School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA.
Nucleic Acids Res. 2021 May 21;49(9):5028-5037. doi: 10.1093/nar/gkab290.
Nucleosomes in all eukaryotic cells are organized into higher order structures that facilitate genome compaction. Visualizing these organized structures is an important step in understanding how genomic DNA is efficiently stored yet remains accessible to information-processing machinery. Arrays of linked nucleosomes serve as useful models for understanding how the properties of both DNA and protein partners affect their arrangement. A number of important questions are also associated with understanding how the spacings between nucleosomes are affected by the histone proteins, chromatin remodelers, or other chromatin-associated protein partners. Contrast variation small angle X-ray scattering (CVSAXS) reports the DNA conformation within protein-DNA complexes and here is applied to measure the conformation(s) of trinucleosomes in solution, with specific sensitivity to the distance between and relative orientation of linked nucleosomes. These data are interpreted in conjunction with DNA models that account for its sequence dependent mechanical properties, and Monte-Carlo techniques that generate realistic structures for comparison with measured scattering profiles. In solution, trinucleosomes segregate into two dominant populations, with the flanking nucleosomes stacked or nearly equilaterally separated, e.g. with roughly equal distance between all pairs of nucleosomes. These populations are consistent with previously observed magnesium-dependent structures of trinucleosomes with shorter linkers.
真核细胞中的核小体组织成更高阶的结构,从而促进基因组的压缩。对这些有组织的结构进行可视化是理解基因组 DNA 如何高效存储但仍可被信息处理机制访问的重要步骤。连接核小体的阵列是理解 DNA 和蛋白质伴侣的特性如何影响它们排列的有用模型。许多重要的问题也与理解核小体之间的间距如何受组蛋白、染色质重塑因子或其他与染色质相关的蛋白质伴侣影响有关。对比度变化小角 X 射线散射 (CVSAXS) 报告了蛋白质-DNA 复合物中的 DNA 构象,这里将其应用于测量溶液中三聚体核小体的构象,特别敏感于连接核小体之间的距离和相对取向。这些数据与考虑 DNA 序列依赖性力学特性的 DNA 模型以及生成与测量散射图谱进行比较的逼真结构的蒙特卡罗技术相结合进行解释。在溶液中,三聚体核小体分为两个主要群体,侧翼核小体堆叠或几乎等距分开,例如所有核小体对之间的距离大致相等。这些群体与以前观察到的具有较短连接物的三聚体核小体的镁依赖性结构一致。