Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
- The University of Western Australia, Australia
- Zhejiang University, China
- Salk Institute for Biological Studies, United States
- Université d'Aix-Marseille, France
- 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
Reviewing Editor
- Detlef Weigel, Max Planck Institute for Developmental Biology, Germany
Version history
- Received: June 10, 2015
- Accepted: July 20, 2015
- Accepted Manuscript published: July 21, 2015 (version 1)
- 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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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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