Department of Computational Science and Engineering, Nagoya University, Nagoya, Japan.
Biophys J. 2012 Jan 18;102(2):296-304. doi: 10.1016/j.bpj.2011.12.005.
Eukaryotic genome is organized in a set of chromosomes each of which consists of a chain of DNA and associated proteins. Processes involving DNA such as transcription, duplication, and repair, therefore, should be intrinsically related to the three-dimensional organization of the genome. In this article, we develop a computational model of the three-dimensional organization of the haploid genome of interphase budding yeast by regarding chromosomes as chains moving under the constraints of nuclear structure and chromatin-chromatin interactions. The simulated genome structure largely fluctuates with the diffusive movement of chromosomes. This fluctuation, however, is not completely random, as parts of chromosomes distribute in characteristic ways to form "territories" in the nucleus. By suitably taking account of constraints arising from the data of the chromosome-conformation-capture measurement, the model explains the observed fluorescence data of chromosome distributions and motions.
真核生物基因组组织在一组染色体中，每条染色体由 DNA 链和相关蛋白组成。因此，涉及 DNA 的过程，如转录、复制和修复，应该与基因组的三维结构内在相关。在本文中，我们通过将染色体视为在核结构和染色质-染色质相互作用的约束下移动的链，开发了有丝分裂芽殖酵母单倍体基因组三维组织的计算模型。模拟的基因组结构随染色体的扩散运动而大幅波动。然而，这种波动并不是完全随机的，因为染色体的某些部分以特征方式分布，在核内形成“区域”。通过适当考虑来自染色体构象捕获测量数据的约束，该模型解释了观察到的染色体分布和运动的荧光数据。
