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

Abstract 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 MATa 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 MATa site and its target HMLα donor is the relevant structure by which condensin promotes MATa-to-α switching. Competing Interest Statement The authors have declared no competing interest. Footnotes Addition of biological replicates Addition of new HiC data (eg. RE inversion on chr. III and IV) Addition of D-loop capture data showing a functional impact of the condensin-mediated looping in donor selection during recombination. Expanded results and discussion sections