Fig. 4: Loss of H3K36me3 results in an excessive gain of CG methylation in genomic regions with specific histone marks.

a Scatter plots showing CG methylation levels in control and Setd2 KO FGOs. Fifty thousand randomly selected 10 kb bins were plotted. b Heatmaps showing H3K36me3, H3K36me2, H3K27me3, and H3K4me3 enrichment and CG methylation levels in 10 kb bins in control and Setd2 KO FGOs^{11, 14}. CG methylation differences between Setd2 KO and control FGOs (ΔCGme). The data were sorted in the same order as in Fig. 3a. c Heatmaps showing H3K4me3 enrichment in 10 kb bins in control and Mll2 KO FGOs¹². d Violin plots showing CG methylation differences in 10 kb bins of cluster 4 (n = 45,161) between Setd2 KO and control FGOs (left) or between Mll2 KO and control FGOs (right)¹². Boxplots show median value and 25–75th percentiles, and whiskers show 1.5× interquartile range from the box. e Scatter plots showing CG methylation levels in control and Setd2 KO FGOs across the genome (left), autosomes (middle), and X chromosome (right). Fifty thousand (left) or ten thousand randomly selected 10 kb bins (middle and right) were plotted with a color gradient for H3K36me2 enrichment in Setd2 KO FGOs¹¹.