papillomavirus type 16 (HPV16) and other oncoviruses have been shown to block innate immune responses and to persist in the host. However, to avoid viral persistence, the immune response attempts to clear the infection. IL-1&beta; is a powerful cytokine produced when viral motifs are sensed by innate receptors that are members of the inflammasome family. Whether oncoviruses such as HPV16 can activate the inflammasome pathway remains unknown. Here, we show that infection of human keratinocytes with HPV16 induced the secretion of IL-1&beta;. Yet, upon expression of the viral early genes, IL-1&beta; transcription was blocked. We went on to show that expression of the viral oncoprotein E6 in human keratinocytes inhibited IRF6 transcription which we revealed regulated IL-1&beta; promoter activity. Preventing E6 expression using siRNA, or using E6 mutants that prevented degradation of p53, showed that p53 regulated IRF6 transcription. HPV16 abrogation of p53 binding to the IRF6 promoter was shown by ChIP in tissues from patients with cervical cancer. Thus E6 inhibition of IRF6 is an escape strategy used by HPV16 to block the production IL-1&beta;. Our findings reveal a struggle between oncoviral persistence and host immunity; which is centered on IL-1&beta; regulation.</p>',
			'date' => '2018-08-08',
			'pmid' => 'http://www.pubmed.gov/30089163',
			'doi' => '10.1371/journal.ppat.1007158',
			'modified' => '2019-02-28 10:14:30',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '3583',
			'name' => 'Human papillomavirus type 16 antagonizes IRF6 regulation of IL-1β.',
			'authors' => 'Ainouze M, Rochefort P, Parroche P, Roblot G, Tout I, Briat F, Zannetti C, Marotel M, Goutagny N, Auron P, Traverse-Glehen A, Lunel-Potencier A, Golfier F, Masson M, Robitaille A, Tommasino M, Carreira C, Walzer T, Henry T, Zanier K, Trave G, Hasan UA',
			'description' => '<p>Human papillomavirus type 16 (HPV16) and other oncoviruses have been shown to block innate immune responses and to persist in the host. However, to avoid viral persistence, the immune response attempts to clear the infection. IL-1&beta; is a powerful cytokine produced when viral motifs are sensed by innate receptors that are members of the inflammasome family. Whether oncoviruses such as HPV16 can activate the inflammasome pathway remains unknown. Here, we show that infection of human keratinocytes with HPV16 induced the secretion of IL-1&beta;. Yet, upon expression of the viral early genes, IL-1&beta; transcription was blocked. We went on to show that expression of the viral oncoprotein E6 in human keratinocytes inhibited IRF6 transcription which we revealed regulated IL-1&beta; promoter activity. Preventing E6 expression using siRNA, or using E6 mutants that prevented degradation of p53, showed that p53 regulated IRF6 transcription. HPV16 abrogation of p53 binding to the IRF6 promoter was shown by ChIP in tissues from patients with cervical cancer. Thus E6 inhibition of IRF6 is an escape strategy used by HPV16 to block the production IL-1&beta;. Our findings reveal a struggle between oncoviral persistence and host immunity; which is centered on IL-1&beta; regulation.</p>',
			'date' => '2018-08-08',
			'pmid' => 'http://www.pubmed.gov/30089163',
			'doi' => '10.1371/journal.ppat.1007158',
			'modified' => '2019-04-17 15:50:02',
			'created' => '2019-04-16 12:25:30',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '3480',
			'name' => 'CTCF-KDM4A complex correlates with histone modifications that negatively regulate  gene expression in cancer cell lines.',
			'authors' => 'Guerra-Calderas L, González-Barrios R, Patiño CC, Alcaraz N, Salgado-Albarrán M, de León DC, Hernández CC, Sánchez-Pérez Y, Maldonado-Martínez HA, De la Rosa-Velazquez IA, Vargas-Romero F, Herrera LA, García-Carrancá A, Soto-Reyes E',
			'description' => '<p>Histone demethylase KDM4A is involved in H3K9me3 and H3K36me3 demethylation, which are epigenetic modifications associated with gene silencing and RNA Polymerase II elongation, respectively. is abnormally expressed in cancer, affecting the expression of multiple targets, such as the gene. This enzyme localizes at the first intron of , and the dissociation of KDM4A increases gene expression. assays showed that KDM4A-mediated demethylation is enhanced in the presence of CTCF, suggesting that CTCF could increase its enzymatic activity however the specific mechanism by which and might be involved in the gene repression is poorly understood. Here, we show that CTCF and KDM4A form a protein complex, which is recruited into the first intron of . This is related to a decrease in H3K36me3/2 histone marks and is associated with its transcriptional downregulation. Depletion of or KDM4A by siRNA, triggered the reactivation of expression, suggesting that both proteins are involved in the negative regulation of this gene. Furthermore, the knockout of restored the expression and H3K36me3 and H3K36me2 histone marks. Such mechanism acts independently of promoter DNA methylation. Our findings support a novel mechanism of epigenetic repression at the gene body that does not involve promoter silencing.</p>',
			'date' => '2018-03-30',
			'pmid' => 'http://www.pubmed.gov/29682202',
			'doi' => '10.18632/oncotarget.24798',
			'modified' => '2019-02-14 17:12:34',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '3390',
