NMR-measured Per-residue Electrostatic Potentials Reveal the Importance of Arginine-Lysine Balance on the Conformational Ensemble of Disordered Histone H3 Tails in Nucleosome Core Particles

Abstract

Biophysical studies of chromatin have provided key insights into how the genome is regulated. Many atomic resolution structures of the fundamental building block of chromatin, the nucleosome core particle (NCP), as well as larger NCP arrays, both in isolation and in complex with effectors, or with post-translational modifications, have been elucidated. These provide in-depth pictures of key functional interactions. Considerably less information is available on the intrinsically disordered nucleosome tails that are critically important for higher order interactions in chromatin, and for transcription, DNA repair, and phase separation, and that serve as hubs for post-translational modifications. Here we focus on the tail of one of the four histones, histone-3 (H3), and measure electrostatic potentials at each of its amide proton positions in isolated NCPs via solution NMR spectroscopy. Using these potentials, in concert with molecular dynamics simulations, an ensemble of structures is calculated for WT H3 tails, as well as variants where all tail arginines are replaced by lysines (R2K) or vice versa (K2R). Our ensembles reveal that K2R tails have a higher propensity to occupy the most negatively charged region of the NCP between the DNA gyres than R2K or WT tails, while lysine enriched tails have an increased relative preference for the less negative regions near the DNA entry and exit points. The structural ensembles provide insight into differences in interactions between neighboring particles that lead to changes in diffusion and phase separation propensities between the NCP variants.