Literature DB >> 21514197

Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells.

Yufei Xu1, Feizhen Wu, Li Tan, Lingchun Kong, Lijun Xiong, Jie Deng, Andrew J Barbera, Lijuan Zheng, Haikuo Zhang, Stephen Huang, Jinrong Min, Thomas Nicholson, Taiping Chen, Guoliang Xu, Yang Shi, Kun Zhang, Yujiang Geno Shi.   

Abstract

DNA methylation at the 5 position of cytosine (5mC) in the mammalian genome is a key epigenetic event critical for various cellular processes. The ten-eleven translocation (Tet) family of 5mC-hydroxylases, which convert 5mC to 5-hydroxymethylcytosine (5hmC), offers a way for dynamic regulation of DNA methylation. Here we report that Tet1 binds to unmodified C or 5mC- or 5hmC-modified CpG-rich DNA through its CXXC domain. Genome-wide mapping of Tet1 and 5hmC reveals mechanisms by which Tet1 controls 5hmC and 5mC levels in mouse embryonic stem cells (mESCs). We also uncover a comprehensive gene network influenced by Tet1. Collectively, our data suggest that Tet1 controls DNA methylation both by binding to CpG-rich regions to prevent unwanted DNA methyltransferase activity, and by converting 5mC to 5hmC through hydroxylase activity. This Tet1-mediated antagonism of CpG methylation imparts differential maintenance of DNA methylation status at Tet1 targets, ultimately contributing to mESC differentiation and the onset of embryonic development.
Copyright © 2011 Elsevier Inc. All rights reserved.

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Year:  2011        PMID: 21514197      PMCID: PMC3099128          DOI: 10.1016/j.molcel.2011.04.005

Source DB:  PubMed          Journal:  Mol Cell        ISSN: 1097-2765            Impact factor:   17.970


  33 in total

1.  The bases of the nucleic acids of some bacterial and animal viruses: the occurrence of 5-hydroxymethylcytosine.

Authors:  G R WYATT; S S COHEN
Journal:  Biochem J       Date:  1953-12       Impact factor: 3.857

2.  Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b.

Authors:  Akiko Tsumura; Tomohiro Hayakawa; Yuichi Kumaki; Shin-ichiro Takebayashi; Morito Sakaue; Chisa Matsuoka; Kunitada Shimotohno; Fuyuki Ishikawa; En Li; Hiroki R Ueda; Jun-ichi Nakayama; Masaki Okano
Journal:  Genes Cells       Date:  2006-07       Impact factor: 1.891

Review 3.  Molecular control of pluripotency.

Authors:  Laurie A Boyer; Divya Mathur; Rudolf Jaenisch
Journal:  Curr Opin Genet Dev       Date:  2006-08-22       Impact factor: 5.578

Review 4.  DNA methylation landscapes: provocative insights from epigenomics.

Authors:  Miho M Suzuki; Adrian Bird
Journal:  Nat Rev Genet       Date:  2008-06       Impact factor: 53.242

5.  Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation.

Authors:  Shaun D Fouse; Yin Shen; Matteo Pellegrini; Steve Cole; Alexander Meissner; Leander Van Neste; Rudolf Jaenisch; Guoping Fan
Journal:  Cell Stem Cell       Date:  2008-02-07       Impact factor: 24.633

6.  Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome.

Authors:  Michael Weber; Ines Hellmann; Michael B Stadler; Liliana Ramos; Svante Pääbo; Michael Rebhan; Dirk Schübeler
Journal:  Nat Genet       Date:  2007-03-04       Impact factor: 38.330

7.  Severe global DNA hypomethylation blocks differentiation and induces histone hyperacetylation in embryonic stem cells.

Authors:  Melany Jackson; Anna Krassowska; Nick Gilbert; Timothy Chevassut; Lesley Forrester; John Ansell; Bernard Ramsahoye
Journal:  Mol Cell Biol       Date:  2004-10       Impact factor: 4.272

8.  The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid.

Authors:  N W Penn; R Suwalski; C O'Riley; K Bojanowski; R Yura
Journal:  Biochem J       Date:  1972-02       Impact factor: 3.857

9.  Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2).