			'name' => 'The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes.',
			'authors' => 'Ding D, Bergmaier P, Sachs P, Klangwart M, Rückert T, Bartels N, Demmers J, Dekker M, Poot RA, Mermoud JE',
			'description' => '<p>Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has been shown to affect stem cell state, but the mechanistic explanation for this effect is unknown. Here, we set out to gain further insights into the function of SMARCAD1 in mouse ESCs. We identified KRAB-associated protein 1 (KAP1) as the stoichiometric binding partner of SMARCAD1 in ESCs. We found that this interaction occurs on chromatin and that SMARCAD1 binds to different classes of KAP1 target genes, including zinc finger protein (ZFP) and imprinted genes. We also found that the RING B-box coiled-coil (RBCC) domain in KAP1 and the proximal coupling of ubiquitin conjugation to ER degradation (CUE) domain in SMARCAD1 mediate their direct interaction. Of note, retention of SMARCAD1 in the nucleus depended on KAP1 in both mouse ESCs and human somatic cells. Mutations in the CUE1 domain of SMARCAD1 perturbed the binding to KAP1 and Accordingly, an intact CUE1 domain was required for tethering this remodeler to the nucleus. Moreover, mutation of the CUE1 domain compromised SMARCAD1 binding to KAP1 target genes. Taken together, our results reveal a mechanism that localizes SMARCAD1 to genomic sites through the interaction of SMARCAD1's CUE1 motif with KAP1.</p>',
			'date' => '2018-02-23',
			'pmid' => 'http://www.pubmed.gov/29284678',
			'doi' => '10.1074/jbc.RA117.000959',
			'modified' => '2018-11-09 12:27:47',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '3359',
			'name' => 'Miz1 Controls Schwann Cell Proliferation via H3K36me2 Demethylase Kdm8 to Prevent Peripheral Nerve Demyelination',
			'authors' => 'Fuhrmann D. et al.',
			'description' => '<p>Schwann cell differentiation and myelination depends on chromatin remodeling, histone acetylation, and methylation, which all affect Schwann cell proliferation. We previously reported that the deletion of the POZ (POxvirus and Zinc finger) domain of the transcription factor Miz1 (Myc-interacting zinc finger protein; encoded by <i>Zbtb17</i>) in mouse Schwann cells (<i>Miz1</i>&Delta;<i>POZ</i>) causes a neuropathy at 90 d after birth [postnatal day (P) 90], with a subsequent spontaneous regeneration. Here we show that RNA sequencing from <i>Miz1</i>&Delta;<i>POZ</i> and control animals at P30 revealed a set of upregulated genes with a strong correlation to cell-cycle regulation. Consistently, a subset of Schwann cells did not exit the cell cycle as observed in control animals and the growth fraction increased over time. From the RNAseq gene list, two direct Miz1 target genes were identified, one of which encodes the histone H3K36<sup>me2</sup> demethylase Kdm8. We show that the expression of <i>Kdm8</i> is repressed by Miz1 and that its release in <i>Miz1</i>&Delta;<i>POZ</i> cells induces a decrease of H3K36<sup>me2</sup>, especially in deregulated cell-cycle-related genes. The linkage between elevated <i>Kdm8</i> expression, hypomethylation of H3K36 at cell-cycle-relevant genes, and the subsequent re-entering of adult Schwann cells into the cell cycle suggests that the release of <i>Kdm8</i> repression in the absence of a functional Miz1 is a central issue in the development of the <i>Miz1</i>&Delta;<i>POZ</i> phenotype.<b>SIGNIFICANCE STATEMENT</b> The deletion of the Miz1 (Myc-interacting zinc finger protein 1) POZ (POxvirus and Zinc finger) domain in Schwann cells causes a neuropathy. Here we report sustained Schwann cell proliferation caused by an increased expression of the direct Miz1 target gene <i>Kdm8</i>, encoding a H3K36me2 demethylase. Hence, the demethylation of H3K36 is linked to the pathogenesis of a neuropathy.</p>',
			'date' => '2018-01-24',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29217679',
			'doi' => '',
			'modified' => '2018-04-06 09:51:37',
			'created' => '2018-04-06 09:51:37',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '3318',
			'name' => 'The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes ',
			'authors' => 'Dong Ding et. al.',
			'description' => '<p>Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has been shown to affect stem cell state, but the mechanistic explanation for this effect is unknown. Here, we set out to gain further insights into the function of SMARCAD1 in mouse ESCs. We identified KRAB-associated protein 1 (KAP1) as the stoichiometric binding partner of SMARCAD1 in ESCs. We found that this interaction occurs on chromatin and that SMARCAD1 binds to different classes of KAP1 target genes, including zinc finger protein (ZFP) and imprinted genes. We also found that the RING B-box coiled-coil (RBCC) domain in KAP1 and the proximal coupling of ubiquitin conjugation to ER degradation (CUE) domain in SMARCAD1 mediate their direct interaction. Of note, retention of SMARCAD1 in the nucleus depended on KAP1 in both mouse ESCs and human somatic cells. Mutations in the CUE1 domain of SMARCAD1 perturbed the binding to KAP1 <em>in vitro</em> and <em>in vivo</em>. Accordingly, an intact CUE1 domain was required for tethering this remodeler to the nucleus. Moreover, mutation of the CUE1 domain compromised SMARCAD1 binding to KAP1 target genes. Taken together, our results reveal a mechanism that localizes SMARCAD1 to genomic sites through the interaction of SMARCAD1&rsquo;s CUE1 motif with KAP1.</p>',
