Extended Data Fig. 7: Chromatin conformation of monotreme sex chromosomes.

a, Hi-C interactions between platypus sex chromosomes, with chromosome 1 shown as control. a, b, There are unexpected interchromosomal interactions (shown in red) between platypus sex chromosomes detected by Hi-C data (a), whereas most interactions are within the same chromosomes (shown in red in b) for the other chromosomes (b). c, The Hi-C interchromosomal interactions among platypus sex chromosome (inter_XY, n = 2,711 100-kb windows) is significantly higher than that among autosomes (inter_A, n = 14,342,930 100-kb window). Box plots show median, quartiles (boxes) and range (whiskers). ***P < 0.0001 (P < 2.2 × 10⁻¹⁶), one-sided Wilcoxon rank-sum test. d, The interaction strength is higher between Y2 and Y3 than the interaction strengths between Y2 and other chromosomes. n = 1,002, 228, 5,025, 67,313 and 6,904,867 100-kb windows are shown in Y2-Y2, Y2-Y3, Y2-other.sex.chr, Y2-A and A-A, respectively. Box plots show median, quartiles (boxes) and range (whiskers). ***P < 0.0001 (P < 2.2 × 10⁻¹⁶), one-sided Wilcoxon rank-sum test. e, Inferred three-dimensional structure of the platypus sex chromosome system. X chromosomes are shown in red and Y chromosomes in blue, with PARs in light colour. Interchromosomal interactions inferred from Hi-C are shown by dashed lines. f, Hi-C interactions reveal unexpected interchromosomal interactions between the echidna sex chromosomes. g, Putative CTCF-binding sites are enriched at TAD boundaries in platypus and echidna sex chromosomes. For each X chromosome of platypus, we calculated their putative CTCF-binding-site density per 10 kb and plotted them along the ±500 kb of TAD boundaries. Platypus X4 and echidna X5 are not shown because less than 10 TAD boundaries are detected. h, Putative CTCF-binding-site density plot showing its enrichment among the homologous regions of platypus, echidna, human and chicken.