Extended Data Fig. 9: Relationship between H3K27ac distribution, gene expression and DNA methylation in Dnmt3A^KO SSCs (ID4-eGFP^bright+med).

a, Genomic annotation of each category of H3K27ac peaks. b, Quantification of intersection between H3K27ac peaks from Dnmt3A^KO, Dnmt3A^WT and WT SSCs (ID4-eGFP^bright), and progenitors (ID4-eGFP^dim) (from published data³⁶), down-enriched peaks and up-enriched peaks. Intersections lower than 200 were removed from the figure. c, Heatmap focusing on i) Dnmt3A^KO-lost H3K27ac peaks (log2 FC) compared to WT (left), ii) differential expression (log2 FC) of genes associated with these peaks (TSS + /−5 kb from the peak) between Dnmt3A^KO and WT—from ID4-eGFP^bright+med RNA-seq—(right). Rows are ordered according to gene expression changes: Cat. 1: 1,499 peaks associated with 1,561 non differentially expressed genes; Cat. 2: 10 peaks associated with 10 upregulated genes; Cat. 3: 85 peaks associated with 64 downregulated genes. d, (Left) Heatmap showing levels of H3K27ac peak enrichment in RPKM-normalized CUT&RUN signal from Dnmt3A^KO and WT ID4-GFP^bright+med germ cells as in Fig. 5d. (Right) Enrichment in H3K27ac, ATAC-seq and H3K27me3 from public prospermatogonia ChIP-seq data^37,38 (RPKM-normalized signal) at H3K27ac peaks described here in Dnmt3A^KO and WT. e, Heatmap focusing on i) Dnmt3A^KO-gained H3K27ac peaks (log2 FC) compared to WT that in addition lost above 30% DNA methylation in Dnmt3A^KO condition, from E18.5 WGBS (the two first columns), and ii) differential expression (log2 FC) of genes associated with H3K27ac peaks (TSS + /−5 kb from the peak) between Dnmt3A^KO and WT—from ID4-eGFP^bright+med RNA-seq—(center) Rows are ordered according to gene expression changes: top, differentially expressed, n = 1,083; middle, upregulated, n = 142; bottom, downregulated, n = 8. No Dnmt3A^KO-gained H3K27ac peaks were associated with unexpressed genes. f, Genome browser representation of the Gata2 locus, showing H3K27ac enrichment (grey), DNA methylation (yellow) and RNA expression (red) for Dnmt3A^KO and WT. Regions showing Dnmt3A^KO de novo H3K27ac peaks associated with >30% DNA methylation loss are shaded in light blue; regions showing de novo H3K27ac peaks at regions not controlled by DNA methylation are shaded in grey-blue.