Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, Japan.
Department of Complex Systems Science, Nagoya University, Nagoya, Japan.
Methods Mol Biol. 2025;2856:293-308. doi: 10.1007/978-1-0716-4136-1_18.
In order to analyze the three-dimensional genome architecture, it is important to simulate how the genome is structured through the cell cycle progression. In this chapter, we present the usage of our computation codes for simulating how the human genome is formed as the cell transforms from anaphase to interphase. We do not use the global Hi-C data as an input into the genome simulation but represent all chromosomes as linear polymers annotated by the neighboring region contact index (NCI), which classifies the A/B type of each local chromatin region. The simulated mitotic chromosomes heterogeneously expand upon entry to the G1 phase, which induces phase separation of A and B chromatin regions, establishing chromosome territories, compartments, and lamina and nucleolus associations in the interphase nucleus. When the appropriate one-dimensional chromosomal annotation is possible, using the protocol of this chapter, one can quantitatively simulate the three-dimensional genome structure and dynamics of human cells of interest.
为了分析三维基因组结构，模拟基因组如何随着细胞周期的进展而构建是很重要的。在本章中，我们介绍了如何使用我们的计算代码来模拟人类基因组的形成过程，即细胞从后期转变为间期的过程。我们没有将全局 Hi-C 数据作为基因组模拟的输入，而是将所有染色体表示为线性聚合物，这些聚合物由相邻区域接触指数（NCI）注释，该指数对每个局部染色质区域的 A/B 类型进行分类。模拟有丝分裂染色体在进入 G1 期时不均匀地扩张，这会导致 A 和 B 染色质区域的相分离，从而在间期核中建立染色体区域、隔室和板层以及核仁的关联。当可以使用适当的一维染色体注释时，可以使用本章中的协议来定量模拟感兴趣的人类细胞的三维基因组结构和动力学。
