Fig. 1

Higher interaction frequency at mid-/long-range distances in male chrX. a Male over female log₂ ratio of normalized (chromosome-wise ICE) Hi-C matrices of contact frequencies binned at 25 kb resolution is shown for a representative 5 Mb region of chrX. b Interaction frequency decay with distance is shown in a log–log plot. Normalized (genome-wide ICE) Hi-C data binned at 25 kb were converted to contact frequencies as described in Methods for both sex-sorted embryos (left column) and cell lines (right column) datasets, for male (clone-8, upper row) and female (Kc167, lower row) samples. For any given genomic distance (log₁₀ genomic distance on x-axis) the median log₁₀ Hi-C interaction frequency is reported (y-axis). Distances ranging from 50 kb (2 bins distance in the 25 kb bins matrix) to 2.5 Mb are shown. c Heatmap showing the pairwise difference (deltas) of the rate of Hi-C signal decay (slope coefficient). The slope coefficients were computed considering distances <400 kb (≤5.6 in log₁₀ distance). The colour scale and the numeric values report the differences between chromosomes indicated in the horizontal vs vertical axes labels. Layout as in (b) panel (male samples in upper row, female samples in lower row). d Boxplot of slope coefficient deltas for rate of Hi-C decay grouped by autosome pairwise comparisons (the first three columns in panel (c) heatmaps) and chrX comparisons to autosomes (the fourth column in panel (c) heatmaps) in male and female embryos (left) or cell lines (right). The difference in rate of decay between autosomes and chrX is highly significant in male samples only (** marks Wilcoxon test p-value < 0.01). For each box the median is marked as horizontal line, the boxes mark the interquartile range (IQR), the whiskers extend up to 1.5 IQR.