1. Biochemistry and Chemical Biology
  2. Cell Biology

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
https://doi.org/10.7554/eLife.31311
Share this article
Cite this article
  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
  2. Download BibTeX
  3. Download .RIS

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.

Reviewing Editor

  1. Nick J Proudfoot, University of Oxford, United Kingdom

Version history

  1. Received: August 17, 2017
  2. Accepted: October 4, 2017
  3. Accepted Manuscript published: October 6, 2017 (version 1)
  4. Version of Record published: October 19, 2017 (version 2)

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

  • 10,299
    views
  • 1,922
    downloads
  • 785
    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

Categories and tags

Research organism

Further reading

    1. Biochemistry and Chemical Biology

    A multi-hierarchical approach reveals d-serine as a hidden substrate of sodium-coupled monocarboxylate transporters

    Pattama Wiriyasermkul, Satomi Moriyama ... Shushi Nagamori
    Research Article

    Transporter research primarily relies on the canonical substrates of well-established transporters. This approach has limitations when studying transporters for the low-abundant micromolecules, such as micronutrients, and may not reveal physiological functions of the transporters. While d-serine, a trace enantiomer of serine in the circulation, was discovered as an emerging biomarker of kidney function, its transport mechanisms in the periphery remain unknown. Here, using a multi-hierarchical approach from body fluids to molecules, combining multi-omics, cell-free synthetic biochemistry, and ex vivo transport analyses, we have identified two types of renal d-serine transport systems. We revealed that the small amino acid transporter ASCT2 serves as a d-serine transporter previously uncharacterized in the kidney and discovered d-serine as a non-canonical substrate of the sodium-coupled monocarboxylate transporters (SMCTs). These two systems are physiologically complementary, but ASCT2 dominates the role in the pathological condition. Our findings not only shed light on renal d-serine transport, but also clarify the importance of non-canonical substrate transport. This study provides a framework for investigating multiple transport systems of various trace micromolecules under physiological conditions and in multifactorial diseases.

    1. Biochemistry and Chemical Biology
    2. Cell Biology

    MEMO1 binds iron and modulates iron homeostasis in cancer cells

    Natalia Dolgova, Eva-Maria E Uhlemann ... Oleg Y Dmitriev
    Research Article

    Mediator of ERBB2-driven Cell Motility 1 (MEMO1) is an evolutionary conserved protein implicated in many biological processes; however, its primary molecular function remains unknown. Importantly, MEMO1 is overexpressed in many types of cancer and was shown to modulate breast cancer metastasis through altered cell motility. To better understand the function of MEMO1 in cancer cells, we analyzed genetic interactions of MEMO1 using gene essentiality data from 1028 cancer cell lines and found multiple iron-related genes exhibiting genetic relationships with MEMO1. We experimentally confirmed several interactions between MEMO1 and iron-related proteins in living cells, most notably, transferrin receptor 2 (TFR2), mitoferrin-2 (SLC25A28), and the global iron response regulator IRP1 (ACO1). These interactions indicate that cells with high MEMO1 expression levels are hypersensitive to the disruptions in iron distribution. Our data also indicate that MEMO1 is involved in ferroptosis and is linked to iron supply to mitochondria. We have found that purified MEMO1 binds iron with high affinity under redox conditions mimicking intracellular environment and solved MEMO1 structures in complex with iron and copper. Our work reveals that the iron coordination mode in MEMO1 is very similar to that of iron-containing extradiol dioxygenases, which also display a similar structural fold. We conclude that MEMO1 is an iron-binding protein that modulates iron homeostasis in cancer cells.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX

    Isabelle Petit-Hartlein, Annelise Vermot ... Franck Fieschi
    Research Article

    NADPH oxidases (NOX) are transmembrane proteins, widely spread in eukaryotes and prokaryotes, that produce reactive oxygen species (ROS). Eukaryotes use the ROS products for innate immune defense and signaling in critical (patho)physiological processes. Despite the recent structures of human NOX isoforms, the activation of electron transfer remains incompletely understood. SpNOX, a homolog from Streptococcus pneumoniae, can serves as a robust model for exploring electron transfers in the NOX family thanks to its constitutive activity. Crystal structures of SpNOX full-length and dehydrogenase (DH) domain constructs are revealed here. The isolated DH domain acts as a flavin reductase, and both constructs use either NADPH or NADH as substrate. Our findings suggest that hydride transfer from NAD(P)H to FAD is the rate-limiting step in electron transfer. We identify significance of F397 in nicotinamide access to flavin isoalloxazine and confirm flavin binding contributions from both DH and Transmembrane (TM) domains. Comparison with related enzymes suggests that distal access to heme may influence the final electron acceptor, while the relative position of DH and TM does not necessarily correlate with activity, contrary to previous suggestions. It rather suggests requirement of an internal rearrangement, within the DH domain, to switch from a resting to an active state. Thus, SpNOX appears to be a good model of active NOX2, which allows us to propose an explanation for NOX2’s requirement for activation.