Fig. 5. CTCF recruits Cp190 to a subset of Cp190-bound domain boundaries.

a Overlap between CTCF (green) and Cp190 (blue) peaks in WT, and regions with reduced Cp190 binding in CTCF⁰ relative to WT (red). Some peaks were split for three-way comparisons (see “Methods”). b Cp190 ChIP-seq signal in WT or CTCF⁰ around CTCF peaks, ranked by CTCF occupancy in WT. c Distribution of indicated datasets around CD boundaries defined in any genotype (n = 3970 boundaries) ranked by insulation defects in CTCF⁰. (1) Insulation score differences in CTCF⁰ minus WT. Visibly weaker boundaries in CTCF⁰ (score > +0.1) or in WT (score < −0.1) are bracketed. On the right, boundaries are classified as in Fig. 2d. (2–4) ChIP occupancy of CTCF peaks in WT, Cp190 peaks in WT or Cp190 peaks in CTCF⁰. (5) Differential Cp190 ChIP occupancy in CTCF⁰ minus WT. (6) Expressed TSSs in WT and CTCF⁰ with similar (gray), increased (red) or decreased (blue) expression in CTCF⁰ relative to WT. d As above for CD boundaries with a CTCF peak within ±2 kb (n = 349 boundaries) centered on the closest CTCF peak classified as TSS-proximal (within ±200 bp of a TSS) or distal (lane 7). e Numbers of CD boundaries bound by CTCF in WT (n = 349 boundaries) that are present or absent in CTCF⁰ mutants, and whose associated CTCF peak overlaps or not a residual Cp190 peak in CTCF⁰ mutants (p-val = 3.1e−6, two-sided Fisher’s Exact Test for Count Data). f Physical insulation score differences in CTCF⁰ minus WT at CTCF-bound CD boundaries (n = 349 boundaries) are higher when the associated CTCF peak does not overlap a residual Cp190 peak in CTCF⁰ mutants, or a TSS within 200 bp (indicated p values and W-statistics from two-sided Wilcoxon rank-sum test with continuity correction). Box plot: center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile ranges; points, outliers; n = CTCF peaks of each category (in x). g Example locus like Fig. 2c also displaying Cp190 ChIP-seq signal in WT and CTCF⁰ mutant larval CNSs. Asterisks mark Cp190 peaks in CTCF⁰ mutants with reduced occupancy relative to WT revealed by differential analysis. Solid arrowheads mark strictly CTCF-dependent boundaries (the second boundary was not called by TopDom), empty arrowheads mark partially CTCF-dependent boundaries.