From fibers to the sea of nuclesomes: Computer simulations of the regulation of the spatial structure of Mbp chromatin domains in the nucleus

在真核生物的细胞核中，DNA包裹在组蛋白周围，形成称为核小体的圆柱形单位。核小体通过接头DNA连接并形成称为染色质的串珠状结构。在体外染色质采用直径为30 nm的纤维状结构，而在体内通常没有观察到这种结构。在拟议的研究中，我们将应用粗粒度的染色质计算机模拟来阐明这种折叠的条件和性质，其调节和变化的后果。连接DNA和核小体是由弹性和静电力相互作用的圆柱形单元模拟的。大都会蒙特卡罗和副本交换方法被用来采样的平衡态的配置合奏。在模拟中，将通过对1.5 Mbp范围内的长核小体链进行建模，并应用周期性边界条件，来模拟核中的高核小体密度条件。核小体的间距将基于合成的和来自实验的真实的核小体位置。高阶模型的折叠的基本空间特性将从这些模拟中提取。该模型将扩展的潜力描述成环蛋白cohesin和CTCF。来自模拟的数据的分析将阐明例如在染色体构象捕获技术中观察到的接触概率的分布，并解释与基因调控相关的核小体重新定位和/或CTCF/粘着蛋白耗尽引起的空间结构的变化。来自健康和恶性细胞的ATAC-Seq和Hi-C数据提供了有关转录因子结合、染色质可及性和空间结构的信息。我们将联合收割机在染色质大区域模型中结合这些数据，即所谓的TADS，以阐明基因的顺式和反式调节机制以及恶性细胞中基因的失调。

In the nucleus of eukaryotes DNA is wrapped around histone proteins forming cylindrical units called nucleosomes. Nucleosomes are connected by linker DNA and form a bead-on-a-string like structure termed chromatin. In vitro chromatin adopts a fiber-like structure with a diameter of 30 nm while in general in vivo no such structure is observed. In the proposed research we will apply coarse-grained computer simulations of chromatin to elucidate conditions and properties of this folding, its regulation and the consequences of the changes. Linker DNA and the nucleosomes are modelled by cylindrical units interacting by elastic and electrostatic forces. Metropolis Monte Carlo and replica exchange methods are used to sample an ensemble of configurations in equilibrium. The conditions of high nucleosome density as in the nucleus will be mimicked in the simulations by modelling long nucleosome chains in the range of 1.5 Mbp and larger applying periodic boundary conditions. The spacing of the nucleosomes will be based on synthetic and real nucleosome positions from experiments. Fundamental spatial properties of the folding of higher order models will be extracted from these simulations. The model will be extended by potentials describing the loop-forming proteins cohesin and CTCF. The analysis of data from simulations will elucidate the distribution of contact probabilities as observed e.g. in chromosome conformation capture techniques and explain changes of the spatial structure by nucleosome repositioning and/or CTCF/cohesin depletion connected with gene regulation. Data from ATAC-Seq and Hi-C from healthy and malign cells provides information about transcription factor binding, chromatin accessibility and spatial structure. We will combine these data in models of large domains of chromatin, so called TADS, to elucidate cis- and trans-regulation mechanisms of genes and the deregulation of genes in malign cells.