			'date' => '2017-12-28',
			'pmid' => 'http://www.jbc.org/content/early/2017/12/28/jbc.RA117.000959',
			'doi' => 'doi: 10.1074/jbc.RA117.000959 ',
			'modified' => '2018-01-14 07:43:01',
			'created' => '2018-01-14 07:43:01',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '3304',
			'name' => 'Individual effects of the copia and gypsy enhancer and insulator on chromatin marks, eRNA synthesis, and binding of insulator proteins in transfected genetic constructs.',
			'authors' => 'Fedoseeva D.M. et al.',
			'description' => '<p>Enhancers and insulators are involved in the regulation of gene expression, but the basic underlying mechanisms of action of these elements are unknown. We analyzed the individual effects of the enhancer and the insulator from Drosophila mobile elements copia [enh(copia)] and gypsy using transfected genetic constructs in S2 cells. This system excludes the influence of genomic cis regulatory elements. The enhancer-induced synthesis of 350-1050-nt-long enhancer RNAs (eRNAs) and H3K4me3 and H3K18ac marks, mainly in the region located about 300bp downstream of the enhancer. Insertion of the insulator between the enhancer and the promoter reduced these effects. We also observed the binding of dCTCF to the enhancer and to gypsy insulator. Our data indicate that a single gypsy insulator interacts with both the enhancer and the promoter, while two copies of the gypsy insulator preferentially interact with each other. Our results suggest the formation of chromatin loops that are shaped by the enhancer and the insulator.</p>',
			'date' => '2017-10-16',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29045822',
			'doi' => '',
			'modified' => '2018-01-03 10:13:37',
			'created' => '2018-01-03 10:13:37',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '3277',
			'name' => 'UV Radiation Activates Toll-Like Receptor 9 Expression in Primary Human Keratinocytes, an Event Inhibited by Human Papillomavirus 38 E6 and E7 Oncoproteins',
			'authors' => 'Pacini L. et al.',
			'description' => '<p>Several lines of evidence indicate that cutaneous human papillomavirus (HPV) types belonging to the beta genus of the HPV phylogenetic tree synergize with UV radiation in the development of skin cancer. Accordingly, the E6 and E7 oncoproteins from some beta HPV types are able to deregulate pathways related to immune response and cellular transformation. Toll-like receptor 9 (TLR9), in addition to playing a role in innate immunity, has been shown to be involved in the cellular stress response. Using primary human keratinocytes as experimental models, we have shown that UV irradiation (and other cellular stresses) activates TLR9 expression. This event is closely linked to p53 activation. Silencing the expression of p53 or deleting its encoding gene affected the activation of TLR9 expression after UV irradiation. Using various strategies, we have also shown that the transcription factors p53 and c-Jun are recruited onto a specific region of the TLR9 promoter after UV irradiation. Importantly, the E6 and E7 oncoproteins from beta HPV38, by inducing the accumulation of the p53 antagonist &Delta;Np73&alpha;, prevent the UV-mediated recruitment of these transcription factors onto the TLR9 promoter, with subsequent impairment of TLR9 gene expression. This study provides new insight into the mechanism that mediates TLR9 upregulation in response to cellular stresses. In addition, we show that HPV38 E6 and E7 are able to interfere with this mechanism, providing another explanation for the possible cooperation of beta HPV types with UV radiation in skin carcinogenesis.<b>IMPORTANCE</b> Beta HPV types have been suggested to act as cofactors in UV-induced skin carcinogenesis by altering several cellular mechanisms activated by UV radiation. We show that the expression of TLR9, a sensor of damage-associated molecular patterns produced during cellular stress, is activated by UV radiation in primary human keratinocytes (PHKs). Two transcription factors known to be activated by UV radiation, p53 and c-Jun, play key roles in UV-activated TLR9 expression. The E6 and E7 oncoproteins from beta HPV38 strongly inhibit UV-activated TLR9 expression by preventing the recruitment of p53 and c-Jun to the TLR9 promoter. Our findings provide additional support for the role that beta HPV types play in skin carcinogenesis by preventing activation of specific pathways upon exposure of PHKs to UV radiation.</p>',
			'date' => '2017-09-12',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28724760',
			'doi' => '',
			'modified' => '2017-10-16 10:19:04',
			'created' => '2017-10-16 10:19:04',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '3249',
			'name' => 'The cardiac calsequestrin gene transcription is modulated at the promoter by NFAT and MEF-2 transcription factors',
			'authors' => 'Rafael Estrada-Avilés, Gabriela Rodríguez, Angel Zarain-Herzberg',
