Fig. 6: Extensive alignment of chromosome ends during early meiotic prophase.

a–c Boxplots quantify interactions among the 5 Mb sub-telomeric regions on different chromosomes. Each box shows the distribution of average interaction frequency per genomic 50-kb bin in sub-telomeric regions for 171 pairwise combinations of autosomes. Leptotene and zygotene stages exhibit the highest interactions between sub-telomeric regions at the centromere-proximal ends of different chromosomes (CEN-CEN, a) and between the centromere-distal ends of different chromosomes (TEL-TEL, b), but the lowest interactions between sub-telomeric regions at different chromosome ends (CEN-TEL, c). Box limits, upper and lower quartiles. Centre bars, median. Whiskers, 1.5× interquartile range. d Boxplots quantify the polarity of interactions among the sub-telomeric regions by calculating (CEN-CEN + TEL-TEL)/(2 × CEN-TEL) for each of 171 pairwise combinations of autosomes. Leptotene and zygotene stages exhibit the highest polarity. For all boxplots in a–d, n = 171 pairwise combinations of autosomes. e Averaged trans observed/expected heatmaps of all 171 pairwise combinations of autosomes. Interpolation was performed to normalize for different chromosome lengths. Matrices were scaled to 500 bins × 500 bins. f Plots quantifying the signals along the diagonals of the heatmaps in e indicate the extent of inter-chromosomal alignment along chromosomes. Regions of ~20% chromosome length from either chromosome end exhibit prominent inter-chromosomal alignment in leptotene and zygotene stages. g Plots quantify zygotene-stage inter-homolog alignment scores versus chromosome position for A and B compartment regions. Inter-homolog alignment patterns are similar to the inter-chromosomal alignment patterns in f.