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Within the nucleus, structural maintenance of chromosome protein complexes,namely condensin and cohesin, create an architecture to facilitate theorganization and proper function of the genome. Condensin, in addition toperforming loop extrusion, creates localized clusters of chromatin in thenucleolus through transient crosslinks. Large-scale simulations revealed threedifferent dynamic behaviors as a function of timescale: slow crosslinking leadsto no clusters, fast crosslinking produces rigid slowly changing clusters,while intermediate timescales are optimal for producing flexible clusters thatmediate gene interaction. By mathematically analyzing different relativescalings of the two sources of stochasticity, thermal fluctuations and theforce induced by the transient crosslinks, we predict these three distinctregimes of cluster behavior. Standard time-averaging that takes thefluctuations of the transient crosslink force to zero can predict the existenceof clusters, but not their timescale-dependent lifetimes. Accounting for theinteraction of both fluctuations from the crosslinks and thermal noise with aneffective energy landscape does capture the timescale-dependent flexiblecluster lifetimes. No clusters are predicted when the fluctuations of thetransient crosslink force are taken to be large relative to thermalfluctuations. This mathematical perturbation analysis illuminates theimportance of accounting for stochasticity in local incoherent transient forcesto predict emergent complex biological behavior.

Different relative scalings between transient forces and thermal fluctuations tune regimes of chromatin organization