Department of Biomedical Engineering, Northwestern University, Evanston, United States.
Magnetism and Interface Physics & Computational Polymer Physics, Department of Materials, ETH Zurich, Zurich, Switzerland.
Elife. 2024 Sep 27;13:RP97604. doi: 10.7554/eLife.97604.
We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions. The SR-EV generate conformationally defined domains observed by single-cell imaging techniques. From nucleosome to chromosome scales, the model captures the overall chromatin organization as a corrugated system, with dense and dilute regions alternating in a manner that resembles the mixing of two disordered bi-continuous phases. This particular organizational topology is a consequence of the multiplicity of interactions and processes occurring in the nuclei, and mimicked by the proposed return rules. Single configuration properties and ensemble averages show a robust agreement between theoretical and experimental results including chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. Model and experimental results suggest that there is an inherent chromatin organization regardless of the cell character and resistant to an external forcing such as RAD21 degradation.
我们提出了基于随机规则和物理相互作用的染色质结构的自归巢排斥体积 (SR-EV) 模型。SR-EV 产生通过单细胞成像技术观察到的构象定义的域。从核小体到染色体尺度，该模型将整体染色质组织捕获为波纹系统，密集和稀疏区域以类似于两种无序双连续相混合的方式交替。这种特殊的组织拓扑结构是核内发生的多种相互作用和过程的结果，并通过提出的返回规则来模拟。单个构型特性和整体平均值表明理论和实验结果之间存在稳健的一致性，包括染色质体积浓度、接触概率、包装域识别和大小特征以及包装缩放行为。模型和实验结果表明，存在内在的染色质组织，无论细胞特征如何，并且不受 RAD21 降解等外部强制的影响。
