Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

  1. David Secco
  2. Chuang Wang
  3. Huixia Shou
  4. Matthew D Schultz
  5. Serge Chiarenza
  6. Laurent Nussaume
  7. Joseph R Ecker
  8. James Whelan
  9. Ryan Lister  Is a corresponding author
  1. The University of Western Australia, Australia
  2. Zhejiang University, China
  3. Salk Institute for Biological Studies, United States
  4. Université d'Aix-Marseille, France
  5. La Trobe University, Australia

Abstract

Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes in mC occurred after changes in nearby gene transcription, were mostly DCL3a-independent, could partially be propagated through mitosis, however no evidence of meiotic transmission was observed. Similar analyses performed in Arabidopsis revealed a very limited effect of phosphate starvation on mC, suggesting a species-specific mechanism. Overall, this suggests that TEs in proximity to environmentally induced genes are silenced via hypermethylation, and establishes the temporal hierarchy of transcriptional and epigenomic changes in response to stress.

Article and author information

Author details

  1. David Secco

    ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
    Competing interests
    The authors declare that no competing interests exist.
  2. Chuang Wang

    State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  3. Huixia Shou

    State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China
    Competing interests
    The authors declare that no competing interests exist.
  4. Matthew D Schultz

    Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Serge Chiarenza

    UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes, Université d'Aix-Marseille, Saint-Paul-lez-Durance, France
    Competing interests
    The authors declare that no competing interests exist.
  6. Laurent Nussaume

    UMR 6191 CEA, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement des Plantes, Université d'Aix-Marseille, Saint-Paul-lez-Durance, France
    Competing interests
    The authors declare that no competing interests exist.
  7. Joseph R Ecker

    Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. James Whelan

    Department of Botany, School of Life Science, ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Australia
    Competing interests
    The authors declare that no competing interests exist.
  9. Ryan Lister

    ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
    For correspondence
    ryanlister@gmail.com
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Detlef Weigel, Max Planck Institute for Developmental Biology, Germany

Publication history

  1. Received: June 10, 2015
  2. Accepted: July 20, 2015
  3. Accepted Manuscript published: July 21, 2015 (version 1)
  4. Version of Record published: August 18, 2015 (version 2)

Copyright

© 2015, Secco 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. David Secco
  2. Chuang Wang
  3. Huixia Shou
  4. Matthew D Schultz
  5. Serge Chiarenza
  6. Laurent Nussaume
  7. Joseph R Ecker
  8. James Whelan
  9. Ryan Lister
(2015)
Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
eLife 4:e09343.
https://doi.org/10.7554/eLife.09343
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