Activity-driven chromatin organization during interphase: compaction, segregation, and entanglement suppression

Abstract

ABSTRACTIn mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that active loop extrusion causes the apparent fractal dimension of chromatin to cross over between two and four at contour lengths on the order of 30 kilo-base pairs (kbp). The anomalously high fractal dimensionD= 4 is due to the inability of extruded loops to fully relax during active extrusion. Compaction on longer contour length scales extends within topologically associated domains (TADs), facilitating gene regulation by distal elements. Extrusion-induced compaction segregates TADs such that overlaps between TADs are reduced to less than 35% and increases the entanglement strand of chromatin by up to a factor of 50 to several Mega-base pairs. Furthermore, active loop extrusion couples cohesin motion to chromatin conformations formed by previously extruding cohesins and causes the mean square displacement of chromatin loci during lag times (Δt) longer than tens of minutes to be proportional to Δt1/3. We validate our results with hybrid molecular dynamics – Monte Carlo simulations and show that our theory is consistent with experimental data. This work provides a theoretical basis for the compact organization of interphase chromatin, explaining the physical reason for TAD segregation and suppression of chromatin entanglements which contribute to efficient gene regulation.SIGNIFICANCE STATEMENTDuring interphase, cells must compact chromatin such that gene promoters and their regulatory elements frequently contact each other in space. However, cells also need to insulate promoters from regulatory elements in other genomic sections. Using polymer physics theory and computer simulations, we propose that the cohesin protein complex actively extrudes chromatin into topologically associated domains (TADs) with an anomalously high fractal dimension ofD≈ 4 while suppressing spatial overlap between different TADs. Our model suggests that the fast kinetics of active loop extrusion compared to the slow relaxation of chromatin loops maintains a dense chromatin organization. This work presents a physical framework explaining how cohesin contributes to effective transcriptional regulation.