Literature DB >> 33658714

The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity.

Jiadong Liu1,2,3, Mingwei Gao1,2,3, Jiangping He4, Kaixin Wu1,5,6, Siyuan Lin1,2, Lingmei Jin1,2,3, Yaping Chen1,2,3, He Liu4,7, Junjie Shi1,2,3, Xiwei Wang4, Lei Chang4, Yingying Lin8, Yu-Li Zhao9, Xiaofei Zhang1,2,4, Man Zhang4, Guan-Zheng Luo9, Guangming Wu4, Duanqing Pei1,4,10, Jie Wang1,2, Xichen Bao1,2,4, Jiekai Chen11,12,13,14,15.   

Abstract

The RNA modification N6-methyladenosine (m6A) has critical roles in many biological processes1,2. However, the function of m6A in the early phase of mammalian development remains poorly understood. Here we show that the m6A reader YT521-B homology-domain-containing protein 1 (YTHDC1) is required for the maintenance of mouse embryonic stem (ES) cells in an m6A-dependent manner, and that its deletion initiates cellular reprogramming to a 2C-like state. Mechanistically, YTHDC1 binds to the transcripts of retrotransposons (such as intracisternal A particles, ERVK and LINE1) in mouse ES cells and its depletion results in the reactivation of these silenced retrotransposons, accompanied by a global decrease in SETDB1-mediated trimethylation at lysine 9 of histone H3 (H3K9me3). We further demonstrate that YTHDC1 and its target m6A RNAs act upstream of SETDB1 to repress retrotransposons and Dux, the master inducer of the two-cell stage (2C)-like program. This study reveals an essential role for m6A RNA and YTHDC1 in chromatin modification and retrotransposon repression.

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Year:  2021        PMID: 33658714     DOI: 10.1038/s41586-021-03313-9

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  52 in total

1.  Stem cells. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation.

Authors:  Shay Geula; Sharon Moshitch-Moshkovitz; Dan Dominissini; Abed AlFatah Mansour; Nitzan Kol; Mali Salmon-Divon; Vera Hershkovitz; Eyal Peer; Nofar Mor; Yair S Manor; Moshe Shay Ben-Haim; Eran Eyal; Sharon Yunger; Yishay Pinto; Diego Adhemar Jaitin; Sergey Viukov; Yoach Rais; Vladislav Krupalnik; Elad Chomsky; Mirie Zerbib; Itay Maza; Yoav Rechavi; Rada Massarwa; Suhair Hanna; Ido Amit; Erez Y Levanon; Ninette Amariglio; Noam Stern-Ginossar; Noa Novershtern; Gideon Rechavi; Jacob H Hanna
Journal:  Science       Date:  2015-01-01       Impact factor: 47.728

2.  Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain.

Authors:  Shukun Luo; Liang Tong
Journal:  Proc Natl Acad Sci U S A       Date:  2014-09-08       Impact factor: 11.205

Review 3.  Gene expression regulation mediated through reversible m⁶A RNA methylation.

Authors:  Ye Fu; Dan Dominissini; Gideon Rechavi; Chuan He
Journal:  Nat Rev Genet       Date:  2014-03-25       Impact factor: 53.242

4.  Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain.

Authors:  Chao Xu; Xiao Wang; Ke Liu; Ian A Roundtree; Wolfram Tempel; Yanjun Li; Zhike Lu; Chuan He; Jinrong Min
Journal:  Nat Chem Biol       Date:  2014-09-21       Impact factor: 15.040

5.  YTHDF2/3 Are Required for Somatic Reprogramming through Different RNA Deadenylation Pathways.

Authors:  Jiadong Liu; Mingwei Gao; Shuyang Xu; Yaping Chen; Kaixin Wu; He Liu; Jie Wang; Xuejie Yang; Junwei Wang; Weiwei Liu; Xichen Bao; Jiekai Chen
Journal:  Cell Rep       Date:  2020-09-08       Impact factor: 9.423

Review 6.  Reading, writing and erasing mRNA methylation.

Authors:  Sara Zaccara; Ryan J Ries; Samie R Jaffrey
Journal:  Nat Rev Mol Cell Biol       Date:  2019-09-13       Impact factor: 94.444

Review 7.  Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism.

Authors:  Ying Yang; Phillip J Hsu; Yu-Sheng Chen; Yun-Gui Yang
Journal:  Cell Res       Date:  2018-05-22       Impact factor: 25.617

8.  Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development.

Authors:  Seth D Kasowitz; Jun Ma; Stephen J Anderson; N Adrian Leu; Yang Xu; Brian D Gregory; Richard M Schultz; P Jeremy Wang
Journal:  PLoS Genet       Date:  2018-05-25       Impact factor: 5.917

9.  m6A facilitates hippocampus-dependent learning and memory through YTHDF1.

