YTHDC1 Mediates Nuclear Export of N6-methyladenosine Methylated mRNAs

  1. Ian A Roundtree
  2. Guan-Zheng Luo
  3. Zijie Zhang
  4. Xiao Wang
  5. Tao Zhou
  6. Yiquang Cui
  7. Jiahao Sha
  8. Xingxu Huang
  9. Laura Guerrero
  10. Phil Xie
  11. Emily He
  12. Bin Shen  Is a corresponding author
  13. Chuan He  Is a corresponding author
  1. University of Chicago, United States
  2. ShanghaiTech University, China
  3. Nanjing Medical University, China
  4. The University of Chicago, United States

Abstract

N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNA (mRNA), and plays critical roles in RNA biology. The function of this modification is mediated by m6A-selective 'reader' proteins of the YTH family, which incorporate m6A-modified mRNAs into pathways of RNA metabolism. Here, we show that the m6A-binding protein YTHDC1 mediates export of methylated mRNA from the nucleus to the cytoplasm in HeLa cells. Knockdown of YTHDC1 results in an extended residence time for nuclear m6A-containing mRNA, with an accumulation of transcripts in the nucleus and accompanying depletion within the cytoplasm. YTHDC1 interacts with the splicing factor and nuclear export adaptor protein SRSF3, and facilitates RNA binding to both SRSF3 and NXF1. This role for YTHDC1 expands the potential utility of chemical modification of mRNA, and supports an emerging paradigm of m6A as a distinct biochemical entity for selective processing and metabolism of mammalian mRNAs.

Data availability

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Ian A Roundtree

    Department of Chemistry, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Guan-Zheng Luo

    Department of Chemistry, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Zijie Zhang

    Department of Chemistry, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Xiao Wang

    Department of Chemistry, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Tao Zhou

    School of Life Science and Technology, ShanghaiTech University, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.
  6. Yiquang Cui

    State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.
  7. Jiahao Sha

    State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.
  8. Xingxu Huang

    School of Life Science and Technology, ShanghaiTech University, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.
  9. Laura Guerrero

    Department of Chemistry, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Phil Xie

    Department of Chemistry, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Emily He

    Department of Chemistry, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Bin Shen

    State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
    For correspondence
    binshen@njmu.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
  13. Chuan He

    Department of Chemistry, The University of Chicago, Chicago, United States
    For correspondence
    chuanhe@uchicago.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4319-7424

Funding

National Institute of General Medical Sciences (F30GM117646)

  • Ian A Roundtree

Howard Hughes Medical Institute

  • Ian A Roundtree
  • Guan-Zheng Luo
  • Zijie Zhang
  • Xiao Wang
  • Chuan He

National Science Foundation (CHE-1048528)

  • Ian A Roundtree
  • Guan-Zheng Luo
  • Zijie Zhang
  • Xiao Wang
  • Laura Guerrero
  • Phil Xie
  • Emily He
  • Chuan He

National Institute of General Medical Sciences (HG008688)

  • Chuan He

National Institute of General Medical Sciences (GM113194)

  • Chuan He

National Natural Science Foundation of China (31171377)

  • Xingxu Huang

National Natural Science Foundation of China (31471400)

  • Xingxu Huang

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2017, Roundtree et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 11,505
    views
  • 2,089
    downloads
  • 967
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Ian A Roundtree
  2. Guan-Zheng Luo
  3. Zijie Zhang
  4. Xiao Wang
  5. Tao Zhou
  6. Yiquang Cui
  7. Jiahao Sha
  8. Xingxu Huang
  9. Laura Guerrero
  10. Phil Xie
  11. Emily He
  12. Bin Shen
  13. Chuan He
(2017)
YTHDC1 Mediates Nuclear Export of N6-methyladenosine Methylated mRNAs
eLife 6:e31311.
https://doi.org/10.7554/eLife.31311

Share this article

https://doi.org/10.7554/eLife.31311

Further reading

    1. Biochemistry and Chemical Biology
    2. Computational and Systems Biology
    A Sofia F Oliveira, Fiona L Kearns ... Adrian J Mulholland
    Short Report

    The spike protein is essential to the SARS-CoV-2 virus life cycle, facilitating virus entry and mediating viral-host membrane fusion. The spike contains a fatty acid (FA) binding site between every two neighbouring receptor-binding domains. This site is coupled to key regions in the protein, but the impact of glycans on these allosteric effects has not been investigated. Using dynamical nonequilibrium molecular dynamics (D-NEMD) simulations, we explore the allosteric effects of the FA site in the fully glycosylated spike of the SARS-CoV-2 ancestral variant. Our results identify the allosteric networks connecting the FA site to functionally important regions in the protein, including the receptor-binding motif, an antigenic supersite in the N-terminal domain, the fusion peptide region, and another allosteric site known to bind heme and biliverdin. The networks identified here highlight the complexity of the allosteric modulation in this protein and reveal a striking and unexpected link between different allosteric sites. Comparison of the FA site connections from D-NEMD in the glycosylated and non-glycosylated spike revealed that glycans do not qualitatively change the internal allosteric pathways but can facilitate the transmission of the structural changes within and between subunits.

    1. Biochemistry and Chemical Biology
    2. Genetics and Genomics
    Conor J Howard, Nathan S Abell ... Nathan B Lubock
    Research Article

    Deep Mutational Scanning (DMS) is an emerging method to systematically test the functional consequences of thousands of sequence changes to a protein target in a single experiment. Because of its utility in interpreting both human variant effects and protein structure-function relationships, it holds substantial promise to improve drug discovery and clinical development. However, applications in this domain require improved experimental and analytical methods. To address this need, we report novel DMS methods to precisely and quantitatively interrogate disease-relevant mechanisms, protein-ligand interactions, and assess predicted response to drug treatment. Using these methods, we performed a DMS of the melanocortin-4 receptor (MC4R), a G-protein-coupled receptor (GPCR) implicated in obesity and an active target of drug development efforts. We assessed the effects of >6600 single amino acid substitutions on MC4R’s function across 18 distinct experimental conditions, resulting in >20 million unique measurements. From this, we identified variants that have unique effects on MC4R-mediated Gαs- and Gαq-signaling pathways, which could be used to design drugs that selectively bias MC4R’s activity. We also identified pathogenic variants that are likely amenable to a corrector therapy. Finally, we functionally characterized structural relationships that distinguish the binding of peptide versus small molecule ligands, which could guide compound optimization. Collectively, these results demonstrate that DMS is a powerful method to empower drug discovery and development.