Effective model of loop extrusion predicts chromosomal domains

An active loop-extrusion mechanism is regarded as the main out-of-equilibrium mechanism responsible forthe structuring of megabase-sized domains in chromosomes. We developed a model to study the dynamics ofthe chromosome fiber by solving the kinetic equations associated with the motion of the extruder. By averagingout the position of the extruder along the chain, we build an effective equilibrium model capable of reproducingexperimental contact maps based solely on the positions of extrusion-blocking proteins. We assessed the qualityof the effective model using numerical simulations of chromosomal segments and comparing the results withexplicit-extruder models and experimental data.