Confinement-Induced Glassy Dynamics in a Model for Chromosome Organization

Area of Science:

• Genomics
• Biophysics
• Computational Biology

Background:

• Intrachromosomal contact probability (P(s)) scaling suggests fractal-like chromosome organization.
• Observed variations in P(s) scaling across organisms necessitate a unifying explanation.

Purpose of the Study:

• To investigate dynamical arrest in confined spaces as a key factor in genome organization.
• To model nuclear chromosomes as a homopolymer within a sphere of variable size.

Main Methods:

• Utilized Brownian dynamics simulations to model polymer chains within spherical confinement.
• Analyzed the effect of polymer volume fraction (ϕ) on chain dynamics and the approach to a critical value (ϕ(c)).

Main Results:

• Simulations revealed that polymer dynamics slow down as ϕ approaches a critical value, ϕ(c)≈0.44.
• This critical value is universal for sufficiently long polymers (N≫1).
• Human chromosomes (large N, high ϕ) exhibit glassy dynamics and segregated organization, unlike yeast chromosomes (smaller N, lower ϕ).

Conclusions:

• Dynamical arrest due to high polymer volume fraction explains the distinct chromosome organization in humans.
• Equilibrated dynamics, not glassy arrest, characterize yeast chromosome organization.
• Polymer volume fraction (ϕ) serves as a critical parameter for understanding genome dynamics and organization across species.