DNA-loop extruding SMC complexes can traverse one another in vivo

Chromosome organization by structural maintenance of chromosomes (SMC) complexes is vital to living organisms. SMC complexes were recently found to be motors that extrude DNA loops. However, it remains unclear what happens when multiple complexes encounter one another in vivo on the same DNA and how interactions help organize an active genome. We created a crash-course track system to study SMC complex encounters in vivo by engineering the Bacillus subtilis chromosome to have defined SMC loading sites. Chromosome conformation capture (Hi-C) analyses of over 20 engineered strains show an amazing variety of never-before-seen chromosome folding patterns. Via 3D polymer simulations and theory, we find that these patterns require SMC complexes to bypass each other in vivo, contrary to the common assumption that SMC complexes mutually block each other’s loop extrusion activity. We posit that the bypassing activity enables SMC complexes to spatially organize a functional and busy genome.