High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion [RCMC]

Cohesin-mediated DNA loop extrusion enables gene regulation by distal enhancers through the establishment of chromosome structure and long-range enhancer-promoter interactions. The best characterized cohesin-related structures, such as topologically associating domains (TADs) anchored at convergent CTCF binding sites, represent static conformations. Consequently, loop extrusion dynamics remain poorly understood. To better characterize static and dynamically extruding chromatin loop structures, we use MNase-based 3D genome assays to simultaneously determine CTCF and cohesin localization as well as the 3D contacts they mediate. Here we present CTCF Analyzer (with) Multinomial Estimation (CAMEL), a tool that identifies CTCF footprints at near base-pair resolution in CTCF MNase HiChiP. We also use Region Capture Micro-C to identify a CTCF-adjacent footprint that is attributed to cohesin occupancy. We leverage this substantial advance in resolution to determine that the fully extruded (CTCF-CTCF loop) state is rare genome-wide with locus-specific variation from ~1-10%. We further investigate the impact of chromatin state on loop extrusion dynamics and find that active regulatory elements impede cohesin extrusion. These findings support a model of topological regulation whereby the transient, partially extruded state facilitates enhancer-promoter contacts that can regulate transcription. Overall design: We employed K562 CTCF MNase HiChIP to footprint CTCF & cohesin and investigate cohesin extrusion dynamics at the fragment level. We additionally re-sequenced the mESC RCMC libraries from Goel et al. Nature Genetics 2023 to 150bp reads (WT, DMSO, and IAA conditions for Fbn2, Klf1, and Ppm1g loci) to verify the cohesin footprint we observed in CTCF HiChIP.