Zc3h13 Regulates Nuclear RNA m6A Methylation and Mouse Embryonic Stem Cell Self-Renewal

Jing Wen; Ruitu Lv; Honghui Ma; Hongjie Shen; Chenxi He; Jiahua Wang; Fangfang Jiao; Hang Liu; Pengyuan Yang; Li Tan; Fei Lan; Yujiang Geno Shi; Chuan He; Yang Shi; Jianbo Diao

doi:10.1016/j.molcel.2018.02.015

Zc3h13 Regulates Nuclear RNA m⁶A Methylation and Mouse Embryonic Stem Cell Self-Renewal

Mol Cell. 2018 Mar 15;69(6):1028-1038.e6. doi: 10.1016/j.molcel.2018.02.015.

Authors

Jing Wen¹, Ruitu Lv¹, Honghui Ma¹, Hongjie Shen¹, Chenxi He¹, Jiahua Wang¹, Fangfang Jiao¹, Hang Liu¹, Pengyuan Yang², Li Tan¹, Fei Lan³, Yujiang Geno Shi⁴, Chuan He⁵, Yang Shi⁶, Jianbo Diao⁷

Affiliations

¹ Institute of Clinical Science, Zhongshan Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China.
² Department of Systems Biology, Institutes of Biomedical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China.
³ Institute of Clinical Science, Zhongshan Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China; Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai 201102, China.
⁴ Institute of Clinical Science, Zhongshan Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China; Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai 201102, China; Division of Endocrinology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. Electronic address: yujiang_shi@hms.harvard.edu.
⁵ Department of Chemistry, and Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA. Electronic address: chuanhe@uchicago.edu.
⁶ Institute of Clinical Science, Zhongshan Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China; Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai 201102, China; Newborn Medicine Division, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: yshi@hms.harvard.edu.
⁷ Institute of Clinical Science, Zhongshan Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China; Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, China. Electronic address: diao2010@gmail.com.

Abstract

N⁶-methyladenosine (m⁶A) is an abundant modification in eukaryotic mRNA, regulating mRNA dynamics by influencing mRNA stability, splicing, export, and translation. However, the precise m⁶A regulating machinery still remains incompletely understood. Here we demonstrate that ZC3H13, a zinc-finger protein, plays an important role in modulating RNA m⁶A methylation in the nucleus. We show that knockdown of Zc3h13 in mouse embryonic stem cell significantly decreases global m⁶A level on mRNA. Upon Zc3h13 knockdown, a great majority of WTAP, Virilizer, and Hakai translocate to the cytoplasm, suggesting that Zc3h13 is required for nuclear localization of the Zc3h13-WTAP-Virilizer-Hakai complex, which is important for RNA m⁶A methylation. Finally, Zc3h13 depletion, as does WTAP, Virilizer, or Hakai, impairs self-renewal and triggers mESC differentiation. Taken together, our findings demonstrate that Zc3h13 plays a critical role in anchoring WTAP, Virilizer, and Hakai in the nucleus to facilitate m⁶A methylation and to regulate mESC self-renewal.

Keywords: Zc3h13; m(6)A; mESC self-renewal; nuclear localization.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

3' Untranslated Regions
Active Transport, Cell Nucleus
Adenosine / analogs & derivatives*
Adenosine / metabolism
Animals
Carrier Proteins / genetics
Carrier Proteins / metabolism
Cell Cycle Proteins
Cell Differentiation
Cell Nucleus / metabolism*
Cell Proliferation*
Cell Self Renewal*
DNA-Binding Proteins / genetics
DNA-Binding Proteins / metabolism
Gene Expression Regulation, Developmental
HEK293 Cells
Humans
Methylation
Mice
Mouse Embryonic Stem Cells / metabolism*
Nuclear Proteins / genetics
Nuclear Proteins / metabolism*
RNA Processing, Post-Transcriptional*
RNA Splicing Factors
RNA Stability
RNA, Messenger / genetics
RNA, Messenger / metabolism*
RNA-Binding Proteins
Signal Transduction
Ubiquitin-Protein Ligases / genetics
Ubiquitin-Protein Ligases / metabolism

Substances

3' Untranslated Regions
Carrier Proteins
Cell Cycle Proteins
DNA-Binding Proteins
Nuclear Proteins
RNA Splicing Factors
RNA, Messenger
RNA-Binding Proteins
Wtap protein, mouse
Zc3h13 protein, mouse
N-methyladenosine
Ubiquitin-Protein Ligases
Adenosine

Abstract

Publication types

MeSH terms

Substances

Grants and funding