Extended domains of co-regulation correlate with the subdivision of the genome into topological domains. (A–C) Outlines of loci, with genes displayed as arrows and insertions as drawings of the transposon. Regulatory domains and transition zones are labeled, TADs (identified by Hi-C in mouse ES cells) are indicated by green and brown bars and unstructured regions by dashed lines. Hi-C interaction frequencies are represented as a two-dimensional heat map (from Dixon et al. 2012). (A) Multiple insertions in the chr3:7.3–8.3M interval outlined an extended regulatory domain characterized by shared expression in the facial and trunk mesenchyme, and in neural crest derivatives. This domain extends into the adjacent unstructured region (insertion 201179e9), but two telomeric insertions, located in a different TAD, showed different patterns (the proximal limb expression of 181912bc-133 is anterior, whereas insertions in the flanking RD have a more medial expression), defining two transition zones. (B) Multiple insertions in the vicinity of the Foxg1 gene display the typical forebrain (fb) expression of the gene (adapted from Chen et al. 2013, with permission from Elsevier © 2013). Expression in the ear (*) is due to another insertion also present in 177175-emb7. The regulatory domain defined by the gene and the insertions is contained within a single TAD. A more detailed version of this panel is shown in Supplemental Figure 5E. (C) Two insertions in a gene desert between Kcnt2 and Cdc73 are divergently expressed in the limb bud (lb) and forebrain (fb), delineating a transition zone. This coincides with the respective insertions being located in different TADs. (D) Size distribution (y-axis) and relationship with TADs (color-coded) of functionally defined intervals. Only a single regulatory domain (RD) overlaps a TAD boundary. Random permutation of regions 200 kb–1 Mb in length (boxed area), where the size distribution of the different functional categories is not statistically different (Kolmogorov-Smirnov test, P = 0.8560 for RD vs. TZ + A + B; P = 0.9240 for RD vs. TZ), showed that RDs are significantly underrepresented in the “separated TADs” category. (E) Unlike control regions (classes A, B) and transition zones (TZ), RDs show depletion in topological boundaries compared with equally sized, randomly distributed fragments. Gray box-plots represent the results of randomization; red dots, the position of the real data. The depletion is statistically significant (P = 0.009), as indicated by the blue star.
