Fig. 2

Signature of chromatin accessibility changes upon acute CTCF loss. A Volcano plots of motif enrichment analysis of ATAC-seq comparing control nucleosome-free regions (NFRs) versus decreased differential accessibility regions (DARs). Fisher exact tests comparing motif frequency generated the p values and odds ratios. Each dot represents a motif in the database. Dots in the top left corner indicate motifs enriched for decreased DARs. B Volcano plots of motif enrichment analysis of ATAC-seq for increased DARs versus control NFRs. Fisher exact tests comparing motif frequency generated the p values and odds ratios. Each dot represents a motif in the database. Dots in the top right corner indicate motifs enriched for increased DARs. C ATAC-seq footprint profiles of the top motifs enriched for decreased DARs. Ratios between the nearest summit and the center indicate the probability of motifs protected from Tn5 insertion. Stronger dips in the center indicate higher confidence in binding. The height of the nearest summit to the center indicates chromatin accessibility. The number of matched motifs we used for each footprint profiling was attached at the end of each TF motif. D ATAC-seq footprint profiles of the top motifs enriched for increased DARs. E Log₂ fold change of normalized contact numbers from Hi-C (+IAA versus -IAA) at loops grouped by whether the loop anchors overlapped the DARs or control NFRs. ***p value < 0.001; ****p value < 0.0001, Student’s t test. F Density plot measures the distance from DARs to the closest TAD boundaries