Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso di Monte Sant'Angelo, Naples, Italy.
Berlin Institute for Medical Systems Biology, Max-Delbrück Centre (MDC) for Molecular Medicine, Berlin, Germany.
Methods Mol Biol. 2023;2655:57-66. doi: 10.1007/978-1-0716-3143-0_5.
Human chromosomes have a complex 3D spatial organization in the cell nucleus, which comprises a hierarchy of physical interactions across genomic scales. Such an architecture serves important functional roles, as genes and their regulators have to physically interact to control gene regulation. However, the molecular mechanisms underlying the formation of those contacts remain poorly understood. Here, we describe a polymer-physics-based approach to investigate the machinery shaping genome folding and function. In silico model predictions on DNA single-molecule 3D structures are validated against independent super-resolution single-cell microscopy data, supporting a scenario whereby chromosome architecture is controlled by thermodynamics mechanisms of phase separation. Finally, as an application of our methods, the validated single-polymer conformations of the theory are used to benchmark powerful technologies to probe genome structure, such as Hi-C, SPRITE, and GAM.
人类染色体在细胞核中有一个复杂的三维空间组织，它包含基因组尺度上的物理相互作用的层次结构。这种结构具有重要的功能作用，因为基因及其调控因子必须进行物理相互作用才能控制基因调控。然而，形成这些接触的分子机制仍知之甚少。在这里，我们描述了一种基于聚合物物理的方法来研究塑造基因组折叠和功能的机制。对 DNA 单分子三维结构的计算机模型预测与独立的超分辨率单细胞显微镜数据进行了验证，支持了这样一种情景，即染色体结构受相分离热力学机制控制。最后，作为我们方法的一个应用，理论的经过验证的单聚合物构象被用于基准强大的技术来探测基因组结构，如 Hi-C、SPRITE 和 GAM。
