Center for 3D Structure and Physics of the Genome

项目摘要 人类基因组在细胞核内的动态三维折叠，称为4D折叠。 核组在基因组的许多过程中发挥作用，包括基因调控和基因组的维持 稳定染色体组织的缺陷与人类疾病如癌症有关， 过早衰老随着细胞在发育过程中改变状态，4D核组被广泛重组， 随着细胞的衰老为了了解基因组如何工作，我们需要全面的4D核组图 针对不同的细胞状态。我们还需要详细的分子和生物物理机制的知识， 染色体折叠和洞察4D核组在基因组功能中的作用，特别是在 在发育过程中建立和维持细胞状态，以及在衰老和疾病中丧失细胞状态 为了应对这些挑战，我们组建了一个高度跨学科的中心，其目标是 生成全面的4D核组图，其代表空间、物理、动态和功能 在早期和晚期阶段，在4D核组的关键转变期间，人类基因组的组织 生活我们的中心有丰富的经验，并制作了4DN参考Hi-C和Micro-C交互地图， 和FISH数据集来与Hi-C数据比较。我们有绘制基因组折叠的基准技术， 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），绘制核周边的基因座（Protect-seq），检测 拓扑连锁（多接触3C）和映射亚核蛋白质组和转录组（C-BERST）。 凭借一套全面的基准基因组学、成像、蛋白质组学分析和建模工具， 我们将应用这些方法，并整合和建模产生的数据，以确定 4D核组如何在生命周期中发育：从胚胎干细胞的不成熟状态到成熟状态 在细胞分化成肝细胞的过程中，然后4D核组如何再次改变并恶化， 细胞（过早）老化。我们将绘制基因组和相关蛋白质和RNA的3D结构， 亚核结构附近的位点，识别组织中的细胞间变异，量化动态和生物物理 染色质相互作用的性质，并将染色体和核组织与基因表达联系起来。 这些不同的数据集将被整合，以确定4DN核子组在 随着细胞分化和老化，单个基因座的分辨率。染色体折叠的机制模型将是 配方和实验测试。最后，我们将开发新的平台，以可视化和广泛分享 在细胞转变期间动态4D核组和4D核组轨迹的可导航图。

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.