DNA methylation in Arabidopsis is found in different target sequences, besides of the CpG dinucleotide. The DNA demethylation process is very active and it is mediated by the DEMETER (DME) family if helix- hairpin- helix DNA glycosilases, that also have an additional apurinic/apyrimidinic (AP) lyase activity. This family has four known members: DME, REPRESSOR OF SILENCING1 (ROS1, a DME homolog), DEMETER- LIKE2 (DML2) and DML3; and demethylation can occur by mediation of DME but also by ROS1; the activity of the two other members of this family has not been reported. In this paper, Penterman et al. (2007) used microarrays to identify loci demethylated by ROS1, DML2 and DML3. To this end, they first confirmed the 5meC demethylase activity of DML2 and DML3. Then, they compared the genome- wide methylation pattern changes when wild- type or single- knock out mutants were screened for expression; here, they found "~179 loci were methylation and demethylation pathways converge". These results were confirmed by bisulfite sequencing. Comparison between bisulfite sequencing data from a triple mutant, and from single mutants and wild type plants showed that hypermethylation at the majority of these loci was regulated by this family of glycosilases; and also that redundancy of this regulation exists for DML enzymes at some loci (i.e., a loci can be demethylated by more than one DML enzyme). Crosses between single mutants and wild type individuals restored the demethylation levels in most loci (11 out of 14), and methylation levels were intermediate between mutant and wild type in the remaining loci, with a parental origin- specificity. Thus these were epilalleles, and hence DML demethylation "prevents the formation of stable epialleles" in some loci, a very interesting housekeeping function for this family.
Penterman J. et al. 2007. Proc Natl Acad Sci USA 104(16):6752-57
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