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N6-methyladenosine-dependent regulation of messenger RNA stability

Nature volume 505, pages 117120 (02 January 2014) | Download Citation

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Abstract

N6-methyladenosine (m6A) is the most prevalent internal (non-cap) modification present in the messenger RNA of all higher eukaryotes1,2. Although essential to cell viability and development3,4,5, the exact role of m6A modification remains to be determined. The recent discovery of two m6A demethylases in mammalian cells highlighted the importance of m6A in basic biological functions and disease6,7,8. Here we show that m6A is selectively recognized by the human YTH domain family 2 (YTHDF2) ‘reader’ protein to regulate mRNA degradation. We identified over 3,000 cellular RNA targets of YTHDF2, most of which are mRNAs, but which also include non-coding RNAs, with a conserved core motif of G(m6A)C. We further establish the role of YTHDF2 in RNA metabolism, showing that binding of YTHDF2 results in the localization of bound mRNA from the translatable pool to mRNA decay sites, such as processing bodies9. The carboxy-terminal domain of YTHDF2 selectively binds to m6A-containing mRNA, whereas the amino-terminal domain is responsible for the localization of the YTHDF2–mRNA complex to cellular RNA decay sites. Our results indicate that the dynamic m6A modification is recognized by selectively binding proteins to affect the translation status and lifetime of mRNA.

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Change history

  • 01 January 2014

    Minor changes were made to the Author Information section.

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Referenced accessions

Gene Expression Omnibus

Data deposits

RNA sequencing data were deposited in the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under accession number GSE49339 and the processed results were presented as Supplementary Table 1. Processed files were deposited in the Gene Expression Omnibus under accession no. GSE46705.

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Acknowledgements

This work is supported by National Institutes of Health GM071440 (C.H.) and EUREKA GM088599 (T.P. and C.H.). The Mass Spectrometry Facility of the University of Chicago is funded by National Science Foundation (CHE-1048528). We thank A. E. Kulozik, W. Filipowicz and J. A. Steitz for providing the sequence and plasmids of the tether reporter. We thank Dr. G. Zheng and W. Clark for help in polysome profiling. We also thank S. F. Reichard for editing the manuscript.

Author information

Affiliations

  1. Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA

    • Xiao Wang
    • , Zhike Lu
    • , Adrian Gomez
    • , Yanan Yue
    • , Dali Han
    • , Ye Fu
    • , Qing Dai
    • , Guifang Jia
    •  & Chuan He
  2. Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, UCSD Moores Cancer Center and Institute of Genome Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA

    • Gary C. Hon
    •  & Bing Ren
  3. Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA

    • Marc Parisien
    •  & Tao Pan
  4. Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China

    • Guifang Jia

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Contributions

C.H. conceived the project. X.W. designed and performed most experiments. Z.L. and X.W. performed data analyses of high-throughput sequencing data. A.G. assisted with the experiments. Y.Y. and D.H. conducted the experimental and data analysis part of m6A profiling, respectively. Y.F. performed the RNA-affinity pull-down experiment of YTHDF1 and YTHDF3. M.P. and G.J. provided valuable discussions. G.C.H. and B.R. performed high throughput sequencing. Q.D. assisted in m6A synthesis. X.W. and C.H. interpreted the results and wrote the manuscript with input from T.P.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Chuan He.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Data

    This file contains processed results of RNA sequencing data.

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DOI

https://doi.org/10.1038/nature12730

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