Synergistic Coordination of Chromatin Torsional Mechanics and Topoisomerase Activity

Due to the intrinsic twist of DNA, eukaryotic replication generates DNA supercoiling as the replisome unravels parental DNA. If not resolved, this supercoiling may intertwine chromatin fibers and result in significant topological challenges during chromosome replication. Since the replisome alone is incapable of driving its substrates out of torsional equilibrium, the generated supercoiling partitions ahead of or behind the replication fork to maintain a balance of torque. By making direct torque measurements, we demonstrated that a single chromatin fiber (as would be located ahead of a replisome) is torsionally soft, while a braided chromatin fiber (as would be located behind the replisome) is relatively stiff. These results imply that supercoiling on chromatin substrates is preferentially directed in front of the replication fork. We further showed that topoisomerase II relaxation displays a strong preference for a single chromatin fiber over a braided fiber, suggesting a synergistic coordination – the mechanical properties of chromatin inherently suppress intertwining during replication elongation by driving DNA supercoiling ahead of the fork, where it is more efficiently removed by topoisomerase II. This work highlights the fundamental role of physical principles in the cell.