The dynamics of individual nucleosomes controls the chromatin condensation pathway: direct AFM visualization of variant chromatin

TL;DR

This study combines biochemical assays, single molecule imaging, and modeling to reveal how nucleosome variants influence chromatin structure and condensation pathways, highlighting the role of individual nucleosome dynamics in higher-order organization.

Contribution

It provides the first direct visualization and quantitative analysis of how histone variants alter nucleosomal array organization and chromatin condensation mechanisms.

Findings

H2A.Bbd variant drastically changes nucleosomal array structure

Conventional arrays show 'beads on a string' organization

Nucleosome fluctuation properties influence higher-order chromatin structure

Abstract

Chromatin organization and dynamics is studied in this work at scales ranging from single nucleosome to nucleosomal array by using a unique combination of biochemical assays, single molecule imaging technique and numerical modeling. We demonstrate that a subtle modification in the nucleosome structure induced by the histone variant H2A.Bbd drastically modifies the higher order organization of the nucleosomal arrays. Importantly, as directly visualized by AFM, conventional H2A nucleosomal arrays exhibit specific local organization, in contrast to H2A.Bbd arrays, which show "beads on a string" structure. The combination of systematic image analysis and theoretical modeling allows a quantitative description relating the observed gross structural changes of the arrays to their local organization. Our results strongly suggest that higher-order organization of H1-free nucleosomal arrays is mainly determined by the fluctuation properties of individual nucleosomes. Moreover, numerical simulations suggest the existence of attractive interactions between nucleosomes to provide the degree of compaction observed for conventional chromatin fibers.