CHH methylation in CRP4 coding region. A) Average percent methylation of cytosines in a CHH context in different parts of the SAT5 repeat monomer containing the CRP4 gene. CHH methylation is highest in the CRP4 coding region. B) Overall levels of methylation in CG (Black), CHG (blue) and CHH (red) nucleotide groups in the CRP4 coding region in wild type plants (WT) and mutants defective in RNA-directed DNA methylation (nrpe1 dcl3 double mutant and dms4, nrpd1, and rdr2 single mutants). Primarily CHH methylation is lost in the mutants.