New automated experimental and computational pipeline for high coverage single-cell Hi-C and its integration with single cell RNA-seq: enabling 4D Nucleomics at single cell resolution

 描述(申请人提供)：在这个项目中，我们将开发新的方法来研究小鼠骨髓中各种细胞类型的基因组的三维排列。基因组的三维结构，即它在细胞核中的物理排列方式，被认为是基因组控制的重要组成部分。在正确的细胞或组织类型中，以及在正确的发育阶段，基因被开启和关闭的机制包括基因组空间组织的变化。我们将开发一种新的方法，可以评估数千个单个细胞中的三维基因组组织，并同时测量其中大量细胞的实际基因表达谱。我们将对这些数据进行系统的数学和统计分析，以寻找基因组组织的新原理，这些原理可能在控制健康和疾病的基因组方面发挥未知的作用。我们还将使用这些数据来生成单个染色体和整个基因组的3D计算机模型，因为它存在于单个细胞核中。然后，我们将使用这些模型来寻找在基因控制中可能重要的基因组的空间模式、重复结构和可变结构区域。对于这些实验，我们将使用小鼠骨髓细胞，这是人类骨髓细胞的重要代表。骨髓是一种临床上重要的复杂组织，含有成体干细胞，这些干细胞可以产生血液和免疫系统的所有细胞。 通过系统分析这些重要细胞类型的3D基因组构象和基因表达谱，我们将提供这些细胞类型如何作用于创造血液的基本知识。我们将与其他研究小组合作，确保他们能够获得这些强大的技术和计算机分析包，这将加速更全面地了解基因组是如何控制的。这些信息对于设计治疗血液和其他组织疾病的新的有效治疗策略至关重要，对于了解癌症的分子基础以更有效地治疗和预防癌症至关重要。

 DESCRIPTION (provided by applicant): In this project we will develop new methods to investigate the three dimensional arrangement of the genome in various cell types from mouse bone marrow. The three dimensional organization of the genome, how it is physically arranged in the nucleus of cells, is recognized as an important component of genome control. The mechanisms by which genes get switched on and off in the correct cells or tissue type, and during the correct stages of development include changes in the spatial organization of the genome. We will develop a new method that can assess three dimensional genome organizations in thousands of individual cells and simultaneously measure the actual gene expression profile of a large number of those cells. We will systematically analyze the data mathematically and statistically to look for new principles of genome organization that may play unknown roles in controlling the genome in health and disease. We will also use the data to generate 3D computer models of individual chromosomes and the entire genome as it exists in the individual cell nucleus. We will then use these models to look for spatial patterns, recurring structures and variable structured regions of the genome that may be important in gene control. For these experiments we will use mouse bone marrow cells, which are an important representative of human bone marrow cells. Bone marrow is a clinically important, complex tissue containing the adult stems cells that give rise to all cells of the blood and immune system. By systematically analyzing the 3D genome conformation and gene expression profiles of these important cell types we will be providing fundamental knowledge of how these cell types function to create the blood. We will cooperate with other research groups to ensure that they have access to these powerful technologies and computer analysis packages that will accelerate a fuller understanding of how the genome is controlled. This information is vital to design new effective therapeutic strategies for the treatment of diseases of the blood and other tissues, and to understand the molecular basis of cancers for more effective treatments and prevention.