			'description' => '<p>Calsequestrin-2 (CASQ2) is the main Ca<sup>2+</sup>-binding protein inside the sarcoplasmic reticulum of cardiomyocytes. Previously, we demonstrated that MEF-2 and SRF binding sites within the human <em>CASQ2</em> gene (<em>hCASQ2</em>) promoter region are functional in neonatal cardiomyocytes. In this work, we investigated if the calcineurin/NFAT pathway regulates <em>hCASQ2</em> expression in neonatal cardiomyocytes. The inhibition of NFAT dephosphorylation with CsA or INCA-6, reduced both the luciferase activity of <em>hCASQ2</em> promoter constructs (-3102/+176 bp and -288/+176 bp) and the CASQ2 mRNA levels in neonatal rat cardiomyocytes. Additionally, NFATc1 and NFATc3 over-expressing neonatal cardiomyocytes showed a 2-3-fold increase in luciferase activity of both <em>hCASQ2</em> promoter constructs, which was prevented by CsA treatment. Site-directed mutagenesis of the -133 bp MEF-2 binding site prevented trans-activation of <em>hCASQ2</em> promoter constructs induced by NFAT overexpression. Chromatin Immunoprecipitation (ChIP) assays revealed NFAT and MEF-2 enrichment within the -288 bp to +76 bp of the <em>hCASQ2</em> gene promoter. Besides, a direct interaction between NFAT and MEF-2 proteins was demonstrated by protein co-immunoprecipitation experiments. Taken together, these data demonstrate that NFAT interacts with MEF-2 bound to the -133 bp binding site at the <em>hCASQ2</em> gene promoter. In conclusion, in this work, we demonstrate that the Ca<sup>2+</sup>-calcineurin/NFAT pathway modulates the transcription of the <em>hCASQ2</em> gene in neonatal cardiomyocytes.</p>',
			'date' => '2017-09-08',
			'pmid' => 'http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0184724',
			'doi' => 'https://doi.org/10.1371/journal.pone.0184724 ',
			'modified' => '2017-09-26 07:16:08',
			'created' => '2017-09-26 07:16:08',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '3300',
			'name' => 'The cardiac calsequestrin gene transcription is modulated at the promoter by NFAT and MEF-2 transcription factors.',
			'authors' => 'Estrada-Avilés R. et al.',
			'description' => '<p>Calsequestrin-2 (CASQ2) is the main Ca2+-binding protein inside the sarcoplasmic reticulum of cardiomyocytes. Previously, we demonstrated that MEF-2 and SRF binding sites within the human CASQ2 gene (hCASQ2) promoter region are functional in neonatal cardiomyocytes. In this work, we investigated if the calcineurin/NFAT pathway regulates hCASQ2 expression in neonatal cardiomyocytes. The inhibition of NFAT dephosphorylation with CsA or INCA-6, reduced both the luciferase activity of hCASQ2 promoter constructs (-3102/+176 bp and -288/+176 bp) and the CASQ2 mRNA levels in neonatal rat cardiomyocytes. Additionally, NFATc1 and NFATc3 over-expressing neonatal cardiomyocytes showed a 2-3-fold increase in luciferase activity of both hCASQ2 promoter constructs, which was prevented by CsA treatment. Site-directed mutagenesis of the -133 bp MEF-2 binding site prevented trans-activation of hCASQ2 promoter constructs induced by NFAT overexpression. Chromatin Immunoprecipitation (ChIP) assays revealed NFAT and MEF-2 enrichment within the -288 bp to +76 bp of the hCASQ2 gene promoter. Besides, a direct interaction between NFAT and MEF-2 proteins was demonstrated by protein co-immunoprecipitation experiments. Taken together, these data demonstrate that NFAT interacts with MEF-2 bound to the -133 bp binding site at the hCASQ2 gene promoter. In conclusion, in this work, we demonstrate that the Ca2+-calcineurin/NFAT pathway modulates the transcription of the hCASQ2 gene in neonatal cardiomyocytes.</p>',
			'date' => '2017-09-08',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28886186',
			'doi' => '',
			'modified' => '2017-12-05 10:13:23',
			'created' => '2017-12-05 10:13:23',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '3264',
			'name' => 'Viral driven epigenetic events alter the expression of cancer-related genes in Epstein-Barr-virus naturally infected Burkitt lymphoma cell lines',
			'authors' => 'Hernandez-Vargas H. et al.',
			'description' => '<p>Epstein-Barr virus (EBV) was identified as the first human virus to be associated with a human malignancy, Burkitt&rsquo;s lymphoma (BL), a pediatric cancer endemic in sub-Saharan Africa. The exact mechanism of how EBV contributes to the process of lymphomagenesis is not fully understood. Recent studies have highlighted a genetic difference between endemic (EBV+) and sporadic (EBV&minus;) BL, with the endemic variant showing a lower somatic mutation load, which suggests the involvement of an alternative virally-driven process of transformation in the pathogenesis of endemic BL. We tested the hypothesis that a global change in DNA methylation may be induced by infection with EBV, possibly thereby accounting for the lower mutation load observed in endemic BL. Our comparative analysis of the methylation profiles of a panel of BL derived cell lines, naturally infected or not with EBV, revealed that the presence of the virus is associated with a specific pattern of DNA methylation resulting in altered expression of cellular genes with a known or potential role in lymphomagenesis. These included ID3, a gene often found to be mutated in sporadic BL. In summary this study provides evidence that EBV may contribute to the pathogenesis of BL through an epigenetic mechanism.</p>',
			'date' => '2017-07-19',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517637/',
			'doi' => '',