Authors:  Victoria Valinluck; Hsin-Hao Tsai; Daniel K Rogstad; Artur Burdzy; Adrian Bird; Lawrence C Sowers
Journal:  Nucleic Acids Res       Date:  2004-08-09       Impact factor: 16.971

10.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

Authors:  Tarjei S Mikkelsen; Manching Ku; David B Jaffe; Biju Issac; Erez Lieberman; Georgia Giannoukos; Pablo Alvarez; William Brockman; Tae-Kyung Kim; Richard P Koche; William Lee; Eric Mendenhall; Aisling O'Donovan; Aviva Presser; Carsten Russ; Xiaohui Xie; Alexander Meissner; Marius Wernig; Rudolf Jaenisch; Chad Nusbaum; Eric S Lander; Bradley E Bernstein
Journal:  Nature       Date:  2007-07-01       Impact factor: 49.962

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  303 in total

1.  Epigenetic dysregulation of Oxtr in Tet1-deficient mice has implications for neuropsychiatric disorders.

Authors:  Aaron J Towers; Martine W Tremblay; Leeyup Chung; Xin-Lei Li; Alexandra L Bey; Wenhao Zhang; Xinyu Cao; Xiaoming Wang; Ping Wang; Lara J Duffney; Stephen K Siecinski; Sonia Xu; Yuna Kim; Xiangyin Kong; Simon Gregory; Wei Xie; Yong-Hui Jiang
Journal:  JCI Insight       Date:  2018-12-06

Review 2.  Epigenetic control on cell fate choice in neural stem cells.

Authors:  Xiao-Ling Hu; Yuping Wang; Qin Shen
Journal:  Protein Cell       Date:  2012-05-02       Impact factor: 14.870

3.  Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.

Authors:  Miao Yu; Gary C Hon; Keith E Szulwach; Chun-Xiao Song; Liang Zhang; Audrey Kim; Xuekun Li; Qing Dai; Yin Shen; Beomseok Park; Jung-Hyun Min; Peng Jin; Bing Ren; Chuan He
Journal:  Cell       Date:  2012-05-17       Impact factor: 41.582

4.  Effect of valproic acid on mitochondrial epigenetics.

Authors:  Hu Chen; Svetlana Dzitoyeva; Hari Manev
Journal:  Eur J Pharmacol       Date:  2012-06-20       Impact factor: 4.432

Review 5.  Epigenetic regulation of early neural fate commitment.

Authors:  Yunbo Qiao; Xianfa Yang; Naihe Jing
Journal:  Cell Mol Life Sci       Date:  2016-01-22       Impact factor: 9.261

6.  Hydrogen Sulfide Promotes Tet1- and Tet2-Mediated Foxp3 Demethylation to Drive Regulatory T Cell Differentiation and Maintain Immune Homeostasis.

Authors:  Ruili Yang; Cunye Qu; Yu Zhou; Joanne E Konkel; Shihong Shi; Yi Liu; Chider Chen; Shiyu Liu; Dawei Liu; Yibu Chen; Ebrahim Zandi; Wanjun Chen; Yanheng Zhou; Songtao Shi
Journal:  Immunity       Date:  2015-08-11       Impact factor: 31.745

Review 7.  The role of DNA methylation in aging, rejuvenation, and age-related disease.

Authors:  Adiv A Johnson; Kemal Akman; Stuart R G Calimport; Daniel Wuttke; Alexandra Stolzing; João Pedro de Magalhães
Journal:  Rejuvenation Res       Date:  2012-10       Impact factor: 4.663

Review 8.  Nucleic acid modifications with epigenetic significance.

Authors:  Ye Fu; Chuan He
Journal:  Curr Opin Chem Biol       Date:  2012-10-22       Impact factor: 8.822

Review 9.  Breathing-in epigenetic change with vitamin C.

Authors:  Asun Monfort; Anton Wutz
Journal:  EMBO Rep       Date:  2013-03-15       Impact factor: 8.807

Review 10.  5-Hydroxymethylcytosine: generation, fate, and genomic distribution.

Authors:  Li Shen; Yi Zhang
Journal:  Curr Opin Cell Biol       Date:  2013-03-13       Impact factor: 8.382

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