H3K36me3-coupled DNA Demethylation by DNMT3A Is Essential for Hypoxia-Induced EMT of Cancer Cells [ChIP-Seq]
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PROVIDER: PRJNA1057948 | ENA |
REPOSITORIES: ENA
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Project description:The epithelial-to-mesenchymal transition (EMT) and metastasis of the cancer cells are closely associated with epigenetic changes of chromatin and reprogramming of transcriptomes. The DNA methyltransferases DNMT3A and DNMT3B possess DNA demethylation/dehydroxymethylation activities. Here, we show, by a range of molecular/cellular approaches, that active DNA demethylation activity of DNMT3A is required for hypoxia-induced EMT of the primary colon carcinoma SW480 cells, its genome-wide DNA demethylation, and promoter DNA demethylation/transcriptional activation of the EMT genes TWIST1 and SNAIL1. DNMT3A also positively regulates hypoxia-induced TWIST1 activation in other types of cancer cells. Mechanistic analysis supports a regulatory model, in which hypoxia-induced H3K36me3 mark recruits DNMT3A to demethylate CpG in the hypoxia-responsive element (HRE), thereby facilitating HIF-1α binding and TWIST1 activation. This study demonstrates for the first time an in vivo functional role of the active DNA demethylation activity of DNMT3A and its potential as a novel therapeutic target of anti-cancer development.
2025-08-13 | GSE252166 | GEO
Project description:The epithelial-to-mesenchymal transition (EMT) and metastasis of the cancer cells are closely associated with epigenetic changes of chromatin and reprogramming of transcriptomes. The DNA methyltransferases DNMT3A and DNMT3B possess DNA demethylation/dehydroxymethylation activities. Here, we show, by a range of molecular/cellular approaches, that active DNA demethylation activity of DNMT3A is required for hypoxia-induced EMT of the primary colon carcinoma SW480 cells, its genome-wide DNA demethylation, and promoter DNA demethylation/transcriptional activation of the EMT genes TWIST1 and SNAIL1. DNMT3A also positively regulates hypoxia-induced TWIST1 activation in other types of cancer cells. Mechanistic analysis supports a regulatory model, in which hypoxia-induced H3K36me3 mark recruits DNMT3A to demethylate CpG in the hypoxia-responsive element (HRE), thereby facilitating HIF-1α binding and TWIST1 activation. This study demonstrates for the first time an in vivo functional role of the active DNA demethylation activity of DNMT3A and its potential as a novel therapeutic target of anti-cancer development.
2025-08-13 | GSE251863 | GEO
Project description:H3K36me3-coupled DNA Demethylation by DNMT3A Is Essential for Hypoxia-Induced EMT of Cancer Cells
| PRJNA1057944 | ENA
Project description:H3K36me3-coupled DNA Demethylation by DNMT3A Is Essential for Hypoxia-Induced EMT of Cancer Cells [Bisulfite Sequencing]
| PRJNA1055568 | ENA
Project description:The DNA methylation program is at the bottom layer of the epigenetic regulatory cascade of vertebrate development. While the methylation at C-5 position of the cytosine (C) residues on the vertebrate genomes is achieved through the catalytic activities of the DNA methyltransferases (DNMTs), the conversion of the methylated cytosine (5mC) could be accomplished by the combined actions of the TET enzyme and DNA repair. Interestingly, it has been found recently that the mouse and human DNMTs also possess active DNA demethylation activity in vitro in a Ca2+- and redox condition-dependent manner. We report here the study of tracking down the fate of the methyl group removed from 5mC on DNA during in vitro demethylation reaction by mouse de novo DNMTs, i.e. DNMT3A and DNMT3B. Remarkably, the methyl group becomes covalently linked to the catalytic cysteines utilized by the two de novo DNMTs in their DNA methylation reactions. Thus, the forward and reverse reactions of DNA methylations by the DNMTs may utilize the same cysteine residue(s) as the active site despite of their distinctive pathways. Secondly, we demonstrate that active DNA demethylation of a heavily methylated GFP reporter plasmid by ectopically expressed DNMT3A or DNMT3B occurs in vivo in transfected human HEK 293 cells in culture. Furthermore, the extent of DNA demethylation by the DNMTs in this cell-based system is affected by Ca2+ homeostasis as well as by mutation of their putative active cysteines. These findings substantiate the roles of the vertebrate DNMTs as double-edged swords in DNA methylation-demethylation in vitro as well as in a cellular context.
