Fig. 4: Specific epigenetic marks associated with recombination hotspot formation.

a UCSC genome browser view of the ChIP-seq read coverage at a known CO hotspot; H3K27ac, H3K36me3, H3K9me2, and H3K4me3 (as control) ChIP-seq data were included. The known DSB hotspot and CO hotspot (HS59.5) were highlighted with light black shading. Region shown represents chromosome 19 (chr19): 59,415,641–59,455,641. b UCSC genome browser view of the ChIP-seq read coverage at the same known CO hotspot as a in leptotene and mid-zygotene spermatocytes of Prdm9^−/− mice; H3K27ac, H3K36me3, H3K9me2, and H3K4me3 (as control) ChIP-seq data were included. c Venn diagram showing the overlap of hotspot-associated H3K4me3, H3K36me3, and H3K27ac peaks in mid-zygotene spermatocytes. d–g Heatmaps (top) and profiles (bottom) of H3K4me3 (d), H3K27ac (e), H3K36me3 (f), and H3K9me2 (g) on the SPO11-oligo defined DSB hotspots in spermatogenic cells. Each row in heatmaps represents a DSB hotspot of ±5 kb around the center and ranked by H3K4me3 tag density from the highest to the lowest. Color indicates ChIP-seq tag density. Average ChIP-seq tag density was calculated using ChIP-seq reads with 50-bp resolution. h Pie chart showing that the minority of DSB hotspots are positioned within NDRs, most of which are distal NDRs. i Boxplot showing the ratio of chromatin accessibility level (chromatin accessibility level in SPO11-oligo defined DSB hotspots versus that in the whole genome) in the WT, Prdm9^−/−, Spo11^−/−, and Dmc1^−/− mid-zygotene spermatocytes. Only regions with at least three GCH sites were considered. Undiff undifferentiated spermatogonia, A1 type A1 spermatogonia, B type B spermatogonia, mpL mid-preleptotene spermatocytes, L leptotene spermatocytes, mZ mid-zygotene spermatocytes, mP mid-pachytene spermatocytes, D diplotene spermatocytes, Ctrl control.