			'modified' => '2017-10-09 16:04:14',
			'created' => '2017-10-09 16:04:14',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '3255',
			'name' => 'SOX2 as a New Regulator of HPV16 Transcription',
			'authors' => 'Martínez-Ramírez I. et al.',
			'description' => '<p>Persistent infections with high-risk human papillomavirus (HPV) constitute the main risk factor for cervical cancer development. HPV16 is the most frequent type associated to squamous cell carcinomas (SCC), followed by HPV18. The long control region (LCR) in the HPV genome contains the replication origin and sequences recognized by cellular transcription factors (TFs) controlling viral transcription. Altered expression of <i>E6</i> and <i>E7</i> viral oncogenes, modulated by the LCR, causes modifications in cellular pathways such as proliferation, leading to malignant transformation. The aim of this study was to identify specific TFs that could contribute to the modulation of high-risk HPV transcriptional activity, related to the cellular histological origin. We identified sex determining region Y (SRY)-box 2 (SOX2) response elements present in HPV16-LCR. SOX2 binding to the LCR was demonstrated by in vivo and in vitro assays. The overexpression of this TF repressed HPV16-LCR transcriptional activity, as shown through reporter plasmid assays and by the down-regulation of endogenous HPV oncogenes. Site-directed mutagenesis revealed that three putative SOX2 binding sites are involved in the repression of the LCR activity. We propose that SOX2 acts as a transcriptional repressor of HPV16-LCR, decreasing the expression of <i>E6</i> and <i>E7</i> oncogenes in a SCC context.</p>',
			'date' => '2017-07-05',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/28678184',
			'doi' => '',
			'modified' => '2017-10-02 15:11:26',
			'created' => '2017-10-02 15:11:26',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '3079',
			'name' => 'Biphasic regulation of chondrocytes by Rela through induction of anti-apoptotic and catabolic target genes',
			'authors' => 'Kobayashi H. et al.',
			'description' => '<p>In vitro studies have shown that Rela/p65, a key subunit mediating NF-&kappa;B signalling, is involved in chondrogenic differentiation, cell survival and catabolic enzyme production. Here, we analyse in vivo functions of Rela in embryonic limbs and adult articular cartilage, and find that Rela protects chondrocytes from apoptosis through induction of anti-apoptotic genes including Pik3r1. During skeletal development, homozygous knockout of Rela leads to impaired growth through enhanced chondrocyte apoptosis, whereas heterozygous knockout of Rela does not alter growth. In articular cartilage, homozygous knockout of Rela at 7 weeks leads to marked acceleration of osteoarthritis through enhanced chondrocyte apoptosis, whereas heterozygous knockout of Rela results in suppression of osteoarthritis development through inhibition of catabolic gene expression. Haploinsufficiency or a low dose of an IKK inhibitor suppresses catabolic gene expression, but does not alter anti-apoptotic gene expression. The biphasic regulation of chondrocytes by Rela contributes to understanding the pathophysiology of osteoarthritis.</p>',
			'date' => '2016-11-10',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27830706',
			'doi' => '',
			'modified' => '2016-12-12 16:46:36',
			'created' => '2016-12-12 16:46:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '3053',
			'name' => 'Esrrb directly binds to Gata6 promoter and regulates its expression with Dax1 and Ncoa3',
			'authors' => 'Uranishi K et al.',
			'description' => '<p>Estrogen-related receptor beta (Esrrb) is expressed in embryonic stem (ES) cells and is involved in self-renewal ability and pluripotency. Previously, we found that Dax1 is associated with Esrrb and represses its transcriptional activity. Further, the disruption of the Dax1-Esrrb interaction increases the expression of the extra-embryonic endoderm marker Gata6 in ES cells. Here, we investigated the influences of Esrrb and Dax1 on Gata6 expression. Esrrb overexpression in ES cells induced endogenous Gata6 mRNA and Gata6 promoter activity. In addition, the Gata6 promoter was found to contain the Esrrb recognition motifs ERRE1 and ERRE2, and the latter was the responsive element of Esrrb. Associations between ERRE2 and Esrrb were then confirmed by biotin DNA pulldown and chromatin immunoprecipitation assays. Subsequently, we showed that Esrrb activity at the Gata6 promoter was repressed by Dax1, and although Dax1 did not bind to ERRE2, it was associated with Esrrb, which directly binds to ERRE2. In addition, the transcriptional activity of Esrrb was enhanced by nuclear receptor co-activator 3 (Ncoa3), which has recently been shown to be a binding partner of Esrrb. Finally, we showed that Dax1 was associated with Ncoa3 and repressed its transcriptional activity. Taken together, the present study indicates that the Gata6 promoter is activated by Esrrb in association with Ncoa3, and Dax1 inhibited activities of Esrrb and Ncoa3, resulting maintenance of the undifferentiated status of ES cells.</p>',
			'date' => '2016-09-04',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27601327',
			'doi' => '',
			'modified' => '2016-10-24 14:26:35',
