Conditions for positioning of nucleosomes on DNA

TL;DR

This study investigates the factors influencing nucleosome positioning on DNA, emphasizing the interplay of binding preferences and interactions, and derives conditions for optimal positioning relevant to in vivo scenarios.

Contribution

It provides a theoretical framework analyzing how binding strength, energy landscape correlation, and nucleosome interactions affect positioning accuracy.

Findings

Weak binding preferences can still lead to good positioning with strong interactions.

Synergistic effects are crucial for nucleosome positioning on correlated energy landscapes.

Theoretical results are discussed in the context of in vivo nucleosome positioning.

Abstract

Positioning of nucleosomes along eukaryotic genomes plays an important role in their organization and regulation. There are many different factors affecting the location of nucleosomes. Some can be viewed as preferential binding of a single nucleosome to different locations along the DNA and some as interactions between neighboring nucleosomes. In this study we analyzed how well nucleosomes are positioned along the DNA as a function of strength of the preferential binding, correlation length of the binding energy landscape, interactions between neighboring nucleosomes and others relevant system properties. We analyze different scenarios: designed energy landscapes and generically disordered ones and derive conditions for good positioning. Using analytic and numerical approaches we find that, even if the binding preferences are very weak, synergistic interplay between the interactions and the binding preferences is essential for a good positioning of nucleosomes, especially on correlated energy landscapes. Analyzing empirical energy landscape, we discuss relevance of our theoretical results to positioning of nucleosomes on DNA \emph{in vivo.}