Fig. 2

Dissecting the relative contributions of CG and non-CG methylation to the H3K9me2 pattern. a Upset plot displaying the number of unique and overlapping H3K9me2 loci between the wild type and indicated mutants. Bars represent the intersection size for overlapping H3K9me2 loci between Col-0, met1, ddcc, and mddcc. Numbers (> 10) of H3K9me2 loci in different subgroups are shown. All H3K9me2 loci were classified into eight types as indicated. b Heatmaps of H3K9me2 levels and DNA methylation enrichments of the indicated H3K9me2 types in (a). The number of H3K9me2 loci in the wild type is defined as 100%, and the percentages of type I–IV are shown. c Representative examples of H3K9me2 changes caused by DNA methylation loss. d Peak intensities of the indicated H3K9me2 types in different genotypes. e H3K9me2 intensities of the indicated categories in ddcc (left) and met1 (right) compared with the wild type. The horizontal column at the bottom shows the proportion of H3K9me2 in different categories. Boxplots in d and e include a median with quartiles and outliers above the top whisker. The statistical analysis was performed using two-side Wilcoxon test. NS, no significant difference. **p < 2.2e−16 from Wilcoxon test. f Distribution of DNA methylation at the H3K9me2 loci gained in ddcc (type V) and met1 (type VI) compared with the wild type