Authors:  Hailing Shi; Xuliang Zhang; Yi-Lan Weng; Hongjun Song; Chuan He; Tao Zhou; Zongyang Lu; Yajing Liu; Zhike Lu; Jianan Li; Piliang Hao; Yu Zhang; Feng Zhang; You Wu; Jary Y Delgado; Yijing Su; Meera J Patel; Xiaohua Cao; Bin Shen; Xingxu Huang; Guo-Li Ming; Xiaoxi Zhuang
Journal:  Nature       Date:  2018-10-31       Impact factor: 49.962

10.  The RNA m6A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence.

Authors:  Ivayla Ivanova; Christian Much; Monica Di Giacomo; Chiara Azzi; Marcos Morgan; Pedro N Moreira; Jack Monahan; Claudia Carrieri; Anton J Enright; Dónal O'Carroll
Journal:  Mol Cell       Date:  2017-08-31       Impact factor: 17.970

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  53 in total

1.  Dynamic control of chromatin-associated m6A methylation regulates nascent RNA synthesis.

Authors:  Wenqi Xu; Chenxi He; Emily G Kaye; Jiahui Li; Mandi Mu; Geoffrey M Nelson; Li Dong; Jiahua Wang; Feizhen Wu; Yujiang Geno Shi; Karen Adelman; Fei Lan; Yang Shi; Hongjie Shen
Journal:  Mol Cell       Date:  2022-02-25       Impact factor: 17.970

2.  Estimating the prognosis of esophageal squamous cell carcinoma based on The Cancer Genome Atlas (TCGA) of m6A methylation-associated genes.

Authors:  Yu Pu; Xianfeng Lu; Xueqin Yang; Yi Yang; Dong Wang; Mengxia Li; Wei Guan; Mingfang Xu
Journal:  J Gastrointest Oncol       Date:  2022-02

Review 3.  Epigenetics as "conductor" in "orchestra" of pluripotent states.

Authors:  Ishita Baral; Pallavi Chinnu Varghese; Debasree Dutta
Journal:  Cell Tissue Res       Date:  2022-07-15       Impact factor: 4.051

4.  Histone H1 regulates non-coding RNA turnover on chromatin in a m6A-dependent manner.

Authors:  José Miguel Fernández-Justel; Cristina Santa-María; Sara Martín-Vírgala; Shreya Ramesh; Alberto Ferrera-Lagoa; Mónica Salinas-Pena; Javier Isoler-Alcaraz; Magdalena M Maslon; Albert Jordan; Javier F Cáceres; María Gómez
Journal:  Cell Rep       Date:  2022-09-13       Impact factor: 9.995

Review 5.  Hidden codes in mRNA: Control of gene expression by m6A.

Authors:  Shino Murakami; Samie R Jaffrey
Journal:  Mol Cell       Date:  2022-06-16       Impact factor: 19.328

6.  Nuclear m6A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos.

Authors:  Chuan Chen; Wenqiang Liu; Jiayin Guo; Yuanyuan Liu; Xuelian Liu; Jun Liu; Xiaoyang Dou; Rongrong Le; Yixin Huang; Chong Li; Lingyue Yang; Xiaochen Kou; Yanhong Zhao; You Wu; Jiayu Chen; Hong Wang; Bin Shen; Yawei Gao; Shaorong Gao
Journal:  Protein Cell       Date:  2021-04-22       Impact factor: 14.870

7.  RNA demethylation increases the yield and biomass of rice and potato plants in field trials.

Authors:  Qiong Yu; Shun Liu; Lu Yu; Yu Xiao; Shasha Zhang; Xueping Wang; Yingying Xu; Hong Yu; Yulong Li; Junbo Yang; Jun Tang; Hong-Chao Duan; Lian-Huan Wei; Haiyan Zhang; Jiangbo Wei; Qian Tang; Chunling Wang; Wutong Zhang; Ye Wang; Peizhe Song; Qiang Lu; Wei Zhang; Shunqing Dong; Baoan Song; Chuan He; Guifang Jia
Journal:  Nat Biotechnol       Date:  2021-07-22       Impact factor: 68.164

8.  p53 convergently activates Dux/DUX4 in embryonic stem cells and in facioscapulohumeral muscular dystrophy cell models.

Authors:  Bradley D Weaver; Christina M Smith; Edward J Grow; Jingtao Guo; Paula Stein; Sean C Shadle; Peter G Hendrickson; Nicholas E Johnson; Russell J Butterfield; Roberta Menafra; Susan L Kloet; Silvère M van der Maarel; Carmen J Williams; Bradley R Cairns
Journal:  Nat Genet       Date:  2021-07-15       Impact factor: 38.330

9.  N6-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation.

Authors:  Yuanming Cheng; Wei Xie; Brian F Pickering; Karen L Chu; Angela M Savino; Xuejing Yang; Hanzhi Luo; Diu Tt Nguyen; Shanlan Mo; Ersilia Barin; Anthony Velleca; Thomas M Rohwetter; Dinshaw J Patel; Samie R Jaffrey; Michael G Kharas
Journal:  Cancer Cell       Date:  2021-05-27       Impact factor: 38.585

10.  RNA methylation preserves ES cell identity by chromatin silencing of retrotransposons.

Authors:  Zhaofa Xu; Annabel Ma; Yongchao C Ma
Journal:  Signal Transduct Target Ther       Date:  2021-07-07
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