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DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells

Chromatin remodeling is important for the epigenetic reprogramming of human primordial germ cells. However, the comprehensive chromatin state has not yet been analyzed for human fetal germ cells (FGCs). Here we use nucleosome occupancy and methylation sequencing method to analyze both the genome-wid...

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Autores principales: Guo, Hongshan, Hu, Boqiang, Yan, Liying, Yong, Jun, Wu, Yan, Gao, Yun, Guo, Fan, Hou, Yu, Fan, Xiaoying, Dong, Ji, Wang, Xiaoye, Zhu, Xiaohui, Yan, Jie, Wei, Yuan, Jin, Hongyan, Zhang, Wenxin, Wen, Lu, Tang, Fuchou, Qiao, Jie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5339845/
https://www.ncbi.nlm.nih.gov/pubmed/27824029
http://dx.doi.org/10.1038/cr.2016.128
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author Guo, Hongshan
Hu, Boqiang
Yan, Liying
Yong, Jun
Wu, Yan
Gao, Yun
Guo, Fan
Hou, Yu
Fan, Xiaoying
Dong, Ji
Wang, Xiaoye
Zhu, Xiaohui
Yan, Jie
Wei, Yuan
Jin, Hongyan
Zhang, Wenxin
Wen, Lu
Tang, Fuchou
Qiao, Jie
author_facet Guo, Hongshan
Hu, Boqiang
Yan, Liying
Yong, Jun
Wu, Yan
Gao, Yun
Guo, Fan
Hou, Yu
Fan, Xiaoying
Dong, Ji
Wang, Xiaoye
Zhu, Xiaohui
Yan, Jie
Wei, Yuan
Jin, Hongyan
Zhang, Wenxin
Wen, Lu
Tang, Fuchou
Qiao, Jie
author_sort Guo, Hongshan
collection PubMed
description Chromatin remodeling is important for the epigenetic reprogramming of human primordial germ cells. However, the comprehensive chromatin state has not yet been analyzed for human fetal germ cells (FGCs). Here we use nucleosome occupancy and methylation sequencing method to analyze both the genome-wide chromatin accessibility and DNA methylome at a series of crucial time points during fetal germ cell development in both human and mouse. We find 116 887 and 137 557 nucleosome-depleted regions (NDRs) in human and mouse FGCs, covering a large set of germline-specific and highly dynamic regulatory genomic elements, such as enhancers. Moreover, we find that the distal NDRs are enriched specifically for binding motifs of the pluripotency and germ cell master regulators such as NANOG, SOX17, AP2γ and OCT4 in human FGCs, indicating the existence of a delicate regulatory balance between pluripotency-related genes and germ cell-specific genes in human FGCs, and the functional significance of these genes for germ cell development in vivo. Our work offers a comprehensive and high-resolution roadmap for dissecting chromatin state transition dynamics during the epigenomic reprogramming of human and mouse FGCs.
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spelling pubmed-53398452017-03-09 DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells Guo, Hongshan Hu, Boqiang Yan, Liying Yong, Jun Wu, Yan Gao, Yun Guo, Fan Hou, Yu Fan, Xiaoying Dong, Ji Wang, Xiaoye Zhu, Xiaohui Yan, Jie Wei, Yuan Jin, Hongyan Zhang, Wenxin Wen, Lu Tang, Fuchou Qiao, Jie Cell Res Original Article Chromatin remodeling is important for the epigenetic reprogramming of human primordial germ cells. However, the comprehensive chromatin state has not yet been analyzed for human fetal germ cells (FGCs). Here we use nucleosome occupancy and methylation sequencing method to analyze both the genome-wide chromatin accessibility and DNA methylome at a series of crucial time points during fetal germ cell development in both human and mouse. We find 116 887 and 137 557 nucleosome-depleted regions (NDRs) in human and mouse FGCs, covering a large set of germline-specific and highly dynamic regulatory genomic elements, such as enhancers. Moreover, we find that the distal NDRs are enriched specifically for binding motifs of the pluripotency and germ cell master regulators such as NANOG, SOX17, AP2γ and OCT4 in human FGCs, indicating the existence of a delicate regulatory balance between pluripotency-related genes and germ cell-specific genes in human FGCs, and the functional significance of these genes for germ cell development in vivo. Our work offers a comprehensive and high-resolution roadmap for dissecting chromatin state transition dynamics during the epigenomic reprogramming of human and mouse FGCs. Nature Publishing Group 2017-02 2016-11-08 /pmc/articles/PMC5339845/ /pubmed/27824029 http://dx.doi.org/10.1038/cr.2016.128 Text en Copyright © 2016 Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 Unported License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Original Article
Guo, Hongshan
Hu, Boqiang
Yan, Liying
Yong, Jun
Wu, Yan
Gao, Yun
Guo, Fan
Hou, Yu
Fan, Xiaoying
Dong, Ji
Wang, Xiaoye
Zhu, Xiaohui
Yan, Jie
Wei, Yuan
Jin, Hongyan
Zhang, Wenxin
Wen, Lu
Tang, Fuchou
Qiao, Jie
DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells
title DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells
title_full DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells
title_fullStr DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells
title_full_unstemmed DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells
title_short DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells
title_sort dna methylation and chromatin accessibility profiling of mouse and human fetal germ cells
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5339845/
https://www.ncbi.nlm.nih.gov/pubmed/27824029
http://dx.doi.org/10.1038/cr.2016.128
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