DNA Sequence and Histone Core Composition Determine the Unwrapping Pathways in Nucleosomes

Abstract

Interactions with histone core proteins in the cell efficiently store DNA and regulate access by partner molecules. In this process multiple histone core variants interact with a myriad of diverse sequences of DNA. Understanding how these interactions are influenced by histone composition and DNA sequence is crucial for unraveling their regulatory and packaging mechanisms. We use small angle X-ray scattering with contrast variation (CV-SAXS) to measure DNA unwrapping from nucleosomes as they are electrostatically destabilized by salt. This process allows many different unwrapping states to become accessible. The unwrapping states that are sampled in any given condition are determined from the scattering profiles using an ensemble optimization method. With this method we are able to map the unfolding landscape from fully wrapped to fully unwrapped, allowing the protein-nucleic acid interactions to be probed. We report on the results of multiple sequences and histone variants, including both natural and synthetic DNA sequences.