Jeppsson, K. | bioRxiv Science

bioRxiv2022

The Smc5/6 complex is a DNA loop extruding motor

Structural Maintenance of Chromosomes (SMC) protein complexes are essential for the spatial organization of chromosomes. While cohesin and condensin organize chromosomes by extruding DNA loops, the molecular functions of the third eukaryotic SMC complex, Smc5/6, remain largely unknown. Using single-molecule imaging, we reveal that Smc5/6 forms DNA loops by extrusion. Upon ATP-hydrolysis, Smc5/6 symmetrically reels DNA into loops at a force-dependent rate of 1 kilobase pairs per second. Smc5/6 extrudes loops in the form of a dimer, while monomeric Smc5/6 unidirectionally translocate along DNA. We also find that Nse5 and Nse6 (Nse5/6) subunits act as negative regulators of Smc5/6-mediated loop initiation and stability. Our findings reveal Smc5/6s molecular functions, and establish loop extrusion as a conserved mechanism among eukaryotic SMC complexes. One-Sentence SummarySmc5/6 is a DNA-loop-extruding motor, establishing loop extrusion as a conserved mechanism among eukaryotic SMC complexes.

biophysics↗

bioRxiv2020

Transcription and replication organize cohesin-dependent chromosome loops

Genome function and stability is strictly dependent on regulated folding of chromosomes in space and time. Chromosome loop formation by the protein complex cohesin is a central feature of this multilayer organization1. Accumulating evidence indicates that cohesin creates loops by extruding chromosomal DNA through its ring-like structure in a process that is controlled by the cohesin loading factor Scc2 and the unloader Wpl11-4. Cohesins chromosomal positioning is affected by transcription in both yeast and human cells5,6, and the complex localizes in the vicinity of replication forks7. However, if transcription directly influences chromosome looping remains an unresolved question, and the threedimensional organization of replicating chromosomes is unknown. Here we show that transcription and replication machineries create chromosome loop boundaries. We find that drug-induced depletion of chromosome-bound RNA polymerases triggers a rapid expansion of cohesin-dependent chromosome loops in the budding yeast Saccharomyces cerevisiae. New loop boundaries also form at a few highly expressed genes induced by the cellular stress response caused by the drug. The results also reveal that S-phase chromosomes are shaped by cohesin-dependent loops organized by transcription, with additional loop anchors at replication forks. Together, our results show that replication and transcription control the three-dimensional organization of the genome by blocking the progression of loop-forming cohesin. They also open for the possibility that the resulting positioning of loop-forming cohesin in the vicinity of transcription and replication machineries is part of cohesins functions in transcription control, sister chromatid cohesion and maintenance of fork stability.

molecular biology↗