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Published on October 19, 2007; 10.1104/pp.107.107730

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Received August 21, 2007
Accepted September 24, 2007

Genetic Interactions between DNA demethylation and methylation in Arabidopsis thaliana

Jon Penterman , Rie Uzawa , and Robert L. Fischer *

Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA

* Corresponding author; email: rfischer{at}berkeley.edu.

DNA demethylation in Arabidopsis is mediated by DNA glycosylases of the DEMETER (DME) family. Three DEMETER-LIKE proteins, REPRESSOR OF SILENCING 1 (ROS1), DML2, and DML3, function to protect genes from potentially deleterious methylation. In Arabidopsis, much of the DNA methylation is directed by RNA interference (RNAi) pathways and used to defend the genome from transposable elements and their remnants, repetitive sequences. Here we investigated the relationship between DML demethylation and RNAi-mediated DNA methylation. We found that genic regions demethylated by DML enzymes are enriched for small interfering RNAs (siRNAs) and generally contain sequence repeats, transposons, or both. The most common class of siRNA was 24-nucleotides long, suggesting a role for an RNAi pathway that depends on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2). We show that ROS1 removes methylation that has multiple, independent origins, including de novo methylation directed by RDR2-dependent and independent RNAi pathways. Interestingly, in rdr2 and drm2 mutant plants, we found that genes demethylated by ROS1 accumulate CG methylation, and we propose that this hypermethylation is due to the ROS1 down-regulation that occurs in these mutant backgrounds. Our observations support the hypothesis that DNA demethylation by DML enzymes is one mechanism by which Arabidopsis genes are protected from genome defense pathways.




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