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PMID: 27797352 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications.

Nature plants ·Vol. 2 ·No. 11 ·2016-00-31 ·Pages 16169

Tang K, Lang Z, Zhang H, Zhu JK

Abstract

The Arabidopsis ROS1/DEMETER family of 5-methylcytosine (5mC) DNA glycosylases are the first genetically characterized DNA demethylases in eukaryotes. However, the features of ROS1-targeted genomic loci are not well understood. In this study, we characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. We found that ROS1 preferentially targets transposable elements (TEs) and intergenic regions. Compared with most TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting that ROS1 may prevent DNA methylation spreading from TEs to nearby genes. ROS1-targeted TEs are specifically enriched for H3K18Ac and H3K27me3, and depleted of H3K27me and H3K9me2. Importantly, we identified thousands of previously unknown RNA-directed DNA methylation (RdDM) targets following depletion of ROS1, suggesting that ROS1 strongly antagonizes RdDM at these loci. In addition, we show that ROS1 also antagonizes RdDM-independent DNA methylation at some loci. Our results provide important insights into the genome-wide targets of ROS1 and the crosstalk between DNA methylation and ROS1-mediated active DNA demethylation.

MeSH Terms
Arabidopsis/genetics,metabolism Arabidopsis Proteins/genetics,metabolism Chromatin/metabolism Demethylation Nuclear Proteins/genetics,metabolism
Chemicals
Arabidopsis Proteins Chromatin Nuclear Proteins ROS1 protein, Arabidopsis
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Tang Kai ORCID
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA.
Lang Zhaobo
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA. | Shanghai Centre for Plant Stress Biology, and Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
Zhang Heng
Shanghai Centre for Plant Stress Biology, and Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
Zhu Jian-Kang ORCID
Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA. | Shanghai Centre for Plant Stress Biology, and Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
Conflict of Interest

The authors declare no competing financial interests.

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Article Info
Journal
Nature plants
Abbr.
Nat Plants
ISSN
2055-0278
DOI
10.1038/nplants.2016.169
Published
2016-00-31
Epub
2016-00-31
Pages
16169
Language
English
Region
England
NLM ID
101651677
PMCID
PMC5123759
Subset
IM
Grants
NIGMS NIH HHS · R01 GM070795 · United States
Corrections
CommentIn
PMID: 27808234
External Links
PubMed source DOI: 10.1038/nplants.2016.169 PMC Full Text View journal details
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