Active Nucleosome Displacement: A Theoretical Approach

Abstract

Three-quarters of eukaryotic DNA are wrapped around protein cylinders forming so-called nucleosomes that block the access to the genetic information. Nucleosomes need therefore to be repositioned, either passively (by thermal fluctuations) or actively (by molecular motors). Here we introduce a theoretical model that allows us to study the interplay between a motor protein that moves along DNA (e.g., an RNA polymerase) and a nucleosome that it encounters on its way. We aim at describing the displacement mechanisms of the nucleosome and the motor protein on a microscopic level to understand better the intricate interplay between the active step of the motor and the nucleosome-repositioning step. Different motor types (Brownian ratchet versus power-stroke mechanism) that perform very similarly under a constant load are shown to have very different nucleosome repositioning capacities.