Author
Listed:
- Jingyi Wu
(Tsinghua University
Massachusetts General Hospital and Harvard Medical School
Broad Institute of MIT and Harvard)
- Jiawei Xu
(The First Affiliated Hospital of Zhengzhou University)
- Bofeng Liu
(Tsinghua University)
- Guidong Yao
(The First Affiliated Hospital of Zhengzhou University)
- Peizhe Wang
(Tsinghua University)
- Zili Lin
(Tsinghua University)
- Bo Huang
(Peking University)
- Xuepeng Wang
(Chinese Academy of Sciences
University of Chinese Academy of Sciences)
- Tong Li
(The First Affiliated Hospital of Zhengzhou University)
- Senlin Shi
(The First Affiliated Hospital of Zhengzhou University)
- Nan Zhang
(The First Affiliated Hospital of Zhengzhou University)
- Fuyu Duan
(Tsinghua University)
- Jia Ming
(Tsinghua University)
- Xiangyang Zhang
(The First Affiliated Hospital of Zhengzhou University)
- Wenbin Niu
(The First Affiliated Hospital of Zhengzhou University)
- Wenyan Song
(The First Affiliated Hospital of Zhengzhou University)
- Haixia Jin
(The First Affiliated Hospital of Zhengzhou University)
- Yihong Guo
(The First Affiliated Hospital of Zhengzhou University)
- Shanjun Dai
(The First Affiliated Hospital of Zhengzhou University)
- Linli Hu
(The First Affiliated Hospital of Zhengzhou University)
- Lanlan Fang
(The First Affiliated Hospital of Zhengzhou University)
- Qiujun Wang
(Tsinghua University)
- Yuanyuan Li
(Tsinghua University)
- Wei Li
(Chinese Academy of Sciences
University of Chinese Academy of Sciences)
- Jie Na
(Tsinghua University)
- Wei Xie
(Tsinghua University)
- Yingpu Sun
(The First Affiliated Hospital of Zhengzhou University)
Abstract
Upon fertilization, drastic chromatin reorganization occurs during preimplantation development 1 . However, the global chromatin landscape and its molecular dynamics in this period remain largely unexplored in humans. Here we investigate chromatin states in human preimplantation development using an improved assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) 2 . We find widespread accessible chromatin regions in early human embryos that overlap extensively with putative cis-regulatory sequences and transposable elements. Integrative analyses show both conservation and divergence in regulatory circuitry between human and mouse early development, and between human pluripotency in vivo and human embryonic stem cells. In addition, we find widespread open chromatin regions before zygotic genome activation (ZGA). The accessible chromatin loci are readily found at CpG-rich promoters. Unexpectedly, many others reside in distal regions that overlap with DNA hypomethylated domains in human oocytes and are enriched for transcription factor-binding sites. A large portion of these regions then become inaccessible after ZGA in a transcription-dependent manner. Notably, such extensive chromatin reorganization during ZGA is conserved in mice and correlates with the reprogramming of the non-canonical histone mark H3K4me3, which is uniquely linked to genome silencing3–5. Taken together, these data not only reveal a conserved principle that underlies the chromatin transition during mammalian ZGA, but also help to advance our understanding of epigenetic reprogramming during human early development and in vitro fertilization.
Suggested Citation
Jingyi Wu & Jiawei Xu & Bofeng Liu & Guidong Yao & Peizhe Wang & Zili Lin & Bo Huang & Xuepeng Wang & Tong Li & Senlin Shi & Nan Zhang & Fuyu Duan & Jia Ming & Xiangyang Zhang & Wenbin Niu & Wenyan So, 2018.
"Chromatin analysis in human early development reveals epigenetic transition during ZGA,"
Nature, Nature, vol. 557(7704), pages 256-260, May.
Handle:
RePEc:nat:nature:v:557:y:2018:i:7704:d:10.1038_s41586-018-0080-8
DOI: 10.1038/s41586-018-0080-8
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Citations
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Cited by:
- Julien Pontis & Cyril Pulver & Christopher J. Playfoot & Evarist Planet & Delphine Grun & Sandra Offner & Julien Duc & Andrea Manfrin & Matthias P. Lutolf & Didier Trono, 2022.
"Primate-specific transposable elements shape transcriptional networks during human development,"
Nature Communications, Nature, vol. 13(1), pages 1-13, December.
- Yinuo Wang & Adel Elsherbiny & Linda Kessler & Julio Cordero & Haojie Shi & Heike Serke & Olga Lityagina & Felix A. Trogisch & Mona Malek Mohammadi & Ibrahim El-Battrawy & Johannes Backs & Thomas Wiel, 2022.
"Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function,"
Nature Communications, Nature, vol. 13(1), pages 1-24, December.
- Denis Torre & Nancy J. Francoeur & Yael Kalma & Ilana Gross Carmel & Betsaida S. Melo & Gintaras Deikus & Kimaada Allette & Ron Flohr & Maya Fridrikh & Konstantinos Vlachos & Kent Madrid & Hardik Shah, 2023.
"Isoform-resolved transcriptome of the human preimplantation embryo,"
Nature Communications, Nature, vol. 14(1), pages 1-23, December.
- Saurabh J. Pradhan & Puli Chandramouli Reddy & Michael Smutny & Ankita Sharma & Keisuke Sako & Meghana S. Oak & Rini Shah & Mrinmoy Pal & Ojas Deshpande & Greg Dsilva & Yin Tang & Rakesh Mishra & Giri, 2021.
"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis,"
Nature Communications, Nature, vol. 12(1), pages 1-19, December.
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