Condensin loop extrusion properties, roadblocks, and role in homology search during recombination in S. cerevisiae

Abstract The in vivo mechanism, cis -acting roadblocks, and biological functions of DNA loop extrusion by eukaryotic SMC complexes remain incompletely defined. Here, we identify condensin-dependent Hi-C contact stripes at the recombination enhancer ( RE ) and at rDNA in S. cerevisiae . The RE is an autonomous condensin loading site only active in MAT a cells from which oriented, unidirectional loop extrusion proceeds with an estimated processivity ~150–250 kb and a density ~0.04–0.18 that varies across the cell cycle. Centromeres, replication forks, and highly transcribed RNA PolII-dependent genes represent roadblocks for condensin. Cohesin is not an obstacle for condensin, while Top2 promotes its loop extrusion activity. A DNA double-strand break (DSB) at MAT blocks loop extrusion, resulting in the establishment of a ~170 kb-long RE - MAT loop. The RE and the DSB are required and sufficient to form this site-specific loop, which promotes RE -proximal homology identification in the early stages of recombinational DNA break-repair. We propose that juxtaposition of the broken MAT a site and its target HML α donor is the relevant structure by which condensin promotes a-to-α mating-type switching.