Extended Data Fig. 2: Genome-wide relationship between de novo DNAme in prenatal male germ cells and histone H3 methylation states.

a, Contour scatter plots with outliers showing the relationship between enrichment (RPKM) of the indicated histone marks over 10-kb genomic bins and the difference in the % of DNAme between E16.5 PSG and E13.5 mPGCs³³ in the same regions. The % of genomic coverage for each histone mark in E16.5 PSG is shown in each plot. R indicates Spearman’s rank correlation coefficient. b, Genome browser representation of a region on chromosome 3 showing % DNAme in E13.5 mPGCs and E16.5 PSG³³ as well as RPM values of H3K4me3, H3K27me3, H3K9me3, H3K36me2 and H3K36me3 in E16.5 PSG. c, Violin plots showing % DNAme over H3K9me3 domains of <10 kb (total DNAme genomic coverage, 0.1 Gb) or >20 kb (total DNAme genomic coverage, 0.2 Gb) in E13.5 mPGCs, E16.5 PSG³³ and P0 PSG⁴³ (n = 1). The % of the genome in E16.5 PSG showing H3K9me3 enrichment in domains of <10 kb or >20 kb is shown in each plot. Box (25-75th percentile), median (inside the box) and whisker (1.5x interquartile range from the box) are included in the violin plots. d, Violin plots showing the distribution of enrichment of H3K36me2 over 10-kb genomic bins (left) or H3K9me3 domains of <10 kb (middle) or >20 kb (right) in E16.5 PSG (n = 1). Note that H3K36me2 is particularly depleted in regions of broad H3K9me3. Box, median and whisker are included in the violin plots as shown in c. e, Stacked bar chart showing % total of unique or repeat regions in the genome (total) versus H3K9me3 domains of <10 kb or >20 kb. Repeats were identified by RepeatMasker annotation.