人类染色体在细胞核中具有复杂的3D空间组织,它包括跨基因组尺度的物理相互作用的层次结构。这样的架构发挥着重要的功能作用,因为基因和它们的调节因子必须在物理上相互作用来控制基因调节。然而,这些接触形成的分子机制仍然知之甚少。这里,我们描述了一种基于聚合物物理的方法来研究机器塑造基因组折叠和功能。针对独立的超分辨率单细胞显微镜数据验证了对DNA单分子3D结构的计算机模型预测,支持一种方案,即染色体结构受相分离的热力学机制控制。最后,作为我们方法的应用,该理论的经验证的单聚合物构象被用来作为探测基因组结构的强大技术的基准,比如Hi-C,SPRITE,和GAM。
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.