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 (DME) family remove methylcytosines from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic background. However, the extent and function of demethylation 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 DML 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 demethylated by DML 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 WT DNA methylation. Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation.
Penterman
Jon
J
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
Zilberman
Daniel
D
Huh
Jin Hoe
JH
Ballinger
Tracy
T
Henikoff
Steven
S
Fischer
Robert L
RL
D044503:5-Methylcytosine / Q000378:metabolism; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D045647:DNA Glycosylases / Q000235:genetics; D019175:DNA Methylation; D018744:DNA, Plant / Q000378:metabolism*; D005819:Genetic Markers; D018745:Genome, Plant; D018392:Genomic Imprinting; D009699:N-Glycosyl Hydrolases / Q000235:genetics; D015534:Trans-Activators / Q000235:genetics
D029681:Arabidopsis Proteins; D018744:DNA, Plant; D005819:Genetic Markers; D015534:Trans-Activators; D044503:5-Methylcytosine; C463261:DEMETER protein, Arabidopsis; C519856:DML2 protein, Arabidopsis; C519857:DML3 protein, Arabidopsis; D045647:DNA Glycosylases; D009699:N-Glycosyl Hydrolases