Literature DB >> 32675241

Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation.

Wendan Ren1, Huitao Fan2,3, Sara A Grimm4, Yiran Guo2,3, Jae Jin Kim5, Jiekai Yin6, Linhui Li1, Christopher J Petell2,3, Xiao-Feng Tan1, Zhi-Min Zhang1, John P Coan7, Linfeng Gao6, Ling Cai2,3, Brittany Detrick1, Burak Çetin8, Qiang Cui9,10,11, Brian D Strahl2,3, Or Gozani7, Yinsheng Wang6,12, Kyle M Miller5, Seán E O'Leary1,8, Paul A Wade4, Dinshaw J Patel13, Gang Greg Wang14,3, Jikui Song15,6.   

Abstract

In mammals, repressive histone modifications such as trimethylation of histone H3 Lys9 (H3K9me3), frequently coexist with DNA methylation, producing a more stable and silenced chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, through structural and biochemical characterizations, we identified the replication foci targeting sequence (RFTS) domain of maintenance DNA methyltransferase DNMT1, a module known to bind the ubiquitylated H3 (H3Ub), as a specific reader for H3K9me3/H3Ub, with the recognition mode distinct from the typical trimethyl-lysine reader. Disruption of the interaction between RFTS and the H3K9me3Ub affects the localization of DNMT1 in stem cells and profoundly impairs the global DNA methylation and genomic stability. Together, this study reveals a previously unappreciated pathway through which H3K9me3 directly reinforces DNMT1-mediated maintenance DNA methylation.

Entities:  

Keywords:  DNA methylation; DNMT1; H3K9me3; allosteric regulation

Mesh:

Substances:

Year:  2020        PMID: 32675241      PMCID: PMC7414182          DOI: 10.1073/pnas.2009316117

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   12.779


  57 in total

1.  UHRF1 plays a role in maintaining DNA methylation in mammalian cells.

Authors:  Magnolia Bostick; Jong Kyong Kim; Pierre-Olivier Estève; Amander Clark; Sriharsa Pradhan; Steven E Jacobsen
Journal:  Science       Date:  2007-08-02       Impact factor: 47.728

2.  Transcription of IAP endogenous retroviruses is constrained by cytosine methylation.

Authors:  C P Walsh; J R Chaillet; T H Bestor
Journal:  Nat Genet       Date:  1998-10       Impact factor: 38.330

Review 3.  Structure and function of mammalian DNA methyltransferases.

Authors:  Renata Zofia Jurkowska; Tomasz Piotr Jurkowski; Albert Jeltsch
Journal:  Chembiochem       Date:  2010-11-29       Impact factor: 3.164

4.  Mechanism of allosteric regulation of Dnmt1's processivity.

Authors:  Zeljko M Svedruzić; Norbert O Reich
Journal:  Biochemistry       Date:  2005-11-15       Impact factor: 3.162

5.  Crystal Structure of Human DNA Methyltransferase 1.

Authors:  Zhi-Min Zhang; Shuo Liu; Krystal Lin; Youfu Luo; John Jefferson Perry; Yinsheng Wang; Jikui Song
Journal:  J Mol Biol       Date:  2015-06-10       Impact factor: 5.469

6.  The replication focus targeting sequence (RFTS) domain is a DNA-competitive inhibitor of Dnmt1.

Authors:  Farisa Syeda; Rebecca L Fagan; Matthew Wean; George V Avvakumov; John R Walker; Sheng Xue; Sirano Dhe-Paganon; Charles Brenner
Journal:  J Biol Chem       Date:  2011-03-09       Impact factor: 5.157

7.  DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression.

Authors:  Shintaro Yagi; Keiji Hirabayashi; Shinya Sato; Wei Li; Yoko Takahashi; Tsutomu Hirakawa; Guoying Wu; Naoko Hattori; Naka Hattori; Jun Ohgane; Satoshi Tanaka; X Shirley Liu; Kunio Shiota
Journal:  Genome Res       Date:  2008-10-29       Impact factor: 9.043

8.  Role for DNA methylation in genomic imprinting.

Authors:  E Li; C Beard; R Jaenisch
Journal:  Nature       Date:  1993-11-25       Impact factor: 49.962

9.  Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation.

Authors:  Jingdong Cheng; Huirong Yang; Jian Fang; Lixiang Ma; Rui Gong; Ping Wang; Ze Li; Yanhui Xu
Journal:  Nat Commun       Date:  2015-05-11       Impact factor: 14.919

10.  Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition.

