Fig. 6

DDM1 mediates gene body methylation at genes with unconventional chromatin features. A Heatmaps of normalized histone variant levels, modified histone H3 levels, gene expression (exp.), and DNA accessibility (acc.) in 10,332 gene body methylated genes in Col-0. Data were centered to 0 and normalized. GBM^UC; unconventional GBM cluster genes, GBM^C; conventional GBM cluster genes. Red lines indicate overlap to genes with strongly demethylated GBM in ddm1 (GBM^ddm1). B Venn diagram of genes with strongly demethylated GBM in ddm1 (GBM^ddm1) and unconventional GBM cluster genes (GBM^UC). p-value by Fisher’s exact test. C Boxplots of H1 levels of unmethylated genes in both Col-0 and ddm1 (unmethyl), genes with strongly demethylated GBM in ddm1 (GBM^ddm1), and genes with GBM that their methylation levels are weakly affected or not affected in ddm1 (GBM^weak). D A boxplot of gene expression fold change (FC) of differentially expressed genes in h1 plants (compared to Col-0, q-value < 0.05) overlapping with unmethylated genes in both Col-0 and ddm1 (unmethyl), genes with strongly demethylated GBM in ddm1 (GBM^ddm1), and genes with GBM that their methylation levels are weakly affected or not affected in ddm1 (GBM^weak). p-values by Student’s t test. E Boxplots of H1 levels of unmethylated genes both Col-0 and ddm1 (unmethyl), unconventional GBM cluster genes (GBM^UC), and conventional GBM cluster genes (GBM^C). F A boxplot of gene expression fold change (FC) of differentially expressed genes in h1 plants (compared to Col-0, q-value < 0.05) overlapping with unmethylated genes in both Col-0 and ddm1 (unmethyl), unconventional GBM cluster genes (GBM^UC), and conventional GBM cluster genes (GBM^C). p-values by Student’s t test