Extended Data Fig. 6: Preformed 3D chromatin folding in anterior vs. posterior fin.

a. Pearson matrices and eigenvectors showing A/B compartmentalization of the chromosome Leri_12C of skates in the anterior and posterior portions of the pectoral fin. b. Genome-wide eigenvector correlations. c. Quantification of A/B compartment switches between anterior and posterior portions of the fin. d. Comparison of all EV values between anterior and posterior fin. Heatmaps are sorted according to anterior EV values and compartment switches are indicated in the colour bar on top. Most switches are concentrated towards the centre, where EV values are intermediate. e. Comparison of insulation scores and overall TAD structures around the HoxD locus. f. Genome wide insulation score correlations. g. Correlations of number of reads found inside a consensus set of loops consisting of the union of the loops (see Methods) h. Differential loop analysis derived from read counts in g. logFC vs. logCPM plot with the only significant differential loop highlighted in red. i. Snapshot of the Hi-C heatmap around the only significant differential loop located in the Csmd2 locus. Arrowheads indicate the position of the loop. j. Virtual 4C-seq profiles of Hoxa cluster genes derived from the Hi-C experiments. Few differences are appreciated, and no differences are evident in contacts between Hoxa2 and the differential loop predicted by HiChIP (purple asterisk).