A dynamic view of DNA structure within the nucleosome: Biological implications.,Journal of Structural Biology

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A dynamic view of DNA structure within the nucleosome: Biological implications.
Journal of Structural Biology ( IF 3.0 ) Pub Date : 2020-04-18 , DOI: 10.1016/j.jsb.2020.107511
Romain Retureau ₁ , Nicolas Foloppe ₂ , Ahmad Elbahnsi ₃ , Christophe Oguey ₄ , Brigitte Hartmann ₁

Affiliation

Most of eukaryotic cellular DNA is packed in nucleosome core particles (NCPs), in which the DNA (DNANCP) is wrapped around histones. The influence of this organization on the intrinsic local dynamics of DNA is largely unknown, in particular because capturing such information from experiments remains notoriously challenging. Given the importance of dynamical properties in DNA functions, we addressed this issue using MD simulations of a nucleosome containing the NCP positioning 601 sequence and four related free dodecamers. Comparison between DNANCP and free DNA reveals a limited impact of the dense DNA-histone interface on correlated motions of dinucleotide constituents and on fluctuations of inter base pair parameters. A characteristic feature intimately associated with the DNANCP super-helical path is a set of structural periodicities that includes a marked alternation of regions enriched in backbone BI and BII conformers. This observation led to uncover a convincing correspondence between the sequence effect on BI/BII propensities in both DNANCP and free DNA, strengthening the idea that the histone preference for particular DNA sequences relies on those intrinsic structural properties. These results offer for the first time a detailed view of the DNA dynamical behavior within NCP. They show in particular that the DNANCP dynamics is substantial enough to preserve the ability to structurally adjust to external proteins, for instance remodelers. Also, fresh structural arguments highlight the relevance of relationships between DNA sequence and structural properties for NCP formation. Overall, our work offers a more rational framework to approach the functional, biological roles of NCP.

中文翻译：

核小体内 DNA 结构的动态视图：生物学意义。

大多数真核细胞 DNA 包装在核小体核心颗粒 (NCP) 中，其中 DNA (DNANCP) 包裹在组蛋白周围。该组织对 DNA 内在局部动力学的影响在很大程度上是未知的，特别是因为从实验中获取此类信息仍然是众所周知的挑战。鉴于动态特性在 DNA 功能中的重要性，我们使用包含 NCP 定位 601 序列和四个相关游离十二聚体的核小体的 MD 模拟解决了这个问题。DNANCP 和游离 DNA 之间的比较揭示了致密 DNA-组蛋白界面对二核苷酸成分的相关运动和碱基对间参数波动的有限影响。与 DNANCP 超螺旋路径密切相关的一个特征是一组结构周期性，其中包括富含骨干 BI 和 BII 构象异构体的区域的显着交替。这一观察结果揭示了序列对 DNANCP 和游离 DNA 中 BI/BII 倾向的影响之间令人信服的对应关系，加强了组蛋白对特定 DNA 序列的偏好依赖于这些内在结构特性的观点。这些结果首次提供了 NCP 内 DNA 动力学行为的详细视图。他们特别表明，DNANCP 动力学足以保持结构调整外部蛋白质（例如重塑剂）的能力。还，新的结构论点强调了 DNA 序列与 NCP 形成的结构特性之间关系的相关性。总的来说，我们的工作提供了一个更合理的框架来处理 NCP 的功能和生物学作用。

更新日期：2020-04-18

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