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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...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121778/ https://www.ncbi.nlm.nih.gov/pubmed/21731508 http://dx.doi.org/10.1371/journal.pgen.1002154 |
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author | Szulwach, Keith E. Li, Xuekun Li, Yujing Song, Chun-Xiao Han, Ji Woong Kim, SangSung Namburi, Sandeep Hermetz, Karen Kim, Julie J. Rudd, M. Katharine Yoon, Young-Sup Ren, Bing He, Chuan Jin, Peng |
author_facet | Szulwach, Keith E. Li, Xuekun Li, Yujing Song, Chun-Xiao Han, Ji Woong Kim, SangSung Namburi, Sandeep Hermetz, Karen Kim, Julie J. Rudd, M. Katharine Yoon, Young-Sup Ren, Bing He, Chuan Jin, Peng |
author_sort | Szulwach, Keith E. |
collection | PubMed |
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 | Online Article Text |
id | pubmed-3121778 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-31217782011-06-30 Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells Szulwach, Keith E. Li, Xuekun Li, Yujing Song, Chun-Xiao Han, Ji Woong Kim, SangSung Namburi, Sandeep Hermetz, Karen Kim, Julie J. Rudd, M. Katharine Yoon, Young-Sup Ren, Bing He, Chuan Jin, Peng PLoS Genet Research Article 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. Public Library of Science 2011-06-23 /pmc/articles/PMC3121778/ /pubmed/21731508 http://dx.doi.org/10.1371/journal.pgen.1002154 Text en Szulwach et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Szulwach, Keith E. Li, Xuekun Li, Yujing Song, Chun-Xiao Han, Ji Woong Kim, SangSung Namburi, Sandeep Hermetz, Karen Kim, Julie J. Rudd, M. Katharine Yoon, Young-Sup Ren, Bing He, Chuan Jin, Peng Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells |
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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121778/ https://www.ncbi.nlm.nih.gov/pubmed/21731508 http://dx.doi.org/10.1371/journal.pgen.1002154 |
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