Fig. 5: Cohesin extrudes further through quiescent regions than active regions.

A Most CTCF-mediated looping contacts do not reflect the fully extruded state. Estimate is obtained using left fragments that overlap CAMEL identified CBS (+) and have an interaction length greater than 10 kb with start and end at least 5 bp from motif start and end, length <120, and extended fragment end. For each CBS with at least 50 long-range TF-protected fragments overlapping the motif, % convergent is calculated as the number of interaction partners overlapping CTCF (-) motifs / total number of fragments at motif. Because this estimate is conditional on CTCF binding at the anchor, we divide estimates by two to account for the ~50% occupancy of CTCF³³. B Depiction of how 1 MB regions downstream of CBS were annotated using ChromHMM. Density (C) and P(S) curves (D) for chromatin state clusters shown in (Supplementary Fig. 6A), filtered to the top 20%. Chromatin annotations making up each cluster are added together and quantiles are obtained to determine fragments in the top 20% of active chromatin, quiescent chromatin, and bivalent / polycomb chromatin. Left fragments that overlap CAMEL identified CBS (+) and have an interaction length greater than 10 kb with start and end at least 5 bp from motif start and end, length <120, and extended fragment end are used. E Ridge plots for the bottom 10% quantile (“Low”) and top 10% quantile (“High”) of H3K27ac bp and number of RNAPII binding sites. ChIP-seq from ENCODE was used to annotate 1 MB downstream of left fragments overlapping CBS (+) for this figure. Left fragments that overlap CAMEL identified CBS (+) and have an interaction length greater than 10 kb with start and end at least 5 bp from motif start and end, length <120, and extended fragment end are used. Plots are labeled with the average log10 interaction length. F Diagram illustrating differences in extrusion rates between active and quiescent chromatin states, with numbers obtained from Supplementary Fig. 6B.