Novel hotspots have biased H3K4me3 modification.

<p>(A) F1 hybrid hotspots were classified as B6 or CAST depending on parental origin, or labeled novel. (B) H3K4me3 haplotype ratio for BxC TSS (n = 12,903, orange - autosomes, black - chromosome X). (C) H3K4me3 haplotype ratio for BxC hotspots (grey - all BxC hotspots, n = 12,271; green - novel BxC hotspots, n = 2,298). (D) Scatterplot of haplotype-specific H3K4me3 for hotspots shared between progeny from reciprocal B6 and CAST crosses (n = 10,977, r = 0.978 without X chromosome). 163 hotspots in lower right (circle) are all on the chromosome X. Black shading reflects signal density. (E) Left - Haplotype-specific PCR showing from genomic DNA samples for hotspots chr1 185.33 Mb and chr1 171.37 Mb. Right - Haplotype-specific PCR from spermatocytes before or after enrichment for H3K4me3 (n = 4, error bars - S.D.). (F) The parental identity and fraction of hotpots in WxP F1 hybrids. (G) H3K4me3 haplotype ratio for WxP TSS (n = 15,856, orange - autosomes, black - chromosome X). (H) H3K4me3 haplotype ratio for WxP hotspots (grey - all WxP hotspots, n = 8,360; green - novel WxP hotspots, n = 2,325).