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.

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Figure 1: Characterization of the DNA methylomes of ros1 mutants in Col-0 and C24 ecotypes.
Figure 2: Chromatin features associated with ROS1 targets.
Figure 3: Identification and characterization of type II RdDM targets.
Figure 4: Chromatin features associated with type I and type II RdDM targets.
Figure 5: Reduced ROS1 expression contributes to DNA hypermethylation in RdDM mutants.
Figure 6: ROS1 antagonizes RdDM-independent DNA methylation.

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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.).

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Authors

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.

Corresponding author

Correspondence to Zhaobo Lang.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figures 1–6 (PDF 1973 kb)

Supplementary Table 1

Table of the percentiles of the length of ROS1-targeted TEs and all TEs. (XLSX 38 kb)

Supplementary Table 2

Table of previously published data used in this study. (XLSX 37 kb)

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Tang, K., Lang, Z., Zhang, H. et al. The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications. Nature Plants 2, 16169 (2016). https://doi.org/10.1038/nplants.2016.169

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