Encounter time of two loci governed by polymer de-condensation and local chromatin interaction

TL;DR

This study models the mean first encounter time between two DNA loci using polymer physics, revealing that local chromatin decondensation significantly accelerates the search process, with implications for understanding homology search mechanisms.

Contribution

The paper introduces a new asymptotic formula for the mean first encounter time in polymer models, linking chromatin decondensation to faster homology search.

Findings

Decreasing tethering forces reduces MFET by orders of magnitude.

Polymer decondensation accelerates the homologous search process.

New asymptotic formula for MFET confirmed by simulations.

Abstract

The time for a DNA sequence to find its homologous depends on a long random search process inside the cell nucleus. Using polymer models, we model and compute here the mean first encounter time (MFET) between two sites located on two different polymer chains and confined by potential wells. We find that reducing the potential (tethering) forces results in a local polymer decondensation near the loci and numerical simulations of the polymer model show that these changes are associated with a reduction of the MFET by several orders of magnitude. We derive here new asymptotic formula for the MFET, confirmed by Brownian simulations. We conclude that the acceleration of the search process after local chromatin decondensation can be used to analyze the local search step during homology search.