ABSTRACT
This chapter presents how standard modeling software packages such as HooMD or ESPResSo can be modified to simulate supercoiled chromatin fibers. It suggests that chromatin fibers forming topologically associating domains (TADs) are supercoiled. Numerous studies have indicated that portions of deoxyribonucleic acid in interphase chromosomes are torsionally stressed and this results in supercoiling of implicated chromatin fibers. A standard beaded chain model is frequently sufficient for a coarse-grained approach to model equilibrium behavior of thermally fluctuating, torsionally unstressed polymeric chains subject to confinement. Standard beaded chain models permit free swiveling, which makes them unable to maintain torsional tension and thus not suitable to model the effects of supercoiling. Magnetic tweezers experiments have shown that the torsional stiffness of chromatin fibers depe nds on whether the fiber is overwound or underwound. An important part of the loop extrusion mechanism is that the loop extrusion process should stop when the cohesin rings reach the correctly oriented CCCTC-binding factor proteins at the TAD borders.
