In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

Class 2A, but not class 1 or class 2B, sites are Spo11 dependent. (A) Venn diagram showing the overlap of PRDM9 ChIP-seq peaks from B6 (all 3041 specific and common peaks), B6 Spo11^KO (PRDM9^Dom2), and B6 Prdm9^KO mice. (B) PRDM9 B6 peaks (Spo11^+/+) were binned by strength. In each bin, the percentage of B6 Spo11^KO (PRDM9^Dom2) overlapping peaks was plotted. (C) Distribution of classes into bins of PRDM9 peak strength monitored in B6 Spo11^KO mice. (D) Read distribution from PRDM9 ChIP-seq at representative class 1, 2A, and 2B sites found in B6 Spo11^KO mice compared with the read distribution from PRDM9, H3K4me3, and DMC1 ChIP-seq in B6 mice at the same sites. Read distribution was calculated from pooled replicates, in 1-bp windows, and normalized by library size and input. (E) Average read enrichment (RPKM) of PRDM9, in B6 and B6 Spo11^KO mice centered on class 1, 2A, and 2B sites of each strain. (n.d.) Not determined (only one class 2A peak was identified in B6 Spo11^KO). (F) Classification of the PRDM9-positive peaks detected in B6 Spo11^KO mice in subclasses with (+) or without (−) enrichment for DMC1 (measured in B6 mice) and/or H3K4me3 (specifically present in B6 Spo11^KO mice or also present in RJ2). Classes were defined as in Figure 1D. H3K4me3 ChIP-seq data for B6 Spo11^KO (PRDM9^Dom2) are from Brick et al. (2012) and downloaded from the GEO database (GSE35498).