Maintenance of cytosine methylation in plants is controlled by three DNA 
methyltransferases. MET1 maintains CG methylation, and DRM1/2 and CMT3 act 
redundantly to enforce non-CG methylation. RPS, a repetitive hypermethylated DNA 
fragment from Petunia hybrida, attracts DNA methylation when transferred into 
Petunia or other species. In Arabidopsis thaliana, which does not contain any 
RPS homologues, RPS transgenes are efficiently methylated in all sequence 
contexts. To test which DNA methylation pathways regulate RPS methylation, we 
examined maintenance of RPS methylation in various mutant backgrounds. 
Surprisingly, CG methylation was lost in a drm1/2/cmt3 mutant, and non-CG 
methylation was almost completely eliminated in a met1 mutant. An unusual 
cooperative activity of all three DNA methyltransferases is therefore required 
for maintenance of both CG and non-CG methylation in RPS. Other unusual features 
of RPS methylation are the independence of its non-CG methylation from the 
RNA-directed DNA methylation (RdDM) pathway and the exceptional maintenance of 
methylation at a CC(m)TGG site in some epigenetic mutants. This is indicative of 
activity of a methylation system in plants that may have evolved from the DCM 
methylation system that controls CC(m)WGG methylation in bacteria. Our data 
suggest that strict separation of CG and non-CG methylation pathways does not 
apply to all target regions, and that caution is required in generalizing 
methylation data obtained for individual genomic regions.