Uniform dynamics of cohesin-mediated loop extrusion in living human cells

Most animal genomes are partitioned into Topologically Associating Domains (TADs), created by cohesin-mediated loop extrusion and defined by convergently oriented CCCTC-binding factor (CTCF) sites. The dynamics of loop extrusion and its regulation remain poorly characterized in vivo. Here, we tracked the motion of TAD anchors in living human cells to visualize and quantify cohesin-dependent loop extrusion across multiple endogenous genomic regions. We show that TADs are dynamic structures whose anchors are brought in proximity about once per hour and for 6-19 min (~16% of the time). Moreover, TADs are continuously subjected to extrusion by multiple cohesin complexes. Remarkably, despite strong differences of Hi-C patterns between the chromatin regions, their dynamics is consistent with the same density, residence time and speed of cohesin. Our results suggest that TAD dynamics is governed primarily by the location and affinity of CTCF binding sites, which allows genome-wide predictive models of cohesin-dependent chromatin interactions. Overall design: We performed Capture Micro-C in HCT116 cells treated or not with 500 ??M auxin (leading to RAD21 depletion) for 3 hours. We used cell lines with TetO and CuO repeats inserted in the genome at the L1, L2, T1 and No Loop genomic regions.