DNA demethylation in the Arabidopsis genome

Cytosine DNA methylation is considered to be a stable epigenetic mark, but active demethylation has been observed in both plants and animals. In Arabidopsis thaliana, DNA glycosylases of the DEMETER (DIVIE) family remove methylcytosines from DNA. Demethylation by DME is necessary for genomic imprinting, and clemethylation by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic background. However, the extent and function of clemethylation by DEMETER-LIKE (DML) proteins in WT plants is not known. Using genome-tiling microarrays, we mapped DNA methylation in mutant and WT plants and identified 179 loci actively demethylated by DML enzymes. Mutations in DIML genes lead to locus-specific DNA hypermethylation. Reintroducing WT DML genes restores most loci to the normal pattern of methylation, although at some loci, hypermethylated epialleles persist. Of loci clemethylated by DMI-enzymes, > 80% are near or overlap genes. Genic demethylation by DML enzymes primarily occurs at the 5' and 3' ends, a pattern opposite to the overall distribution of VVT DNA methylation. Our results show that clemethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes f rom potentially deleterious methylation.