			'created' => '2016-10-24 14:26:35',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => array(
			'id' => '3048',
			'name' => 'Chromatin remodeling regulates catalase expression during cancer cells adaptation to chronic oxidative stress.',
			'authors' => 'Glorieux C. et al.',
			'description' => '<p>Regulation of ROS metabolism plays a major role in cellular adaptation to oxidative stress in cancer cells, but the molecular mechanism that regulates catalase, a key antioxidant enzyme responsible for conversion of hydrogen peroxide to water and oxygen, remains to be elucidated. Therefore, we investigated the transcriptional regulatory mechanism controlling catalase expression in three human mammary cell lines: the normal mammary epithelial 250MK primary cells, the breast adenocarcinoma MCF-7 cells and an experimental model of MCF-7 cells resistant against oxidative stress resulting from chronic exposure to H<sub>2</sub>O<sub>2</sub> (Resox), in which catalase was overexpressed. Here we identify a novel promoter region responsible for the regulation of catalase expression at -1518/-1226 locus and the key molecules that interact with this promoter and affect catalase transcription. We show that the AP-1 family member JunB and retinoic acid receptor alpha (RAR&alpha;) mediate catalase transcriptional activation and repression, respectively, by controlling chromatin remodeling through a histone deacetylases-dependent mechanism. This regulatory mechanism plays an important role in redox adaptation to chronic exposure to H<sub>2</sub>O<sub>2</sub> in breast cancer cells. Our study suggests that cancer adaptation to oxidative stress may be regulated by transcriptional factors through chromatin remodeling, and reveals a potential new mechanism to target cancer cells.</p>',
			'date' => '2016-08-31',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/27591797',
			'doi' => '',
			'modified' => '2016-10-10 11:15:35',
			'created' => '2016-10-10 11:15:35',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 21 => array(
			'id' => '2996',
			'name' => 'Induction of cell differentiation activates transcription of the Sarco/Endoplasmic Reticulum calcium-ATPase 3 gene (ATP2A3) in gastric and colon cancer cells',
			'authors' => 'Flores-Peredo L et al.',
			'description' => '<p>The Sarco/Endoplasmic Reticulum Ca<sup>2+</sup> -ATPases (SERCAs), pump Ca<sup>2+</sup> into the endoplasmic reticulum lumen modulating cytosolic Ca<sup>2+</sup> concentrations to regulate various cellular processes including cell growth. Previous studies have reported a downregulation of SERCA3 protein expression in gastric and colon cancer cell lines and showed that in vitro cell differentiation increases its expression. However, little is known about the transcriptional mechanisms and transcription factors that regulate SERCA3 expression in epithelial cancer cells. In this work, we demonstrate that SERCA3 mRNA is upregulated up to 45-fold in two epithelial cancer cell lines, KATO-III and Caco-2, induced to differentiate with histone deacetylase inhibitors (HDACi) and by cell confluence, respectively. To evaluate the transcriptional elements responding to the differentiation stimuli, we cloned the human ATP2A3 promoter, generated deletion constructs and transfected them into KATO-III cells. Basal and differentiation responsive DNA elements were located by functional analysis within the first -135&thinsp;bp of the promoter region. Using site-directed mutagenesis and DNA-protein binding assays we found that Sp1, Sp3, and Klf-4 transcription factors bind to ATP2A3 proximal promoter elements and regulate basal gene expression. We showed that these factors participated in the increase of ATP2A3 expression during cancer cell differentiation. This study provides evidence for the first time that Sp1, Sp3, and Klf-4 transcriptionally modulate the expression of SERCA3 during induction of epithelial cancer cell differentiation.</p>',
			'date' => '2016-07-19',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27433831',
			'doi' => '10.1002/mc.22529',
			'modified' => '2016-08-23 16:57:48',
			'created' => '2016-08-23 16:57:48',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '3027',
			'name' => 'Regulatory Interaction between the Cellular Restriction Factor IFI16 and Viral pp65 (pUL83) Modulates Viral Gene Expression and IFI16 Protein Stability',
			'authors' => 'Biolatti M et al.',
			'description' => '<p>A key player in the intrinsic resistance against human cytomegalovirus (HCMV) is the interferon-&gamma;-inducible protein 16 (IFI16), which behaves as a viral DNA sensor in the first hours post infection and as a repressor of viral gene transcription in the later stages. Previous studies on HCMV replication demonstrated that IFI16 binds to the viral protein kinase pUL97, undergoes phosphorylation and relocalizes to the cytoplasm of infected cells. In this study, we demonstrate that the tegument protein pp65 (pUL83) recruits IFI16 to the promoter of the UL54 gene and downregulates viral replication as shown by use of the HCMV mutant v65Stop, which lacks pp65 expression. Interestingly, at late time-points of HCMV infection, IFI16 is stabilized by its interaction with pp65, which stood in contrast to IFI16 degradation, observed in herpes simplex virus (HSV-1)-infected cells. Moreover, we found that its translocation to the cytoplasm, in addition to pUL97, strictly depends on pp65, as demonstrated with the HCMV mutant RV-VM1, which expresses a form of pp65 unable to translocate into the cytoplasm. Thus, these data reveal a dual role for pp65: during early infection, it modulates IFI16 activity at the promoter of immediate-early and early genes; subsequently, it delocalizes IFI16 from the nucleus into the cytoplasm, thereby stabilizing and protecting it from degradation. Overall, these data identify a novel activity of the pp65/IFI16 interactome involved in the regulation of UL54 gene expression and IFI16 stability during early and late phases of HCMV replication.</p>',
