Journal Article

Solution conformational differences between conventional and CENP-A nucleosomes are accentuated by reversible deformation under high pressure

Sapp, Nicklas, Sarachan, Kathryn, Lund, Reidar, Krueger, Susan, Van Duyne, Gregory D., Curtis, Joseph E., Black, Ben E., Christensen, Mikkel, Sekulić, Nikolina, Gupta, Kushol, Gillilan, Richard E., Allu, Praveen Kumar, Huang, Qingqiu

2025

Overview

Solution-based interrogation of the physical nature of nucleosomes has its roots in X-ray and neutron scattering experiments, including those that provided the initial observation that DNA wraps around core histones. In this study, we performed a comprehensive small-angle scattering study to compare canonical nucleosomes with variant centromeric nucleosomes harboring the histone variant, CENP-A. We used nucleosome core particles (NCPs) assembled on an artificial positioning sequence (Widom 601) and compared these to those assembled on a natural α-satellite DNA from human centromeres. We establish the native solution properties of octameric H3 and CENP-A NCPs using analytical ultracentrifugation (AUC), small-angle X-ray scattering (SAXS), and contrast variation small-angle neutron scattering (CV-SANS). Using high-pressure SAXS (HP-SAXS), we discovered that both histone and DNA sequence have an impact on the stability of octameric nucleosomes in solution under high pressure (300 MPa), with evidence of reversible unwrapping in these experimental conditions. Both canonical nucleosomes harboring conventional histone H3 and their centromeric counterparts harboring CENP-A have a substantial increase in their radius of gyration, but this increase is much less prominent for centromeric nucleosomes. More broadly for chromosome-related research, we note that as HP-SAXS methodologies expand in their utility, we anticipate this will provide a powerful solution-based approach to study nucleosomes and higher-order chromatin complexes.

• Publisher: Springer Netherlands,Springer Nature B.V
• Subject: Animal Genetics and Genomics / Autoantigens - chemistry / Autoantigens - genetics / Biomedical and Life Sciences / Cell Biology / Centromere - chemistry / Centromere Protein A / Centromeres / Chromatin / Chromosomal Proteins, Non-Histone - chemistry / Core particles / deformation / DNA / Histone H3 / Histones / Histones - chemistry / Histones - genetics / Human Genetics / Humans / Life Sciences / Neutron scattering / Neutrons / Nucleic Acid Conformation / Nucleosomes / Nucleosomes - chemistry / Nucleosomes - genetics / Nucleosomes - metabolism / Nucleotide sequence / nucleotide sequences / Plant Genetics and Genomics / Pressure / Protein Conformation / Satellite DNA / Scattering, Small Angle / small-angle X-ray scattering / Ultracentrifugation / X-radiation / X-Ray Diffraction / X-ray scattering