Entanglement dilution and high fractal dimension mediated by loop extrusion revealed in simulations of active polymer melts

In simulations of active polymer melts, researchers have found that a process called active loop extrusion can mediate entanglement dilution and high fractal dimensions. Active loop extrusion is a mechanism by which cohesin protein complexes create chromatin loops in eukaryotic cells. This process maintains topologically associated domains (TADs), which are contiguous segments of chromatin that tend to colocalize spatially and are typically bounded by CTCF proteins.

The simulations revealed that active loop extrusion enhances the intra-chain contact probabilities of polymers compared to their equilibrium, passive counterparts. Furthermore, the size of chain segments becomes much smaller in active melts as a result of extrusion, as opposed to passive melts where the overlap parameter increases monotonically with segment length.

However, in active melts, the overlap parameter is nonmonotonic and reaches a value close to unity within the parameters of the study. Active loop extrusion suppresses contacts between TADs, favoring intra-TAD contacts. This reduction of overlaps between chain segments dilutes entanglements in active melts, potentially leading to more compact conformations depending on the parameters.

Interestingly, active extrusion without TADs may induce even more compact conformations due to fractal loopy globule-like dynamics. The study suggests that active loop extrusion plays a role in reducing overlaps between TADs, contributing to effective gene regulation by cis-regulatory elements.