Chromosome folding encodes mechanisms of cohesion maintenance

After DNA replication, sister chromatids are physically linked by the cohesin complex. These cohesin linkages must be maintained for many hours for faithful chromosome segregation and DNA repair. Cohesin interacts with multiple rapidly exchanging cofactors, including SORORIN, which is often described as a molecular lock for cohesin on chromatin. How such transient SORORIN binding can protect cohesin over much longer timescales remains mechanistically unclear. Furthermore, how loop-extruding cohesins interact with and influence the positioning of sister-linking cohesins remains largely unknown. Here we show that changes in sister chromatid folding over time and after perturbations encode distinct signatures of the underlying mechanisms of cohesion maintenance. By integrating biochemical kinetics with polymer modeling, we infer cohesin turnover, motion, and encounter rules from these folding signatures. Repeated transient sequestration by SORORIN enables long-lasting protection yet acts as a quantitative modulator, rather than a binary switch for cohesion maintenance. Prolonging cohesin residence time by WAPL depletion exposes additional mechanisms shaping sister chromatid conformation, including pushing of sister-linking cohesins and diffusion of loop-extruding cohesins. Together, these results reveal how transient cofactor interactions regulate long-lived cohesin maintenance and establish sister chromosome organization as a quantitative readout of otherwise hidden molecular mechanisms.