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

The Arabidopsis family of 5-methylcytosine (5mC) DNA glycosylases are the first genetically characterized DNA demethylases in eukaryotes. However, the features of genomic loci are not well understood. In this study, we characterized target loci in Arabidopsis Col-0 and C24 ecotypes. We found that duanyu16701 preferentially targets transposable elements (TEs) and intergenic regions. Compared with most TEs, duanyu16701-targeted TEs are closer to protein coding genes, suggesting that duanyu16701 may prevent DNA methylation spreading from TEs to nearby genes. duanyu16701-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 suggesting that duanyu16701 strongly antagonizes RdDM at these loci. In addition, we show that duanyu16701 also antagonizes RdDM-independent DNA methylation at some loci. Our results provide important insights into the genome-wide targets of duanyu16701 and the crosstalk between DNA methylation and active DNA demethylation.

KEYWORDS: {{ getKeywords(articleDetailText.words) }}