Fig. 2

Single-read analysis of CHH methylation in CHH methylase and demethylase mutants. a Methylation states of reads from CHH methylation mutants. Binned methylation states of all reads overlapping regions matching the criteria (5 CHH sites, maximum 30 bp length) are plotted, demonstrating differences in methylation intensity between cmt2, drd1 and drm2. Each panel presents regions filtered according to the averaged region methylation level, as indicated above each panel. The methylation state is defined, as in Fig. 1, as the number of CHH sites in the region that are methylated in each read. b Analysis of methylation patterns within reads. Reads were selected from regions containing 5, 10 and 15 CHH sites (as indicated above the panels) and with a maximum length of 100 bp and binned according to read methylation and methylation stochasticity (as defined in Fig. 1b). White areas indicate no data. c, d Comparison of demethylase mutant read methylation and respective wild type samples: c sites methylated in the drd1 mutant (i.e. CMT2-methylated sites) that are hypermethylated in the demethylase mutants; d sites methylated in the cmt2 mutant (i.e. DRM2-methylated sites) that are hypermethylated in the demethylase mutants. To select CMT2- and DRM2-methylated sites in the ros1-4 and rdd mutants, the drd1 and cmt2 mutants from [14] were used, respectively. For dme, drm1/2 and cmt2 mutants from [31] were used