Replisomes restrict SMC translocation in vivo

Structural maintenance of chromosomes (SMC) complexes organize genomes by extruding DNA loops. How collisions between SMC complexes and DNA polymerases are resolved in vivo remains poorly understood. Taking advantage of the ability to load SMC complexes at defined sites in the Bacillus subtilis genome, we investigated this problem. We engineered head-on and head-to-tail collisions between SMC complexes and the replisome, and monitored SMC translocation by time-resolved ChIP-seq and Hi-C and replisome progression by marker frequency analysis. We report that SMC complexes do not affect replication progression. By contrast, the replisome blocks SMC translocation regardless of collision orientation. Combining experimental data with simulations, we determined that SMC is first blocked by the replisome and then released from the chromosome. However, occasionally SMC can bypass the replisome and continue translocating. Our findings establish that the replisome is a barrier to SMC-mediated DNA-loop extrusion, with implications for chromosome organization in all organisms. Hi-C, ChIP-seq and whole genome sequencing expriments were performed on wild type and mutant cells of Bacillus subtilis PY79 growing in rich medium.