University of Washington Center for Nuclear Organization and Function

华盛顿大学核组织与功能中心

• 批准号: 9916567
• 负责人: William Stafford Noble
• 金额: $ 8.44万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-30 至 2021-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9916567
• 关键词: 3-Dimensional; Address; Algorithms; Architecture; Area; Biological; Biological Assay; Biological Models; Biology; Cardiac Myocytes; Cardiomyopathies; Cell Cycle; Cell Differentiation process; Cell Nucleus; Cells; Chromosomes; Computer Simulation; Computer software; Computing Methodologies; Coupled; DNA; DNA biosynthesis; Data; Data Set; Deoxyribonucleases; Development; Dimensions; Diploidy; Disease; Down Syndrome; Endothelial Cells; Gene Expression; Gene Expression Regulation; Genome; Genomics; Human; Human Biology; Human Cell Line; Hybrids; Induced Mutation; Lamin Type A; Link; Methods; Modeling; Molecular Conformation; Mus; Nature; Nuclear; Nuclear Matrix-Associated Proteins; Output; Process; Protocols documentation; Research Personnel; Side; Skeletal Myoblasts; System; Technology; Testing; Time; Tissues; Universities; Validation; Washington; Work; biological systems; combinatorial; embryonic stem cell; genome editing; genomic data; human disease; human embryonic stem cell; improved; in vivo; insight; method development; novel; predictive modeling; programs; response; technology development; three-dimensional modeling; tool

ABSTRACT – UNIVERSITY OF WASHINGTON CENTER FOR NUCLEAR ORGANIZATION AND FUNCTION (UW-CNOF) A current grand challenge in genomics involves accurately assaying, at all relevant scales, the 3D conformation of DNA in vivo and then linking conformational changes to dynamic processes such as the cell cycle, differentiation and disease. Here we propose to create the University of Washington Center for Nuclear Organization and Function, bringing together an interdisciplinary team of investigators whose diverse areas of expertise – technology development, computational modeling, and mouse and human biology – make them ideally suited to this challenge. Our overall hypothesis is that characterizing and understanding changes in genome architecture over time (the 4D nucleome) will lead to fundamental insights into human biology and disease. We will address this hypothesis by developing a combination of experimental and computational methods development, coupled with their systematic biological validation and application to development- and disease-relevant systems. On the experimental side, we will further optimize our recently developed DNase Hi- C assay, including combinatorial methods for single cells, ultimately aiming to concurrently assay nuclear architecture and gene expression within each of many single cells. On the computational side, we will extend our existing 3D modeling algorithms to account for diploidy, cell-to-cell variability, the hierarchical nature of genome architecture, and to explicitly model architectural changes over cell cycle and cell differentiation time scales. We will then employ several complementary computational methods to link our 4D nucleome models to existing, 1D genomics data sets. The outputs of these new experimental and computational technologies will be subjected to orthogonal validation in several well-understood model systems: human cell lines, in vivo tissues from interspecific F1 hybrid mice, mouse embryonic stem cells (ESCs) and skeletal myoblasts. We will also test specific predictions of the models in response to targeted (genome editing) or large-scale (chromosome silencing) perturbations. After initial validation and in parallel with further methods development, we will apply our new tools to the analysis of three biological systems: we will characterize the dynamics of nuclear architecture during the directed differentiation of naïve human ESCs into cardiomyocytes and endothelial cells; we will test the hypothesis that cardiomyopathy-inducing mutations in the nuclear scaffolding protein, lamin A, are associated with derangements in cardiomyocyte nuclear architecture; and we will determine the changes in human cardiomyocyte nuclear architecture induced by trisomy 21. The proposed center will produce new experimental protocols for ascertaining 4D nucleome architecture, two new software toolkits for modeling the 4D nucleome and linking features of the nucleome to other types of genomic data, a variety of publicly available, large-scale 4D nucleome data sets in mouse and human systems, and fundamental insights into human biology and disease. In all of this work, we will work closely and openly with NOFIC and the 4DN Network to maximize the impact of our center and the overall program.

摘要 – 华盛顿大学核组织与功能中心 (UW-CNOF) 当前基因组学领域的一项重大挑战涉及在所有相关尺度上准确分析 3D DNA 体内构象，然后将构象变化与细胞等动态过程联系起来 周期、分化和疾病。在这里，我们提议创建华盛顿大学核中心 组织和职能，汇集了一个跨学科的研究人员团队，他们的不同领域 专业知识——技术开发、计算建模以及小鼠和人类生物学——使它们成为可能 非常适合这一挑战。我们的总体假设是，描述和理解变化 随着时间的推移，基因组结构（4D 核组）将带来对人类生物学和 疾病。我们将通过实验和计算的结合来解决这个假设 方法开发，及其系统的生物学验证和应用到开发和 疾病相关系统。在实验方面，我们将进一步优化我们最近开发的DNase Hi- C 测定，包括单细胞的组合方法，最终目标是同时测定核 许多单细胞中每个细胞的结构和基因表达。在计算方面，我们将扩展 我们现有的 3D 建模算法可以解释二倍体、细胞间的变异性、细胞的层次性质 基因组结构，并明确模拟细胞周期和细胞分化时间的结构变化 秤。然后，我们将采用几种互补的计算方法将我们的 4D 核组模型链接到 现有的一维基因组学数据集。这些新的实验和计算技术的输出将 在几个众所周知的模型系统中进行正交验证：人类细胞系，体内 来自种间 F1 杂交小鼠的组织、小鼠胚胎干细胞 (ESC) 和骨骼肌母细胞。我们将 还测试模型针对目标（基因组编辑）或大规模的具体预测 （染色体沉默）扰动。经过初步验证并与进一步的方法开发同时进行， 我们将应用我们的新工具来分析三个生物系统：我们将表征 原始人类 ESC 定向分化为心肌细胞期间的核结构 内皮细胞；我们将检验以下假设：核支架中诱发心肌病的突变 蛋白质核纤层蛋白 A 与心肌细胞核结构的紊乱有关；我们会 确定 21 三体性引起的人心肌细胞核结构的变化。 该中心将制定用于确定 4D 核组结构的新实验方案、两个新软件 用于对 4D 核组进行建模并将核组特征与其他类型的基因组数据联系起来的工具包， 小鼠和人体系统中各种公开可用的大规模 4D 核组数据集，以及 对人类生物学和疾病的基本见解。在所有这些工作中，我们将与 NOFIC 和 4DN 网络最大限度地发挥我们中心和整个计划的影响。