Fig. 4

TADs are conserved units of genome organization. A Genome size (top panel), average length (middle panel) and number of TADs (bottom panel) in 12 species. B, C Spearman’s correlation between genome size and TAD number (B) or TAD size (C) in 12 species. D 3DR values computed from the 12 genome assemblies. The colored and white boxes represent “convergent ‘→ ←’ and “divergent ‘← →’” contiguous CTCF motifs. E 3DR values of 12 species when accounting for TAD borders. TAD borders were defined as the extended 20 kb regions around the center of each TAD boundary (on each side, 40 kb in total). We only kept CTCF motifs belonging to TAD borders when calculating the 3DR values in the TAD borders. F Distribution of CNEs (conserved non-coding elements) in TADs. G Plot showing the mean intra- and inter-TAD conservation scores in pairwise comparisons between species. H Barplot of the percentage of correlated gene pairs (Pearson’s r > 0.9) (slashed color bars) within the same TADs compared to all gene pairs (blank color bars) based on expression data of fibroblasts from 7 species with at least 3 replicates. The tested gene pairs were stratified based on the number of genes by which they were spatially separated. Distances are indicated underneath the barplot. For (D) and (E), the internal line indicates the median, the box limits indicate the upper and lower quartiles and the whiskers extend to 1.5 IQR from the quartiles. P values were calculated using two-sided Wilcoxon rank-sum test. For (G) and (H), data are presented as mean ± SD