Fractal and knot-free chromosomes facilitate nucleoplasmic transport

TL;DR

This study uses simulations and scaling analysis to show that fractal globule-like chromosome structures facilitate faster macromolecular transport within the nucleus by reducing the walk dimension compared to other geometries.

Contribution

It demonstrates how the fractal globule structure influences transport properties, highlighting the role of network topology and heterogeneity in diffusion dynamics.

Findings

Fractal globule-like chromosomes have a smaller walk dimension, enhancing diffusion.

Chromosome folding determines macromolecular transport characteristics.

Network connectivity in chromosomes resembles percolation clusters regardless of models.

Abstract

Chromosomes in the nucleus assemble into hierarchies of 3D domains that, during interphase, share essential features with a knot-free condensed polymer known as the fractal globule (FG). The FG-like chromosome likely affects macromolecular transport, yet its characteristics remain poorly understood. Using computer simulations and scaling analysis, we show that the 3D folding and macromolecular size of the chromosomes determine their transport characteristics. Large-scale subdiffusion occurs at a critical particle size where the network of accessible volumes is critically connected. Condensed chromosomes have connectivity networks akin to simple Bernoulli bond percolation clusters, regardless of the polymer models. However, even if the network structures are similar, the tracer's walk dimension varies. It turns out that the walk dimension depends on the network topology of the accessible volume and dynamic heterogeneity of the tracer's hopping rate. We find that the FG structure has a smaller walk dimension than other random geometries, suggesting that the FG-like chromosome structure accelerates macromolecular diffusion and target-search.