Article

The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications

  • Nature Plants 2, Article number: 16169 (2016)
  • doi:10.1038/nplants.2016.169
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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.

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Acknowledgements

This work was supported by National Institutes of Health Grant R01GM070795 and by the Chinese Academy of Sciences (to J.-K. Z.).

Author information

Author notes

    • Kai Tang
    •  & Zhaobo Lang

    These authors contributed equally to this work.

Affiliations

  1. Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA

    • Kai Tang
    • , Zhaobo Lang
    •  & Jian-Kang Zhu
  2. Shanghai Centre for Plant Stress Biology, and Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China

    • Zhaobo Lang
    • , Heng Zhang
    •  & Jian-Kang Zhu

Authors

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Contributions

J.-K.Z, Z.L. and K.T. designed the study, interpreted the data and wrote the manuscript. K.T. and Z.L. did the bioinformatics analysis. H.Z. performed sequencing experiments.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Zhaobo Lang.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    Supplementary Figures 1–6

Excel files

  1. 1.

    Supplementary Table 1

    Table of the percentiles of the length of ROS1-targeted TEs and all TEs.

  2. 2.

    Supplementary Table 2

    Table of previously published data used in this study.