Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell Reprogramming
The core pluripotency factor Oct4 plays key roles in somatic cell reprogramming through transcriptional control. Here, we profile Oct4 occupancy, epigenetic changes, and gene expression in reprogramming. We find that Oct4 binds in a hierarchical manner to target sites with primed epigenetic modifica...
Main Authors: | , , , , , , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Elsevier
2016-02-01
|
Series: | Cell Reports |
Subjects: | |
Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124716000334 |
id |
doaj-64084c997e87451f89e4369139d911a5 |
---|---|
record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jun Chen Xiaolong Chen Min Li Xiaoyu Liu Yawei Gao Xiaochen Kou Yanhong Zhao Weisheng Zheng Xiaobai Zhang Yi Huo Chuan Chen You Wu Hong Wang Cizhong Jiang Shaorong Gao |
spellingShingle |
Jun Chen Xiaolong Chen Min Li Xiaoyu Liu Yawei Gao Xiaochen Kou Yanhong Zhao Weisheng Zheng Xiaobai Zhang Yi Huo Chuan Chen You Wu Hong Wang Cizhong Jiang Shaorong Gao Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell Reprogramming Cell Reports Oct4 reprogramming histone modification iPSC |
author_facet |
Jun Chen Xiaolong Chen Min Li Xiaoyu Liu Yawei Gao Xiaochen Kou Yanhong Zhao Weisheng Zheng Xiaobai Zhang Yi Huo Chuan Chen You Wu Hong Wang Cizhong Jiang Shaorong Gao |
author_sort |
Jun Chen |
title |
Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell Reprogramming |
title_short |
Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell Reprogramming |
title_full |
Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell Reprogramming |
title_fullStr |
Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell Reprogramming |
title_full_unstemmed |
Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell Reprogramming |
title_sort |
hierarchical oct4 binding in concert with primed epigenetic rearrangements during somatic cell reprogramming |
publisher |
Elsevier |
series |
Cell Reports |
issn |
2211-1247 |
publishDate |
2016-02-01 |
description |
The core pluripotency factor Oct4 plays key roles in somatic cell reprogramming through transcriptional control. Here, we profile Oct4 occupancy, epigenetic changes, and gene expression in reprogramming. We find that Oct4 binds in a hierarchical manner to target sites with primed epigenetic modifications. Oct4 binding is temporally continuous and seldom switches between bound and unbound. Oct4 occupancy in most of promoters is maintained throughout the entire reprogramming process. In contrast, somatic cell-specific enhancers are silenced in the early and intermediate stages, whereas stem cell-specific enhancers are activated in the late stage in parallel with cell fate transition. Both epigenetic remodeling and Oct4 binding contribute to the hyperdynamic enhancer signature transitions. The hierarchical Oct4 bindings are associated with distinct functional themes at different stages. Collectively, our results provide a comprehensive molecular roadmap of Oct4 binding in concert with epigenetic rearrangements and rich resources for future reprogramming studies. |
topic |
Oct4 reprogramming histone modification iPSC |
url |
http://www.sciencedirect.com/science/article/pii/S2211124716000334 |
work_keys_str_mv |
AT junchen hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT xiaolongchen hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT minli hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT xiaoyuliu hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT yaweigao hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT xiaochenkou hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT yanhongzhao hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT weishengzheng hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT xiaobaizhang hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT yihuo hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT chuanchen hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT youwu hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT hongwang hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT cizhongjiang hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming AT shaoronggao hierarchicaloct4bindinginconcertwithprimedepigeneticrearrangementsduringsomaticcellreprogramming |
_version_ |
1725006151372767232 |
spelling |
doaj-64084c997e87451f89e4369139d911a52020-11-25T01:49:37ZengElsevierCell Reports2211-12472016-02-011461540155410.1016/j.celrep.2016.01.013Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell ReprogrammingJun Chen0Xiaolong Chen1Min Li2Xiaoyu Liu3Yawei Gao4Xiaochen Kou5Yanhong Zhao6Weisheng Zheng7Xiaobai Zhang8Yi Huo9Chuan Chen10You Wu11Hong Wang12Cizhong Jiang13Shaorong Gao14College of Life Science, Beijing Normal University, Beijing 100875, ChinaClinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, ChinaClinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, ChinaNational Institute of Biological Sciences (NIBS), Beijing 102206, ChinaClinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, ChinaClinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, ChinaClinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, ChinaClinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, ChinaClinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, ChinaNational Institute of Biological Sciences (NIBS), Beijing 102206, ChinaClinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, ChinaClinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, ChinaClinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, ChinaClinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, ChinaClinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai 200092, ChinaThe core pluripotency factor Oct4 plays key roles in somatic cell reprogramming through transcriptional control. Here, we profile Oct4 occupancy, epigenetic changes, and gene expression in reprogramming. We find that Oct4 binds in a hierarchical manner to target sites with primed epigenetic modifications. Oct4 binding is temporally continuous and seldom switches between bound and unbound. Oct4 occupancy in most of promoters is maintained throughout the entire reprogramming process. In contrast, somatic cell-specific enhancers are silenced in the early and intermediate stages, whereas stem cell-specific enhancers are activated in the late stage in parallel with cell fate transition. Both epigenetic remodeling and Oct4 binding contribute to the hyperdynamic enhancer signature transitions. The hierarchical Oct4 bindings are associated with distinct functional themes at different stages. Collectively, our results provide a comprehensive molecular roadmap of Oct4 binding in concert with epigenetic rearrangements and rich resources for future reprogramming studies.http://www.sciencedirect.com/science/article/pii/S2211124716000334Oct4reprogramminghistone modificationiPSC |