Statistical mechanics of nucleosome ordering by chromatin structure-induced two-body interactions

TL;DR

This paper presents a thermodynamic model demonstrating that two-body interactions are crucial for the 10-11 base pair periodicity and ordering of nucleosomes in chromatin, aligning with experimental observations.

Contribution

It introduces a novel model incorporating two-body interactions to explain nucleosome positioning and periodicity in chromatin structure.

Findings

Two-body forces are key to 10-11 bp nucleosome periodicity.

The model explains nucleosome ordering in transcribed regions.

Nucleosome positions can be inferred from large-scale maps.

Abstract

One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to 10-11 base pair (bp) discretization of linker lengths caused by the smaller free energy cost of packaging nucleosomes into a regular chromatin fiber if their rotational setting (defined by DNA helical twist) is conserved. We describe nucleosome positions along the fiber using a thermodynamic model of finite-size particles with effective two-body interactions, subject to an arbitrary external potential. We infer both one-body and two-body energies from readily available large-scale maps of nucleosome positions. We show that two-body forces play a leading role in establishing well-known 10-11 bp genome-wide periodicity of nucleosome occupancies. They also explain nucleosome ordering over transcribed regions observed in both in vitro and in vivo high-throughput experiments.