Genetic interactions between DNA demethylation and methylation in Arabidopsis.
DNA demethylation in Arabidopsis (Arabidopsis thaliana) is mediated by DNA glycosylases of the DEMETER family. Three DEMETER-LIKE (DML) proteins, REPRESSOR OF SILENCING1 (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 and generally contain sequence repeats, transposons, or both. The most common class of small interfering RNAs was 24 nucleotides long, suggesting a role for an RNAi pathway that depends on RNA-DEPENDENT RNA POLYMERASE2 (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.
Penterman
Jon
J
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.
Uzawa
Rie
R
Fischer
Robert L
RL
D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000378:metabolism*; D060565:Argonaute Proteins; D045647:DNA Glycosylases / Q000378:metabolism*; D019175:DNA Methylation; D004251:DNA Transposable Elements; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D015536:Down-Regulation; D009154:Mutation; D009687:Nuclear Proteins / Q000378:metabolism*; D034622:RNA Interference; D034741:RNA, Small Interfering; D012324:RNA-Dependent RNA Polymerase / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid; D043244:Ribonuclease III / Q000378:metabolism
C471209:AGO4 protein, Arabidopsis; D029681:Arabidopsis Proteins; D060565:Argonaute Proteins; D004251:DNA Transposable Elements; D009687:Nuclear Proteins; D034741:RNA, Small Interfering; C471271:ROS1 protein, Arabidopsis; C499181:RNA polymerase IV, Arabidopsis; C519655:RDR2 protein, Arabidopsis; D012324:RNA-Dependent RNA Polymerase; D012321:DNA-Directed RNA Polymerases; C519654:DCL3 protein, Arabidopsis; D043244:Ribonuclease III; C519856:DML2 protein, Arabidopsis; C519857:DML3 protein, Arabidopsis; D045647:DNA Glycosylases