Fig. 3

Fig. 3 Features of 3D chromatin organization in the little skate.

a, TAD metaplot displaying focal interactions at the apex of domains. b, Orientation bias of CTCF-binding site motifs inside ATAC–seq peaks at TAD boundary regions. c, Hi-C maps from whole pectoral fins of the skate hoxa locus at 25 kb resolution, denoting the presence of bipartite TAD configuration. Insul., insulation score. d,e, Hi-C maps from the same locus of c from dissected anterior (d) and posterior (e) portions of skate pectoral fins at 10 kb resolution. No changes in TADs or looping patterns were observed. f, The number of TADs detected associated to the different paralogous segments descending from the two rounds of WGD (1 or 2 for the 1R; α or β for the 2R) g, TAD sizes observed in the different paralogous segments from f. The box plots show the median (centre line) and the first and third quartiles (Q1 and Q3; box limits), and the whiskers extend to the last point within 1.5× the interquartile range below and above Q1 and Q3, respectively. The rest of the observations, including the maximum and minimum values, are shown as outliers. n = 626 (1/α), n = 83 (1/β), n = 570 (2/α) and n = 169 (2/β) TADs.