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Jul 21, 2015;4

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

David Secco, Chuang Wang, Huixia Shou, Matthew D Schultz, Serge Chiarenza, Laurent Nussaume, Joseph R Ecker, James Whelan, Ryan Lister
Author Information
  1. David Secco: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.
  2. Chuang Wang: State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China.
  3. Huixia Shou: State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China.
  4. Matthew D Schultz: Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States.
  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.
  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.
  7. Joseph R Ecker: Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States.
  8. James Whelan: Joint Research Laboratory in Genomics and Nutriomics, Zhejiang University, Hangzhou, China.
  9. Ryan Lister: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.
PMID: 26196146 DOI: 10.7554/eLife.09343

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, and 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.

Keywords

DNA methylation arabidopsis epigenome evolutionary biology genomics nutrient stress phosphate starvation plant biology rice transcriptome

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MeSH Term

5-Methylcytosine
Arabidopsis
DNA Methylation
DNA, Plant
Gene Expression Regulation
Genome, Plant
Oryza
Phosphates
Regulatory Elements, Transcriptional
Sequence Analysis, DNA
Stress, Physiological

Chemicals

DNA, Plant
Phosphates
5-Methylcytosine
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

GEN: GEND000299 (Stranded RNA-seq and methylomes for the rice DCL3a RNAi experiment)
GEN: GEND000300 (Stranded RNA-seq for rice after 3, 24 and 52 days of Pi stress)

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