Fig. 3. HiPore-C reveals interchromosomal chromatin clustering.

a Percentage of multiway intra-/inter-chromosome contact reads (top). The blue–red color bar represents the fragment number in reads. Percentage of reads of different numbers of fragments from different chromosomes (bottom). Different colors represent the number of chromosomes that a multiway contact read covers. b Global interchromosome interaction heatmap at 1 Mb resolution. The color bar represents the enrichment of interactions on a log scale. The chromosomes are labeled on top, green squares indicate centromeres, and gray dots indicate telomeres. c Interchromosome interaction counts, including contact bins located within centromere or telomere regions. The number of interactions is shown (Tel indicates telomeres interactions, n = 109,941; Cent indicates centromeres interactions, n = 27,9739; Other, interactions between genomic regions outside of the telomere and centromere sequences, n = 3,683,803). The number of significantly enriched interchromosome interactions was shown in red. Circos diagrams of significant interchromosome interactions between centromeres (d) or telomeres (e) at both anchor ends. f tSNE diagram of the significant interchromosome interaction regions. Two sets of interchromosome interaction regions are separated and labeled in red (active hub) and blue (inactive hub). Circos diagrams of two sets of interchromosome interactions: red, active hub (g), and blue, inactive hub (h). i Boxplots of gene density, enhancer density, DNase-seq, RNA Polymerase II, and histone modification (H3K4me3, H3K27ac, H3K36me3, H3K4me4, and H3K4me1) signals in inactive hub (blue, n = 72), active hub (red, n = 78), and control (yellow, n = 2894, genomic bins not in either of the active and inactive hubs) regions. The center line, median; red dot, mean; boxes, first and third quartiles; whiskers, 5th and 95th percentiles. Significance was calculated by the Kruskal–Wallis test, followed by Dunnett’s t-test for active and inactive hubs. P values are shown in boxplots. P < 2.2 × 10⁻¹⁶ in all of the Kruskal–Wallis tests.