Fig. 5: Variations in intra-chromosomal loop organization correlate with homolog alignment and crossover distribution.

a Z-stage inter-homolog interaction heatmap at 50 kb resolution for the same region shown in Fig. 4b, c. The inter-homolog interaction data are from Patel et al.³². b Boxplots quantify distributions of inter-homolog alignment scores for 50 kb genomic intervals belonging to A (red) or B (blue) compartment. n, total number of 50 kb intervals for A (n = 17,688) and B (n = 27,016). p value is calculated from two-tailed Mann–Whitney U test. c The A compartment regions >1 Mb are ranked based on the averaged interaction frequencies at 500 kb and divided into three groups (A1, A2, A3). Boxplots depict distributions of inter-homolog alignment scores for 50 kb genomic intervals belonging to A1 (red), A2 (orange), A3 (orange), or B (blue) compartment. n, total number of 50 kb intervals for each category (A1, n = 2376; A2, n = 3948; A3, n = 6327; B, n = 20,090). p values are calculated from two-tailed Mann–Whitney U test. d–h Boxplots quantify distributions of DSBs, COs, and the CO/DSB ratios in A1, A2, A3, and B compartment regions >1 Mb. The positions of DSBs and COs are from Davies et al.⁵⁶, Smagulova et al.⁵⁸, and Hinch et al.³⁰. d, e A1 regions do not exhibit significantly higher DSB density than A2 and A3 regions. f A1 regions do not exhibit significantly higher crossover densities than A2 and A3 regions. g, h A1 regions exhibit significantly higher crossover/DSB ratio than the A2 regions. n, total number of A1 (n = 76), A2 (n = 73), A3 (n = 74), and B (n = 377) regions. p values in d–h are calculated from one-tailed Mann–Whitney U test. For boxplots in b–h, center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range. The values beyond the whiskers are not shown in the boxplots.