Fig. 4

Comparison of dCTCF binding in CTCF^wt-HA and CTCF^Δ132–170-HA adult flies. (A) Average signal (RPKM) of ChIP-seq peaks with DNA binding motif (left) and motif logos (right) for CTCF^wt-HA (wt-HA) and CTCF^Δ132–170-HA (Δ132–170-HA). The motifs associated with the peaks in both datasets are the same. (B) UpSet plot showing an overlap of CP190 binding sites in the y¹w¹¹¹⁸ line and dCTCF binding sites in CTCF^wt-HA (wt-HA) and CTCF^Δ132–170-HA (Δ132–170-HA) lines considering all dCTCF sites (top) and only sites with the binding motif (bottom). The bars are colored according to the distribution of the genomic elements in the corresponding regions. Only regions with dCTCF binding sites are shown. (C) Average signals (RPKM) (top) and signal heatmaps (bottom) for CP190 peaks in the y¹w¹¹¹⁸ line and dCTCF peaks in the CTCF^wt-HA (wt-HA) and CTCF^Δ132–170-HA (Δ132–170-HA) lines. Three different sets of peaks are displayed (columns): a combined set of dCTCF binding sites with the binding motif (both wt-HA and Δ132–170-HA) overlapping with CP190 binding sites (denoted as “dCTCF motif; CP190 signal”); a combined set of dCTCF binding sites with the motif and not overlapping with CP190 binding sites (denoted as “dCTCF motif; no CP190 signal”); a combined set of dCTCF binding sites without the motif but overlapping with CP190 binding sites (denoted as “no dCTCF motif; CP190 signal”). The “dCTCF motif; CP190 signal” and “dCTCF motif; no CP190 signal” sets were motif-centered, and “no CTCF motif; CP190 signal” set was centered on the peak summit. (D) Comparison of dCTCF signal (RPKM) in the CTCF^wt-HA (wt-HA) and CTCF^Δ132–170-HA (Δ132–170) lines in the combined set of dCTCF peaks with the binding motif. Outliers were detected using linear regression (see Methods). Regions overlapping with CP190 binding sites are circled in black