Fig. 3: Global hypomethylation leads to ectopic activity of CMT3 at genes present within wild-type and ddm1 haplotypes.

a Genome browser view of a representative gene AT3G59750, in which non-CG methylation was observed in epiRILs with either wild-type or ddm1 derived haplotypes. b Correlation between hypomethylated genome and the number of gbM genes that gain CHG methylation. Genes inherited from WT (blue dots) and ddm1 (yellow dots) parents were calculated separately for each epiRIL. Gray area shows 95% confidence level interval for predictions (shown by lines) from a loess regression model. c Correlation between hypomethylated genomes and the average accumulated CHG methylation level on mCHG-gain genes. Gray area shows 95% confidence level interval for predictions (showing by lines) from a linear regression model. d A union set of total mCHG-gain genes from all epiRIL lines. It shows the number of mCHG-gain genes from each haplotype type as well as those shared by both haplotypes. e An enrichment analysis using Fisher’s Exact test shows that mCHG-gain genes that either from ddm1 (left) or WT haplotypes (right) are enriched in gbM genes. Yellow bars show the ratio of each type of genes with ectopic mCHG. Gray bars show the ratio of each type of genes in comparison with all coding genes. p- value is based on one-sided test with alternative hypothesis that odds ratio is greater than 1. f Genome-wide association of methylation level changes (difference of value compared to WT) at an example gene compared to its hypomethylation index. An example of positive correlation is shown for AT3G59750. For each gene, the epiRILs were grouped based on haplotypes, either WT (blue) or ddm1 (yellow) derived haplotypes. Gray area shows 95% confidence level interval for predictions (showing by lines) from a linear regression model. g Correlation test in f was applied for all genes. The bar plot shows the number of genes with CHG methylation level changes strongly correlated with the hypomethylation index (with Pearson correlation coefficient either >0.35 (above the line) or <−0.35 (below the line)). The number of associated genes is calculated separately based on haplotypes (either WT or ddm1 derived haplotypes) and gene type (gbM, teM and UM). Source data underlying Figs. 3b, 3e, and 3g are provided as a Source Data file.