Gupta Kushol, Sekulić Nikolina, Allu Praveen Kumar, Sapp Nicklas, Huang Qingqiu, Sarachan Kathryn, Christensen Mikkel, Lund Reidar, Krueger Susan, Curtis Joseph E, Gillilan Richard E, Van Duyne Gregory D, Black Ben E
Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA.
Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, Norway.
bioRxiv. 2025 Jan 21:2025.01.16.633457. doi: 10.1101/2025.01.16.633457.
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 cloned 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 identity 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.
基于溶液的核小体物理性质研究源于X射线和中子散射实验,包括那些首次观察到DNA缠绕在核心组蛋白周围的实验。在本研究中,我们进行了一项全面的小角散射研究,以比较含有组蛋白变体CENP-A的典型核小体和着丝粒变体核小体。我们使用在人工定位序列(Widom 601)上组装的核小体核心颗粒(NCPs),并将其与在从人类着丝粒克隆的天然α-卫星DNA上组装的核小体进行比较。我们使用分析超速离心(AUC)、小角X射线散射(SAXS)和对比变化小角中子散射(CV-SANS)来确定八聚体H3和CENP-A NCPs的天然溶液性质。使用高压SAXS(HP-SAXS),我们发现组蛋白身份和DNA序列都对高压(300 MPa)下溶液中八聚体核小体的稳定性有影响,在这些实验条件下有可逆解旋的证据。含有常规组蛋白H3的典型核小体及其含有CENP-A的着丝粒对应物的回转半径都有显著增加,但着丝粒核小体的这种增加不太明显。更广泛地说,对于与染色体相关的研究,我们注意到随着HP-SAXS方法的实用性不断扩展,我们预计这将为研究核小体和高阶染色质复合物提供一种强大的基于溶液的方法。