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

The in vivo mechanism, regulations by cis-acting roadblocks, and biological functions of loop extrusion by eukaryotic SMC complexes are incompletely defined. Here, using Hi-C, we identified two condensin-dependent contact stripes at the Recombination Enhancer (RE) and the rDNA in S. cerevisiae. We show that oriented, unidirectional loop extrusion proceeds from these sites with an estimated processivity ~170 kb and a density ~0.04-0.18 that varies across the cell cycle. Centromeres and highly-transcribed RNA PolII-dependent genes are permeable condensin roadblocks. Other positionally labile elements such as replication forks and Smc5/6 complexes bound to substrates generated in the absence of Top2 also hinder loop extrusion by condensin. Cohesin is not an obstacle for condensin. Finally, a DNA double-strand break at MAT blocks condensin, which results in the rapid establishment of a long-range RE-MAT loop that juxtaposes the recombination machinery with its HMLα donor target. Hence, all budding yeast SMCs are involved in recombinational DNA repair. We propose a revised model for donor selection during MAT switching that exploits specific properties of loop extrusion by condensin. It can serve as a paradigm for the establishment of other types of selective interactions along chromosomes.