			'date' => '2016-07-06',
			'pmid' => 'http://jvi.asm.org/content/early/2016/06/30/JVI.00923-16.abstract',
			'doi' => '',
			'modified' => '2016-09-07 10:42:20',
			'created' => '2016-09-07 10:42:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '2985',
			'name' => 'miR-125b-1 is repressed by histone modifications in breast cancer cell lines',
			'authors' => 'Cisneros-Soberanis F et al.',
			'description' => '<div class="">
<h4>PURPOSE:</h4>
<p><abstracttext label="PURPOSE" nlmcategory="OBJECTIVE">Downregulation of miR-125b-1 is associated with poor prognosis in breast cancer patients. In this work we investigated the effect of histone modifications on the regulation of this gene promoter.</abstracttext></p>
<h4>METHODS AND RESULTS:</h4>
<p><abstracttext label="METHODS AND RESULTS" nlmcategory="RESULTS">We evaluated the enrichment of two histone modifications involved in gene repression, H3K9me3 and H3K27me3, on the miR-125b-1 promoter in two breast cancer cell lines, MCF7 (luminal A subtype) and MDA-MB-231 (triple-negative subtype), compared to the non-transformed breast cell line MCF10A. H3K27me3 and H3K9me3 were enriched in MCF7 and MDA-MB-231 cells, respectively. Next, we used an EZH2 inhibitor to examine the reactivation of miR-125b-1 in MCF7 cells and evaluated the transcriptional levels of pri-miR-125b-1 and mature miR-125b by qRT-PCR. pri-miRNA and mature miRNA transcripts were both increased after treatment of MCF7 cells with the EZH2 inhibitor, whereas no effect on miR-125b-1 expression levels was observed in MDA-MB-231 and MCF10A cells. We subsequently evaluated the effect of miR-125b-1 reactivation on the expression and protein levels of BAK1, a target of miR-125b. We observed 60 and 70&nbsp;% decreases in the expression and protein levels of BAK1, respectively, compared to cells that were not treated with the EZH2 inhibitor. We over-expressed KDM4B/JMJD2B to reactivate this miRNA, resulting in a three-fold increase in miR-125b expression compared with the same cell line without KDM4B/JMJD2B over-expression.</abstracttext></p>
<h4>CONCLUSION:</h4>
<p><abstracttext label="CONCLUSION" nlmcategory="CONCLUSIONS">The miR-125b-1 is repressed by different epigenetic mechanisms depending on the breast cancer subtype and that miR-125b-1 reactivation specifically eliminates the effect of repressive histone modifications on the expression of an pro-apoptotic target.</abstracttext></p>
</div>',
			'date' => '2016-07-02',
			'pmid' => 'http://www.ncbi.nlm.nih.gov/pubmed/27386402',
			'doi' => ' 10.1186/s40064-016-2475-z',
			'modified' => '2016-07-26 09:50:18',
			'created' => '2016-07-26 09:50:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => array(
			'id' => '2913',
			'name' => 'Osterix and RUNX2 are Transcriptional Regulators of Sclerostin in Human Bone',
			'authors' => 'Flor M. Pérez-Campo, Ana Santurtún, Carmen García-Ibarbia, María A. Pascual, Carmen Valero, Carlos Garcés, Carolina Sañudo, María T. Zarrabeitia, José A. Riancho',
			'description' => '<p><span>Sclerostin, encoded by the </span><em class="EmphasisTypeItalic ">SOST</em><span> gene, works as an inhibitor of the Wnt pathway and therefore is an important regulator of bone homeostasis. Due to its potent action as an inhibitor of bone formation, blocking sclerostin activity is the purpose of recently developed anti-osteoporotic treatments. Two bone-specific transcription factors, RUNX2 and OSX, have been shown to interact and co-ordinately regulate the expression of bone-specific genes. Although it has been recently shown that sclerostin is targeted by OSX in mice, there is currently no information of whether this is also the case in human cells. We have identified SP-protein family and AML1 consensus binding sequences at the human </span><em class="EmphasisTypeItalic ">SOST</em><span> promoter and have shown that OSX, together with RUNX2, binds to a specific region close to the transcription start site. Furthermore, we show that OSX and RUNX2 activate </span><em class="EmphasisTypeItalic ">SOST</em><span> expression in a co-ordinated manner in vitro and that </span><em class="EmphasisTypeItalic ">SOST</em><span> expression levels show a significant positive correlation with </span><em class="EmphasisTypeItalic ">OSX/RUNX2</em><span> expression levels in human bone. We also confirmed previous results showing an association of several SOST/RUNX2 polymorphisms with bone mineral density.</span></p>',
			'date' => '2016-05-06',
			'pmid' => 'http://link.springer.com/article/10.1007/s00223-016-0144-4',
			'doi' => '10.1007/s00223-016-0144-4',
			'modified' => '2016-05-11 17:34:19',
