Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation

Epigenetic silenced alleles of the Arabidopsis SUPERMAN locus (the clark ke nt alleles) are associated with dense hypermethylation at noncanonical cyto sines (CpXpG and asymmetric sites, where X = A, T, C, or G). A genetic scre en for suppressors of a hypermethylated clark kent mutant identified nine l oss-of-function alleles of CHROMOMETHYLASE3 (CMT3), a novel cytosine methyl transferase homolog. These cmt3 mutants display a wild-type morphology but exhibit decreased CpXpG methylation of the SUP gene and of other sequences throughout the genome. They also show reactivated expression of endogenous retrotransposon sequences. These results show that a non-CpG DNA methyltran sferase is responsible for maintaining epigenetic gene silencing.