Authors:  Jian Fang; Jingdong Cheng; Jiaolong Wang; Qiao Zhang; Mengjie Liu; Rui Gong; Ping Wang; Xiaodan Zhang; Yangyang Feng; Wenxian Lan; Zhou Gong; Chun Tang; Jiemin Wong; Huirong Yang; Chunyang Cao; Yanhui Xu
Journal:  Nat Commun       Date:  2016-04-05       Impact factor: 14.919

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  20 in total

Review 1.  Mechanisms of chromatin-based epigenetic inheritance.

Authors:  Wenlong Du; Guojun Shi; Chun-Min Shan; Zhiming Li; Bing Zhu; Songtao Jia; Qing Li; Zhiguo Zhang
Journal:  Sci China Life Sci       Date:  2022-06-30       Impact factor: 6.038

Review 2.  Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications.

Authors:  Daniel Desaulniers; Paule Vasseur; Abigail Jacobs; M Cecilia Aguila; Norman Ertych; Miriam N Jacobs
Journal:  Int J Mol Sci       Date:  2021-10-11       Impact factor: 5.923

3.  RNA m6A regulates transcription via DNA demethylation and chromatin accessibility.

Authors:  Shuang Deng; Jialiang Zhang; Jiachun Su; Zhixiang Zuo; Lingxing Zeng; Kaijing Liu; Yanfen Zheng; Xudong Huang; Ruihong Bai; Lisha Zhuang; Ying Ye; Mei Li; Ling Pan; Junge Deng; Guandi Wu; Rui Li; Shaoping Zhang; Chen Wu; Dongxin Lin; Jianjun Chen; Jian Zheng
Journal:  Nat Genet       Date:  2022-09-07       Impact factor: 41.307

4.  Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo.

Authors:  Hui Yang; Dandan Bai; Yanhe Li; Zhaowei Yu; Chenfei Wang; Yifan Sheng; Wenqiang Liu; Shaorong Gao; Yong Zhang
Journal:  Nat Cell Biol       Date:  2022-04-28       Impact factor: 28.213

Review 5.  Making it or breaking it: DNA methylation and genome integrity.

Authors:  Anusha Sriraman; Turja K Debnath; Blerta Xhemalce; Kyle M Miller
Journal:  Essays Biochem       Date:  2020-10-26       Impact factor: 8.000

Review 6.  The interplay between DNA and histone methylation: molecular mechanisms and disease implications.

Authors:  Yinglu Li; Xiao Chen; Chao Lu
Journal:  EMBO Rep       Date:  2021-04-12       Impact factor: 8.807

Review 7.  Chromatin Regulation through Ubiquitin and Ubiquitin-like Histone Modifications.

Authors:  Robert M Vaughan; Ariana Kupai; Scott B Rothbart
Journal:  Trends Biochem Sci       Date:  2020-12-09       Impact factor: 13.807

8.  DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift.

Authors:  Julia Franzen; Theodoros Georgomanolis; Anton Selich; Chao-Chung Kuo; Reinhard Stöger; Lilija Brant; Melita Sara Mulabdić; Eduardo Fernandez-Rebollo; Clara Grezella; Alina Ostrowska; Matthias Begemann; Miloš Nikolić; Björn Rath; Anthony D Ho; Michael Rothe; Axel Schambach; Argyris Papantonis; Wolfgang Wagner
Journal:  Commun Biol       Date:  2021-05-19

Review 9.  Interplay between chromatin marks in development and disease.

Authors:  Sanne M Janssen; Matthew C Lorincz
Journal:  Nat Rev Genet       Date:  2021-10-04       Impact factor: 53.242

10.  Dnmt1 has de novo activity targeted to transposable elements.

Authors:  Chuck Haggerty; Helene Kretzmer; Christina Riemenschneider; Abhishek Sampath Kumar; Alexandra L Mattei; Nina Bailly; Judith Gottfreund; Pay Giesselmann; Raha Weigert; Björn Brändl; Pascal Giehr; René Buschow; Christina Galonska; Ferdinand von Meyenn; Melissa B Pappalardi; Michael T McCabe; Lars Wittler; Claudia Giesecke-Thiel; Thorsten Mielke; David Meierhofer; Bernd Timmermann; Franz-Josef Müller; Jörn Walter; Alexander Meissner
Journal:  Nat Struct Mol Biol       Date:  2021-06-17       Impact factor: 15.369

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