Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells.
Covalent modification of DNA distinguishes cellular identities and is crucial for regulating the pluripotency and differentiation of embryonic stem (ES) cells. The recent demonstration that 5-methylcytosine (5-mC) may be further modified to 5-hydroxymethylcytosine (5-hmC) in ES cells has revealed a...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2011-06-01
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| Series: | PLoS Genetics |
| Online Access: | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1002154&type=printable |
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| _version_ | 1849725723268349952 |
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| author | Keith E Szulwach Xuekun Li Yujing Li Chun-Xiao Song Ji Woong Han SangSung Kim Sandeep Namburi Karen Hermetz Julie J Kim M Katharine Rudd Young-Sup Yoon Bing Ren Chuan He Peng Jin |
| author_facet | Keith E Szulwach Xuekun Li Yujing Li Chun-Xiao Song Ji Woong Han SangSung Kim Sandeep Namburi Karen Hermetz Julie J Kim M Katharine Rudd Young-Sup Yoon Bing Ren Chuan He Peng Jin |
| author_sort | Keith E Szulwach |
| collection | DOAJ |
| description | Covalent modification of DNA distinguishes cellular identities and is crucial for regulating the pluripotency and differentiation of embryonic stem (ES) cells. The recent demonstration that 5-methylcytosine (5-mC) may be further modified to 5-hydroxymethylcytosine (5-hmC) in ES cells has revealed a novel regulatory paradigm to modulate the epigenetic landscape of pluripotency. To understand the role of 5-hmC in the epigenomic landscape of pluripotent cells, here we profile the genome-wide 5-hmC distribution and correlate it with the genomic profiles of 11 diverse histone modifications and six transcription factors in human ES cells. By integrating genomic 5-hmC signals with maps of histone enrichment, we link particular pluripotency-associated chromatin contexts with 5-hmC. Intriguingly, through additional correlations with defined chromatin signatures at promoter and enhancer subtypes, we show distinct enrichment of 5-hmC at enhancers marked with H3K4me1 and H3K27ac. These results suggest potential role(s) for 5-hmC in the regulation of specific promoters and enhancers. In addition, our results provide a detailed epigenomic map of 5-hmC from which to pursue future functional studies on the diverse regulatory roles associated with 5-hmC. |
| format | Article |
| id | doaj-art-d56adc1fb5e94987bfa629575df65a1e |
| institution | DOAJ |
| issn | 1553-7390 1553-7404 |
| language | English |
| publishDate | 2011-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj-art-d56adc1fb5e94987bfa629575df65a1e2025-08-20T03:10:24ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042011-06-0176e100215410.1371/journal.pgen.1002154Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells.Keith E SzulwachXuekun LiYujing LiChun-Xiao SongJi Woong HanSangSung KimSandeep NamburiKaren HermetzJulie J KimM Katharine RuddYoung-Sup YoonBing RenChuan HePeng JinCovalent modification of DNA distinguishes cellular identities and is crucial for regulating the pluripotency and differentiation of embryonic stem (ES) cells. The recent demonstration that 5-methylcytosine (5-mC) may be further modified to 5-hydroxymethylcytosine (5-hmC) in ES cells has revealed a novel regulatory paradigm to modulate the epigenetic landscape of pluripotency. To understand the role of 5-hmC in the epigenomic landscape of pluripotent cells, here we profile the genome-wide 5-hmC distribution and correlate it with the genomic profiles of 11 diverse histone modifications and six transcription factors in human ES cells. By integrating genomic 5-hmC signals with maps of histone enrichment, we link particular pluripotency-associated chromatin contexts with 5-hmC. Intriguingly, through additional correlations with defined chromatin signatures at promoter and enhancer subtypes, we show distinct enrichment of 5-hmC at enhancers marked with H3K4me1 and H3K27ac. These results suggest potential role(s) for 5-hmC in the regulation of specific promoters and enhancers. In addition, our results provide a detailed epigenomic map of 5-hmC from which to pursue future functional studies on the diverse regulatory roles associated with 5-hmC.https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1002154&type=printable |
| spellingShingle | Keith E Szulwach Xuekun Li Yujing Li Chun-Xiao Song Ji Woong Han SangSung Kim Sandeep Namburi Karen Hermetz Julie J Kim M Katharine Rudd Young-Sup Yoon Bing Ren Chuan He Peng Jin Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genetics |
| title | Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. |
| title_full | Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. |
| title_fullStr | Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. |
| title_full_unstemmed | Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. |
| title_short | Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. |
| title_sort | integrating 5 hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells |
| url | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1002154&type=printable |
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