Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

Transcriptional coregulation defines a functional privileged scale. (A) Schematic representation of the definition of statistical enrichment in the number of coregulated domains. A domain is down- (up-) coregulated if its number of down- (up-) coregulated genes is larger than in 95% of cyclic permutated genomes (empirical P ≤ 0.05). A Z-score is calculated as the difference between the number of coregulated domains detected in the real genome (N^obs) and the mean number of coregulated domains detected in 2000 randomized genomes (N^exp), weighted by its standard deviation σ^exp. (B) Distribution of average fold changes in expression level for domains at different RI values. For each RI value, the number of domains that are either up- or down-regulated during differentiation (at the P ≤ 0.05 level) is also shown in the upper part of the graph. Box: 25%–75% range (black line: median). (C) The statistical enrichment in the number of down-regulated domains is plotted as a function of the RI threshold. Transcriptional coregulation is significant at any level below ∼70% RI but maximal at 65%. (D) Same as panel C for up-regulated domains. (E) Same analysis as in panel C when using domains based on Hi-C data in NPCs. (F) Same as panel E for up-regulated domains. (G) Example of domains that were created de novo during differentiation and detected only in the set of NPC TADs (58% RI).