Confinement-induced glassy dynamics in a model for chromosome organization

TL;DR

This study models chromosome organization as a confined polymer and shows that glassy dynamics emerge at high confinement, explaining differences in chromosome organization across species.

Contribution

It introduces a confinement-induced glass transition model to explain chromosome organization, linking dynamics to genome size and confinement volume fraction.

Findings

Glassy dynamics occur at a critical volume fraction in confined polymers.

Human chromosomes exhibit glassy dynamics due to high confinement.

Yeast chromosomes remain equilibrated without glassy behavior.

Abstract

Recent experiments showing scaling of the intrachromosomal contact probability, $P(s)\sim s^{-1}$ with the genomic distance $s$, are interpreted to mean a self-similar fractal-like chromosome organization. However, scaling of $P(s)$ varies across organisms, requiring an explanation. We illustrate dynamical arrest in a highly confined space as a discriminating marker for genome organization, by modeling chromosome inside a nucleus as a homopolymer confined to a sphere of varying sizes. Brownian dynamics simulations show that the chain dynamics slows down as the polymer volume fraction ($\phi$) inside the confinement approaches a critical value $\phi_c$. The universal value of $\phi_c^{\infty}\approx 0.44$ for a sufficiently long polymer ($N\gg 1$) allows us to discuss genome dynamics using $\phi$ as a single parameter. Our study shows that the onset of glassy dynamics is the reason for the segregated chromosome organization in human ($N\approx 3\times 10^9$, $\phi\gtrsim\phi_c^{\infty}$), whereas chromosomes of budding yeast ($N\approx 10^8$, $\phi<\phi_c^{\infty}$) are equilibrated with no clear signature of such organization.