The novel hotspot at chr1 40.6 Mb, activated by PRDM9Cst on the B6 haplotype, shows transmission distortion to the CAST haplotype.

(A) PRDM9Cst motif aligned to the DNA sequence for both B6 and CAST haplotypes at the peak of PRDM9 ChIP-seq signal (B) PRDM9 and H3K4me3 coverage profile at chr1 40.6 Mb (black lines – SNP positions between B6 and CAST, black box – PRDM9Cst motif). (C) Proportion of mapped reads to each haplotype (unassigned reads lack informative SNPs). (D) Cumulative frequency of recombination crossovers at hotspot chr1 40.6 Mb (n = 19 mice). (E) Transmission distortion at hotspot chr1 40.6 Mb favors the CAST haplotype at the PRDM9 binding site.