Fig. 2: Physical insulation defects in CTCF⁰ mutants.

a Percentage of n = 740 CTCF peaks with at least one contact domain (CD) boundary at a given distance (per 2 kb bins) around the CTCF peak. Enrichment of CD boundaries around the same number of random positions (gray) is shown as control. b Percentage of n = 3458 CD boundaries with at least one CTCF peak at a given distance (per 2 kb bins) around the CD boundary. Enrichment of CTCF peaks around the same number of random positions (gray) is shown as a control. c Example locus (dm6 coordinates) Hi-C maps, eigenvector values (positive for A compartment, negative for B compartment), CD boundaries from this study (color-coded as in Fig. 2d) and a Hi-C study in cultured cells¹⁷, physical insulation score (calculated with different window sizes in gray, average in black), CTCF ChIP-seq (CTCF peaks highlighted and numbered), CTCF motif orientations in DNA, and gene tracks in WT (top) and CTCF⁰ (middle) larval CNSs. (Below) Differential (CTCF⁰ minus WT) Hi-C map and physical insulation score. d Position of CTCF peaks around all CD boundaries defined in any genotype (n = 3970 boundaries) ranked by physical insulation score differences measured in CTCF⁰ minus WT Hi-C maps. Visibly weaker boundaries in CTCF⁰ (score > +0.1) or in WT (score < −0.1) are bracketed. Boundaries are color-coded in all figures as present in both WT and CTCF⁰ (blue), only in WT (red) or only in CTCF⁰ (green). e Physical insulation score differences measured in CTCF⁰ minus WT Hi-C maps around CTCF peaks, ranked by CTCF ChIP occupancy in WT. f Average physical insulation scores around CTCF peaks in WT (black) and CTCF⁰ (red). g GFP pull-down of tagged CTCF N-terminus (residues 1–123) that is WT (GFP-CTCF-N^WT) or Y248A F250A point mutant (GFP-CTCF-N^mut) mixed with untagged recombinant cohesin subcomplex (residues 102–1085 of SA and 273-458 of Vtd). Specific retention of cohesin by CTCF (lane 5) is higher than the background binding of SA-Vtd to beads (lanes 4, 6). Asterisks mark GFP-CTCF-N degradation. CES conserved essential surface, ZnF zinc finger.