Spatially accessible chromatin is depleted for crossover formation, particularly at gene bodies. (A) Summary of recombination activity at DSB binding sites (from DMC1-SSDS ChIP-seq), with additional partition into the top and bottom quartiles for crossover likelihood. Top (i.e., crossover-favored) sites have modestly stronger inherent DSB activity and show greater likelihood of crossover formation. Heatmap shows log fold enrichment over genome median, and an asterisk indicates a Bonferroni-adjusted P < 0.01 difference between the top and bottom partitioned sites. (B) Hi-C cis/total ratio (top) and compartment score (bottom), symmetric-averaged across DSB sites, calculated for ES cell, zygonema, and pachynema data sets. Shading represents 95% confidence intervals. Top CO-favored sites are associated with a higher cis/total ratio, particularly during meiosis, indicative of reduced spatial accessibility (black arrow). (C) Normalized chromatin contact matrices, symmetric-averaged across DSB sites, for ES cell, zygonema, and pachynema Hi-C data sets. We observe reduced contact frequency near top CO-favored sites and vice versa, particularly during pachynema. (D) RAD21/RAD21L cohesin subunit (top), CTCF (middle), and RNAPII (bottom) ChIP-seq tracks, symmetric-averaged across DSB sites, calculated for ES cell and meiotic data sets. Elevated RNAPII occupancy during meiosis appears to be associated with decreased crossover formation (black arrow). (E) Overlap of ChromHMM histone annotations with crossover-partitioned DSB sites. Note CO-favored sites are depleted for the H3K36me3 chromatin typical of gene bodies and are enriched for unmarked chromatin. Heatmap shows log fold enrichment over genome-wide mean, and an asterisk indicates a Bonferroni-adjusted P < 0.01 difference between most (top) and least (bottom) CO-favored sites. Insets plot overlap fraction symmetric-averaged around DSB sites; shading represents 95% confidence intervals. (F) Distribution of crossover likelihood scores at DSB sites split by ChromHMM state. Crossover formation is depleted at DSBs in H3K36me3 chromatin, despite abundant DSB activity (see Fig. 2F), indicating that gene-body crossover depletion occurs at the DSB-to-CO stage rather than the PRDM9-to-DSB stage.
