Literature DB >> 33480184

Chromatin accessibility dynamics during cell fate reprogramming.

Dongwei Li1,2,3,4, Xiaodong Shu1,3,4, Ping Zhu2, Duanqing Pei1,3,4,5.   

Abstract

Genome architecture and chromatin dynamics govern the fate and identify of a cell. Recent advances in mapping chromatin landscapes offer valuable tools for the acquisition of accurate information regarding chromatin dynamics. Here we discuss recent findings linking chromatin dynamics to cell fate control. Specifically, chromatin undergoes a binary off/on switch during iPSC reprogramming, closing and opening loci occupied by somatic and pluripotency transcription factors, respectively. This logic of a binary off/on switch may also be operational in cell fate control during normal development and implies that further approaches could potentially be developed to direct cell fate changes both in vitro and in vivo.
© 2021 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

Entities:  

Keywords:  chromatin dynamics; reprogramming; stem cell

Mesh：

Substances：

Year:  2021        PMID： 33480184      PMCID： PMC7857421          DOI： 10.15252/embr.202051644

Source DB:  PubMed          Journal:  EMBO Rep        ISSN： 1469-221X            Impact factor:   8.807


  121 in total

1.  A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts.

Authors:  Ronghui Li; Jialiang Liang; Su Ni; Ting Zhou; Xiaobing Qing; Huapeng Li; Wenzhi He; Jiekai Chen; Feng Li; Qiang Zhuang; Baoming Qin; Jianyong Xu; Wen Li; Jiayin Yang; Yi Gan; Dajiang Qin; Shipeng Feng; Hong Song; Dongshan Yang; Biliang Zhang; Lingwen Zeng; Liangxue Lai; Miguel Angel Esteban; Duanqing Pei
Journal:  Cell Stem Cell       Date:  2010-06-17       Impact factor: 24.633

2.  Genome-wide characterization of the routes to pluripotency.

Authors:  Samer M I Hussein; Mira C Puri; Peter D Tonge; Marco Benevento; Andrew J Corso; Jennifer L Clancy; Rowland Mosbergen; Mira Li; Dong-Sung Lee; Nicole Cloonan; David L A Wood; Javier Munoz; Robert Middleton; Othmar Korn; Hardip R Patel; Carl A White; Jong-Yeon Shin; Maely E Gauthier; Kim-Anh Lê Cao; Jong-Il Kim; Jessica C Mar; Nika Shakiba; William Ritchie; John E J Rasko; Sean M Grimmond; Peter W Zandstra; Christine A Wells; Thomas Preiss; Jeong-Sun Seo; Albert J R Heck; Ian M Rogers; Andras Nagy
Journal:  Nature       Date:  2014-12-11       Impact factor: 49.962

Review 3.  The interplay of chromatin and transcription factors during cell fate transitions in development and reprogramming.

Authors:  Georgina Peñalosa-Ruiz; Ann Rose Bright; Klaas W Mulder; Gert Jan C Veenstra
Journal:  Biochim Biophys Acta Gene Regul Mech       Date:  2019-07-26       Impact factor: 4.490

4.  C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4.

Authors:  Bruno Di Stefano; Samuel Collombet; Janus Schou Jakobsen; Michael Wierer; Jose Luis Sardina; Andreas Lackner; Ralph Stadhouders; Carolina Segura-Morales; Mirko Francesconi; Francesco Limone; Matthias Mann; Bo Porse; Denis Thieffry; Thomas Graf
Journal:  Nat Cell Biol       Date:  2016-03-14       Impact factor: 28.824

5.  The landscape of accessible chromatin in mammalian preimplantation embryos.

Authors:  Jingyi Wu; Bo Huang; He Chen; Qiangzong Yin; Yang Liu; Yunlong Xiang; Bingjie Zhang; Bofeng Liu; Qiujun Wang; Weikun Xia; Wenzhi Li; Yuanyuan Li; Jing Ma; Xu Peng; Hui Zheng; Jia Ming; Wenhao Zhang; Jing Zhang; Geng Tian; Feng Xu; Zai Chang; Jie Na; Xuerui Yang; Wei Xie
Journal:  Nature       Date:  2016-06-15       Impact factor: 49.962

6.  Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency.

Authors:  Davide Cacchiarelli; Cole Trapnell; Michael J Ziller; Magali Soumillon; Marcella Cesana; Rahul Karnik; Julie Donaghey; Zachary D Smith; Sutheera Ratanasirintrawoot; Xiaolan Zhang; Shannan J Ho Sui; Zhaoting Wu; Veronika Akopian; Casey A Gifford; John Doench; John L Rinn; George Q Daley; Alexander Meissner; Eric S Lander; Tarjei S Mikkelsen
Journal:  Cell       Date:  2015-07-16       Impact factor: 41.582

7.  Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis.

Authors:  Fuchou Tang; Catalin Barbacioru; Siqin Bao; Caroline Lee; Ellen Nordman; Xiaohui Wang; Kaiqin Lao; M Azim Surani
Journal:  Cell Stem Cell       Date:  2010-05-07       Impact factor: 24.633

8.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

9.  The corepressor NCOR1 and OCT4 facilitate early reprogramming by suppressing fibroblast gene expression.

Authors:  Georgina Peñalosa-Ruiz; Klaas W Mulder; Gert Jan C Veenstra
Journal:  PeerJ       Date:  2020-04-22       Impact factor: 2.984

10.  Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.

Authors:  Jay R Hesselberth; Xiaoyu Chen; Zhihong Zhang; Peter J Sabo; Richard Sandstrom; Alex P Reynolds; Robert E Thurman; Shane Neph; Michael S Kuehn; William S Noble; Stanley Fields; John A Stamatoyannopoulos
Journal:  Nat Methods       Date:  2009-03-22       Impact factor: 28.547
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  3 in total

Review 1.  Chromatin accessibility dynamics during cell fate reprogramming.

Authors:  Dongwei Li; Xiaodong Shu; Ping Zhu; Duanqing Pei
Journal:  EMBO Rep       Date:  2021-01-22       Impact factor: 8.807

2.  Computational modeling of chromatin accessibility identified important epigenomic regulators.

Authors:  Yanding Zhao; Yadong Dong; Wei Hong; Chongming Jiang; Kevin Yao; Chao Cheng
Journal:  BMC Genomics       Date:  2022-01-08       Impact factor: 3.969

3.  Differentiation-related epigenomic changes define clinically distinct keratinocyte cancer subclasses.

Authors:  Manuel Rodríguez-Paredes; Frank Lyko; Llorenç Solé-Boldo; Günter Raddatz; Julian Gutekunst; Oliver Gilliam; Felix Bormann; Michelle S Liberio; Daniel Hasche; Wiebke Antonopoulos; Jan-Philipp Mallm; Anke S Lonsdorf
Journal:  Mol Syst Biol       Date:  2022-09       Impact factor: 13.068
  3 in total

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