PRDM9 binding shows large haplotype bias in vivo.

(A) Coverage profile for several representative hotspots for both PRDM9 ChIP-seq and H3K4me3 ChIP-seq in BxC F1 hybrids. (B) 96% of BxC F1 PRDM9 peaks overlap with BxC F1 H3K4me3. (C) Parental origin of BxC PRDM9 peaks. (D) Haplotype-specific heat map of ChIP-seq signal for PRDM9 and H3K4me3 from BxC F1 hybrids. Read densities from a 2 kb window centered on the summit of PRDM9 peaks were clustered. SNPs density between B6 and CAST strains across the same 2 kb were arranged in the order of hotspots. The activating PRDM9 protein variant, and whether the hotspot was identified as novel, is indicated by color bar on the right. (E) Aggregation plots of PRDM9 and H3K4me3 signal. (F) Scatterplot of haplotype-specific PRDM9 binding and haplotype-specific H3K4me3.