Hi-C contact matrices for chromosomes 1 and 2 (lower-left and upper-right gold boxes, respectively) showing features of the three-dimensional chromatin architecture within X. tropicalis blood cell nuclei. Blue pixels represent chromatin contacts between X Y pairs of 500 kb genomic loci, with intensity proportional to contact frequency. Hi-C read pairs are mapped stringently (MQ 30) above the diagonal and permissively (MQ 0) below the diagonal. The characteristic A/B-compartment (checkerboard) and Rabl-like (angel wing) interarm contact patterns within each chromosome are evident. Above the diagonal, an increased frequency of interchromosomal chromatin contacts is observed between pericentromeres (connected by dotted lines) and between chromosome arms (Supplementary Tables 18 , 19 , and 21 ), suggesting a centromere-clustered organization of chromosomes in a Rabl-like configuration. Below the diagonal, high-intensity pixels near the ends of chromosomes not present above the diagonal suggest a telomere-proximal spatial bias in the distributions of similar genomic repeats. See Supplementary Fig. 1e for a plot showing all chromosomes.
