Fig. 5: SEs intra-TAD positioning is linked to TADs biological features.

Characterizing TADs fully contained within B compartment or A compartment; A compartment TADs are further divided based upon SE presence/absence and SE position (edge SEs are SEs <5 kb from TAD boundary) (n = 680 TADs in B compartment, n = 670 TADs without SE in A compartment, n = 495 TADs with non-edge SE in A compartment, n = 183 TADs with edge SE in A compartment). These groups vary in [A] mean TAD size (two-sided, one-way ANOVA, F_2,1557 = 270.8, p < 0.001) and TAD boundary insulation (two-sided, one-way ANOVA, F_2,1548 = 91.01, p < 0.001; lower log₂ insulation score corresponds to stronger insulation) as well as in [B] the number of chromatin loops in contact with the TAD (two-sided, one-way ANOVA F_3,2722 = 19.85, p < 0.001), mean size of those loops (two-sided, one-way ANOVA F_3,2722 = 75.47, p < 0.001), and percentage of loops which cross TAD boundaries (two-sided, one-way ANOVA F_3,2722 = 18.66, p < 0.001). * indicates p < 0.05; ** p < 0.01; ***p < 0.001 by ANOVA with Tukey HSD post-hoc test. Error bars represent standard error of the mean. C Enriched Reactome terms among genes with a TSS residing within or in contact via chromatin looping with a non-edge or edge SE. D Chromatin loops, SEs, CREs, log₂ insulation score, TADs, and Hi-C contact maps for the FOS locus. Abbreviations SE: Super-enhancer, TAD: Topologically associating domain; CRE: Cis-regulatory element; TSS: Transcription start site.