Footprints of loop extrusion in statistics of intra-chromosomal distances: An analytically solvable mode

Journal of Chemical Physics. 2024. Vol. 160. No. 12. Article 124901.

Belan S., Parfenyev V.

Active loop extrusion—the process of formation of dynamically growing chromatin loops due to the motor activity of DNA–binding protein complexes—is a firmly established mechanism responsible for chromatin spatial organization at different stages of a cell cycle in eukaryotes and bacteria. The theoretical insight into the effect of loop extrusion on the experimentally measured statistics of chromatin conformation can be gained with an appropriately chosen polymer model. Here, we consider the simplest analytically solvable model of an interphase chromosome, which is treated as an ideal chain with disorder of sufficiently sparse random loops whose conformations are sampled from the
equilibrium ensemble. This framework allows us to arrive at the closed-form analytical expression for the mean-squared distance between pairs of genomic loci, which is valid beyond the one-loop approximation in diagrammatic representation. In addition, we analyze the loop-induced deviation of chain conformations from the Gaussian statistics by calculating kurtosis of probability density of the pairwise separation vector. The presented results suggest the possible ways of estimating the characteristics of the loop extrusion process based on the experimental data on the scale-dependent statistics of intra-chromosomal pair-wise distances.

Keywords: полимеры, организация хроматина, chromatin organization, выпетливание, biopolymers, active loop extrusion