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

The in vivo mechanism, cis -acting roadblocks, and biological functions of loop extrusion by eukaryotic SMC complexes are incompletely defined. Here, we identify condensin-dependent Hi-C contact stripes at the Recombination Enhancer ( RE ) and the 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 are roadblocks for condensin. Cohesin is not an obstacle for condensin while Top2 promotes its loop extrusion activity. A DNA double-strand break 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 the juxtaposition of the broken MAT a site and its target HML α donor is the relevant structure by which condensin promotes MAT a-to-α switching.