Plants maintain cytosine methylation at CG and non-CG residues to control gene 
expression and genome stability. In a screen for Arabidopsis mutants that alter 
methylation and silencing of a densely methylated endogenous reporter gene, we 
recovered 11 loss-of-function alleles in the CMT3 chromomethylase gene. The cmt3 
mutants displayed enhanced expression and reduced methylation of the reporter, 
particularly at non-CG cytosines. CNG methylation was also reduced at repetitive 
centromeric sequences. Thus, CMT3 is a key determinant for non-CG methylation. 
The lack of CMT homologs in animal genomes could account for the observation 
that in contrast to plants, animals maintain primarily CG methylation.