The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status

  1. Dongming Li
  2. Ana Marie S Palanca
  3. So Youn Won
  4. Lei Gao
  5. Ying Feng
  6. Ajay A Vashisht
  7. Li Liu
  8. Yuanyuan Zhao
  9. Xigang Liu
  10. Xiuyun Wu
  11. Shaofang Li
  12. Brandon Le
  13. Yun Ju Kim
  14. Guodong Yang
  15. Shengben Li
  16. Jinyuan Liu
  17. James A Wohlschlegel
  18. Hongwei Guo
  19. Beixin Mo
  20. Xuemei Chen  Is a corresponding author
  21. Julie A Law  Is a corresponding author
  1. University of California, Riverside, United States
  2. Salk Institute for Biological Studies, United States
  3. Rural Development Administration, Republic of Korea
  4. David Geffen School of Medicine at UCLA, United States
  5. Tsinghua University, China
  6. Peking University, China
  7. Shenzhen University, China

Abstract

DNA methylation is associated with gene silencing in eukaryotic organisms. Although pathways controlling the establishment, maintenance and removal of DNA methylation are known, relatively little is understood about how DNA methylation influences gene expression. Here we identified a METHYL-CpG-BINDING DOMAIN 7 (MBD7) complex in Arabidopsis thaliana that suppresses the transcriptional silencing of two LUCIFERASE (LUC) reporters via a mechanism that is largely downstream of DNA methylation. Although mutations in components of the MBD7 complex resulted in modest increases in DNA methylation concomitant with decreased LUC expression, we found that these hyper-methylation and gene expression phenotypes can be genetically uncoupled. This finding, along with genome-wide profiling experiments showing minimal changes in DNA methylation upon disruption of the MBD7 complex, places the MBD7 complex amongst a small number of factors acting downstream of DNA methylation. This complex, however, is unique as it functions to suppress, rather than enforce, DNA methylation-mediated gene silencing.

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The following data sets were generated

Article and author information

Author details

  1. Dongming Li

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Ana Marie S Palanca

    Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. So Youn Won

    National Academy of Agricultural Science, Rural Development Administration, Suwon, Republic of Korea
    Competing interests
    The authors declare that no competing interests exist.
  4. Lei Gao

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Ying Feng

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Ajay A Vashisht

    Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Li Liu

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Yuanyuan Zhao

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Xigang Liu

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Xiuyun Wu

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Shaofang Li

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Brandon Le

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Yun Ju Kim

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Guodong Yang

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Shengben Li

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    Competing interests
    The authors declare that no competing interests exist.
  16. Jinyuan Liu

    Laboratory of Molecular Biology and Protein Science, Tsinghua University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  17. James A Wohlschlegel

    Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Hongwei Guo

    State Key Laboratory of Protein and Plant Gene research, Peking University, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.
  19. Beixin Mo

    College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
    Competing interests
    The authors declare that no competing interests exist.
  20. Xuemei Chen

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, United States
    For correspondence
    xuemei.chen@ucr.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5209-1157
  21. Julie A Law

    Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
    For correspondence
    jlaw@salk.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7472-7753

Funding

Gordon and Betty Moore Foundation (GBMF3046)

  • Xuemei Chen

National Science Foundation of China (91440105)

  • Xuemei Chen

National Science Foundation of China (30970265)

  • Beixin Mo

National Science Foundation of China (31210103901)

  • Beixin Mo

Guangdong Innovation Research Team Fund (2014ZT05S078)

  • Xuemei Chen

National Institutes of Health (GM061146)

  • Xuemei Chen

National Academy of Agricultural Science (PJ008725)

  • So Youn Won

China Scholarship Council

  • Dongming Li

Glenn Center for Aging Research at the Salk Institute

  • Ana Marie S Palanca

Helmsley Charitable Trust

  • Ana Marie S Palanca
  • Julie A Law

National Institutes of Health (GM112966)

  • Julie A Law

National Institutes of Health (GM089778)

  • James A Wohlschlegel

National Institutes of Health (P30 014195)

  • Ana Marie S Palanca
  • Julie A Law

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

Reviewing Editor

  1. Steven Henikoff, Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, United States

Publication history

  1. Received: July 25, 2016
  2. Accepted: April 24, 2017
  3. Accepted Manuscript published: April 28, 2017 (version 1)
  4. Version of Record published: June 7, 2017 (version 2)

Copyright

© 2017, Li 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.

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  1. Dongming Li
  2. Ana Marie S Palanca
  3. So Youn Won
  4. Lei Gao
  5. Ying Feng
  6. Ajay A Vashisht
  7. Li Liu
  8. Yuanyuan Zhao
  9. Xigang Liu
  10. Xiuyun Wu
  11. Shaofang Li
  12. Brandon Le
  13. Yun Ju Kim
  14. Guodong Yang
  15. Shengben Li
  16. Jinyuan Liu
  17. James A Wohlschlegel
  18. Hongwei Guo
  19. Beixin Mo
  20. Xuemei Chen
  21. Julie A Law
(2017)
The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status
eLife 6:e19893.
https://doi.org/10.7554/eLife.19893

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