Center for 3D Structure and Physics of the Genome

项目总结 人类基因组在细胞核内的动态三维折叠，称为4D 核组在许多基因组过程中发挥作用，包括基因调控和基因组的维持 稳定性。染色体组织缺陷与人类疾病有关，如癌症，以及 过早衰老。随着细胞在发育和发育过程中状态的改变，4D核基因组被广泛地重新组织 随着细胞的老化。为了了解基因组是如何工作的，我们需要4D核基因组的全面图谱。 对于不同的细胞状态。我们还需要详细的分子和生物物理机制的知识。 染色体折叠和对4D核组在基因组功能中的作用的洞察，特别是在 建立和维持发育中的细胞状态及其在衰老和疾病中的丧失 为了应对这些挑战，我们组建了一个高度跨学科的中心，目标是 生成全面的4D基因组图，表示空间、物理、动态和功能 人类基因组在4D核组早期和晚期关键转变过程中的组织 生活。我们中心拥有丰富的经验，并制作了4DN参考Hi-C和Micro-C相互作用图， 和FISH数据集，以与Hi-C数据进行比较。我们有标杆技术来绘制基因组折叠图， 开发了数据标准、通用文件格式、Hi-C/Micro-C数据处理和数据可视化 管道和聚合物模拟方法。我们还开发了新的方法来量化 驱动染色体折叠(液体染色质Hi-C)，以定位核外围的基因座(Protect-Seq)，以检测 拓扑链(多接触3C)和绘制亚核蛋白质组和转录组(C-BERST)。 现在拥有一套全面的基准基因组、成像、蛋白质组分析和建模工具 接下来，我们将应用这些方法，并对生成的数据进行集成和建模，以确定 4D核组在生命周期中是如何发育的：从胚胎干细胞的不成熟状态到成熟状态 在细胞分化为肝细胞的过程中，然后4D核组如何再次变化并恶化为 细胞(过早)老化。我们将绘制基因组的3D结构以及相关的蛋白质和RNA 亚核结构附近的基因座，识别组织中细胞到细胞的变异，量化动态和生物物理 染色质相互作用的特性，并将染色体和核组织与基因表达联系起来。 这些不同的数据类型将被整合以确定4dN核组在 随着细胞分化和年龄的增长，单基因座的分辨率。染色体折叠的机械模型将是 配方和实验测试。最后，我们将开发新的平台来可视化和广泛分享 细胞转变过程中动态4D核组和4D核组轨迹的导航图。

PROJECT SUMMARY The dynamic three-dimensional folding of the human genome within the cell nucleus, referred to as the 4D nucleome, plays roles in many genomic processes, including gene regulation and maintenance of genome stability. Defects in chromosome organization are associated with human diseases such as cancer, and premature aging. The 4D nucleome is extensively re-organized as cells change state during development and as cells age. In order to understand how the genome works we need comprehensive maps of the 4D nucleome for different cell states. We also need detailed knowledge of the molecular and biophysical mechanisms of chromosome folding and insight into the role of the 4D nucleome in genome function, and particularly in establishing and maintaining cellular states in development and their loss in aging and disease To address these challenges, we have assembled a highly interdisciplinary Center with the goal of generating comprehensive 4D nucleome maps that represent the spatial, physical, dynamic and functional organization of the human genome during key transitions of the 4D nucleome during early and late stages in life. Our Center has extensive experience and produced 4DN Reference Hi-C and Micro-C Interaction maps, and FISH datasets to compare to Hi-C data. We have benchmarked technologies for mapping genome folding, and developed data standards, common file formats, Hi-C/Micro-C data processing and data visualization pipelines, and polymer simulation approaches. We also developed new methods to quantify the forces that drive chromosome folding (liquid chromatin Hi-C), to map loci at the nuclear periphery (Protect-seq), to detect topological catenations (multi-contact 3C) and to map sub-nuclear proteomes and transcriptomes (C-BERST). With a comprehensive suite of benchmarked genomic, imaging, proteomic assays and modeling tools now in hand, we will apply these approaches, and integrate and model the resulting data to determine pathways of how 4D nucleome develops during life span: from an immature state in embryonic stem cells, to a mature state during cell differentiation into hepatocytes, and then how the 4D nucleome changes again and deteriorates as cells (prematurely) age. We will map the 3D structure of the genome and associated proteins and RNAs, map loci near sub-nuclear structures, identify cell-to-cell variation in organization, quantify dynamic and biophysical properties of chromatin interactions, and relate chromosome and nuclear organization to gene expression. These different datatypes will be integrated to determine dynamic trajectories of the 4DN nucleome at the resolution of single loci as cells differentiate and age. Mechanistic models for chromosome folding will be formulated and experimentally tested. Finally, we will develop new platforms to visualize and widely share navigable maps of the dynamic 4D nucleome and 4D nucleome trajectories during cellular transitions.