Extended Data Fig. 7: NIPBL downregulation leads to alterations in long-range interaction frequency and chromatin architecture.
From: Disruption of TAD hierarchy promotes LTR co-option in cancer
a, Hi-C contact probability plot showing the average contact frequency of valid paired-end reads as a function of genomic distance with NIPBL perturbation. Genomic distance between valid cis read pairs was calculated and the distribution of log10 read pair genomic distance was plotted. b, Hi-C contact map (at 100 kb resolution) of a representative region (chr8) with NIPBL downregulation (shNIPBL_2, right) vs. control (shLuc, left), demonstrating finer segregation in compartments after NIPBL downregulation. c, Number of baseline CTSSs versus differentially regulated CTSSs by shNIPBL_1 and shNIPBL_2 in hierarchical and non-hierarchical TADs defined under control condition (≥ level 3 vs. ≤ level 2 and singleton). d–e, Fraction (d) and number (e) of baseline CTSS versus differentially regulated CTSSs by shNIPBL_4 and shNIPBL_5 in hierarchical and non-hierarchical TADs defined under control condition (≥ level 3 vs. ≤ level 2 and singleton). *P < 0.05, **P < 0.01, two-tailed chi-square test.