2022-02-24 | PXD003401 | Pride
Project description:Epithelial-to-Mesenchymal Transition (EMT) is involved in prostate cancer metastatic progression and its plasticity suggests epigenetic implications. Deregulation of UHRF1/DNMT1, DNMT3A and miRNAs play a role in EMT, but their interplay has not been clarified yet. Here, we identify miR-720 and miR-1260a as new DNMT3A regulators through miRNA microarray performed on UHRF1 silenced Androgen Receptor (AR) non-responsive (PC3) cell extracts, and subsequent target validation and functional overexpression and downregulation in PC3 and AR responsive LNCaP cells, respectively. These miRNAs inversely correlated with DNMT3A in our ex-vivo model of EMT in PC3 but not in LNCaP cells, induced with conditioned media from patient-derived Cancer-Associated Fibroblasts (CM-CAF). miR-720 and miR-1260a were expressed in very few patients from the PRAD TCGA data set expressing an EMT or MET (Mesenchymal-to-Epitelial Transition) signature; miR-200 family (miR-200a/b, -141, -429), along with miR-205 and miR-203, were downregulated in EMT patients as they modulate key EMT factors. These latter miRNAs resulted hyper-methylated at their promoters in our ex-vivo EMT prostate cancer model, while in the EMT PRAD TCGA data set only miR200c and miR141 promoters displayed a diffused hyper-methylated pattern inversely correlated with their transcriptional expression. Chromatin immunoprecipitation experiments performed on CM-CAF induced PC3 cells extracts showed that DNMT3A gets recruited onto the promoters of the latter two miRNAs, coupled with a marked increase of H3K27me3 and H3K9me3 and/or the decrease of H3K4me3 and H3K36me3. Altogether, our results point to a DNMT3A regulatory role of key miRNAs for EMT in prostate cancer.
2021-11-20 | E-MTAB-9835 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2025-08-13 | GSE252167 | GEO
Project description:Establishment of the DNA methylation landscape of mammalian oocytes, mediated by the DNMT3A-DNMT3L complex, is crucial for reproduction and development. In mouse oocytes, high levels of DNA methylation occur exclusively in the transcriptionally active regions, with moderate to low levels of methylation in other regions. Histone H3K36me3 mediates the high levels of methylation in the transcribed regions; however, it is unknown which histone mark guides the methylation in the other regions. Here, we show that, in mouse oocytes, H3K36me2 is highly enriched in the X chromosome and is broadly distributed across all autosomes. Upon H3K36me2 depletion, DNA methylation in moderately methylated regions is selectively affected, and a methylation pattern unique to the X chromosome is switched to an autosome-like pattern. Furthermore, we find that simultaneous depletion of H3K36me2 and H3K36me3 results in global hypomethylation, comparable to that of DNMT3A depletion. Therefore, the two histone marks jointly provide the chromatin platform essential for guiding DNMT3A-dependent DNA methylation in mouse oocytes.
2022-07-07 | GSE183969 | GEO
Project description:Genome-wide DNA demethylation, including the erasure of genome imprints, in primordial germ cells (PGCs), is critical as a first step for creating the totipotent epigenome in the germ line. Here, we provide evidence that contrary to the prevailing model involving active DNA demethylation, imprint erasure in mouse PGCs occurs in a manner consistent with replication-coupled passive DNA demethylation: PGCs erase imprints during their rapid proliferation with little de novo as well as maintenance DNA methylation potential and no major chromatin alterations. Our findings necessitate the re-evaluation of and provide novel insights into the mechanism of genome-wide DNA demethylation in PGCs. We performed expression analysis of primordial germ cells (PGCs) at embryonic days 10.5-13.5. Because the number of PGCs available at these stages were low, cDNAs were amplified by the method that we previously published (Kurimoto et al. 2006, NAR 34: e42 (PMID 16547197)). To include analysis of PGC gene expression at E9.5, we re-normalized the data from our E9.5 PGC samples (GSM744103, GSM744104) from our previous publication (Hayashi et al., 2011, Cell 146: 519-32 (PMD 21820164)) together with the data from this submission.
2013-03-04 | E-GEOD-40412 | biostudies-arrayexpress
Project description:Genome-wide DNA demethylation, including the erasure of genome imprints, in primordial germ cells (PGCs), is critical as a first step for creating the totipotent epigenome in the germ line. Here, we provide evidence that contrary to the prevailing model involving active DNA demethylation, imprint erasure in mouse PGCs occurs in a manner consistent with replication-coupled passive DNA demethylation: PGCs erase imprints during their rapid proliferation with little de novo as well as maintenance DNA methylation potential and no major chromatin alterations. Our findings necessitate the re-evaluation of and provide novel insights into the mechanism of genome-wide DNA demethylation in PGCs.
2013-03-04 | GSE40412 | GEO