Uncovering the Forces between Nucleosomes using a DNA Origami Force Spectrometer

Abstract

Revealing the energy landscape for nucleosome association may contribute to the understanding of higher-order chromatin structures and their impact on genome regulation. Here we accomplish this in a direct measurement by integrating two nucleosomes into a DNA origami-based force spectrometer, which enabled sub-nanometer resolution measurements of nucleosome-nucleosome distance frequencies via single particle electron microscopy imaging. From the data we derived the Boltzmann-weighted distance-dependent energy landscape for nucleosome pair interactions. We find a shallow but long-ranged (∼6 nm) attractive nucleosome pair potential with a minimum of −1.6 kcal/mol close to direct-contact distances. The relative nucleosome orientation had little influence, but histone H4 acetylation or removal of histone tails drastically decreased the interaction strength. Due to the weak and shallow pair potential, higher-order nucleosome assemblies will be compliant and experience dynamic shape fluctuations in the absence of additional co-factors. Our results contribute to a more accurate description of chromatin, while our force spectrometer provides a powerful tool for the direct and high-resolution study of molecular interactions using imaging techniques.