ABSTRACT
This chapter reviews theoretical and experimental studies that suggest how loop extrusion can organize and reorganize chromosomes. One of the main challenges in characterizing chromosome organization is its almost paradoxical duality. As the resolution of Hi-C data increased, new patterns of chromosome organization because apparent, most prominently Topologically Associating Domains. Two phenomena are central to chromosome reorganization during cell division: compaction of individual chromosomes and their concomitant segregation. Chromosome reorganization for cell division constitutes a remarkable multiscale self-organization phenomenon where hundreds of thousands of nanometer-sized molecules act on meter-long polymers, assembling them into regular and organized micron-sized mitotic chromosomes. As an active process acting on polymers it can maintain the polymer system of chromosomes away from equilibrium, leading to new phenomena of self-organization typical for active systems. The goal of a polymer simulation is to sample the statistics of chromatin conformations in the thermal equilibrium, which can be achieved by running the simulation for a sufficiently long time.
