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Elife. 2015 Jul 21;4. doi: 10.7554/eLife.09343.

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

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ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia.
State Key laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China.
Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, United States.
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.
Joint Research Laboratory in Genomics and Nutriomics, Zhejiang University, Hangzhou, China.


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.


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

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