			'created' => '2016-05-11 17:34:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 25 => array(
			'id' => '3036',
			'name' => 'DNMT1 and HDAC2 Cooperate to Facilitate Aberrant Promoter Methylation in Inorganic Phosphate-Induced Endothelial-Mesenchymal Transition',
			'authors' => 'Tan X et al.',
			'description' => '<p>While phosphorus in the form of inorganic or organic phosphate is critically involved in most cellular functions, high plasma levels of inorganic phosphate levels have emerged as independent risk factor for cardiac fibrosis, cardiovascular morbidity and decreased life-expectancy. While the link of high phosphate and cardiovascular disease is commonly explained by direct cellular effects of phospho-regulatory hormones, we here explored the possibility of inorganic phosphate directly eliciting biological responses in cells. We demonstrate that human coronary endothelial cells (HCAEC) undergo an endothelial-mesenchymal transition (EndMT) when exposed to high phosphate. We further demonstrate that such EndMT is initiated by recruitment of aberrantly phosphorylated DNMT1 to the RASAL1 CpG island promoter by HDAC2, causing aberrant promoter methylation and transcriptional suppression, ultimately leading to increased Ras-GTP activity and activation of common EndMT regulators Twist and Snail. Our studies provide a novel aspect for known adverse effects of high phosphate levels, as eukaryotic cells are commonly believed to have lost phosphate-sensing mechanisms of prokaryotes during evolution, rendering them insensitive to extracellular inorganic orthophosphate. In addition, our studies provide novel insights into the mechanisms underlying specific targeting of select genes in context of fibrogenesis.</p>',
			'date' => '2016-01-27',
			'pmid' => 'http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147816',
			'doi' => '',
			'modified' => '2016-09-23 16:44:11',
			'created' => '2016-09-23 16:44:11',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		)
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	'Testimonial' => array(),
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			'countries' => 'GB',
			'modified' => '2020-06-30 18:30:26',
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			'language' => 'en',
			'url' => 'files/SDS/OneDay-ChIP-Kit/SDS-C01010080-OneDay_ChIP_kit-US-en-1_0.pdf',
			'countries' => 'US',
			'modified' => '2020-06-30 18:31:15',
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			'language' => 'nl',
			'url' => 'files/SDS/OneDay-ChIP-Kit/SDS-C01010080-OneDay_ChIP_kit-BE-nl-1_0.pdf',
			'countries' => 'BE',
			'modified' => '2020-06-30 18:28:54',
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<div class="page" title="Page 4">
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<p><span>Diagenode provides kits with optimized reagents and simplified protocols for ChIP including the <a href="https://www.diagenode.com/en/p/ideal-chip-qpcr-kit">iDeal ChIP-qPCR kit</a>, <a href="https://www.diagenode.com/en/p/ideal-chip-ffpe-kit">iDeal ChIP FFPE kit</a>,&nbsp; <a href="https://www.diagenode.com/en/categories/chromatin-ip-chip-seq-kits">iDeal ChIP-seq kits</a>, <a href="https://www.diagenode.com/en/p/true-microchip-kit-x16-16-rxns">True MicroChIP kit</a>, <a href="https://www.diagenode.com/en/p/universal-plant-chip-seq-kit-x24-24-rxns">Universal Plant ChIP-seq kit </a>and <a href="https://www.diagenode.com/en/categories/chromatin-ip-chipmentation">the ChIPmentation for Histones</a>. This protocol describes the use of the OneDay ChIP Kit.</span></p>
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	'description' => '<p>While phosphorus in the form of inorganic or organic phosphate is critically involved in most cellular functions, high plasma levels of inorganic phosphate levels have emerged as independent risk factor for cardiac fibrosis, cardiovascular morbidity and decreased life-expectancy. While the link of high phosphate and cardiovascular disease is commonly explained by direct cellular effects of phospho-regulatory hormones, we here explored the possibility of inorganic phosphate directly eliciting biological responses in cells. We demonstrate that human coronary endothelial cells (HCAEC) undergo an endothelial-mesenchymal transition (EndMT) when exposed to high phosphate. We further demonstrate that such EndMT is initiated by recruitment of aberrantly phosphorylated DNMT1 to the RASAL1 CpG island promoter by HDAC2, causing aberrant promoter methylation and transcriptional suppression, ultimately leading to increased Ras-GTP activity and activation of common EndMT regulators Twist and Snail. Our studies provide a novel aspect for known adverse effects of high phosphate levels, as eukaryotic cells are commonly believed to have lost phosphate-sensing mechanisms of prokaryotes during evolution, rendering them insensitive to extracellular inorganic orthophosphate. In addition, our studies provide novel insights into the mechanisms underlying specific targeting of select genes in context of fibrogenesis.</p>',
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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
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Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
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