title: The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications.
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.
authors: Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA.
authors: Kai
authors: 0000-0003-3913-6426
authors: K
authors: Tang
authors: 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.
authors: Zhaobo
authors: Z
authors: Lang
authors: Shanghai Centre for Plant Stress Biology, and Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
authors: Heng
authors: H
authors: Zhang
authors: 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.
authors: Jian-Kang
authors: 0000-0001-5134-731X
authors: JK
authors: Zhu
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism*; D000073398:Demethylation; D009687:Nuclear Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D009687:Nuclear Proteins; C471271:ROS1 protein, Arabidopsis