Mapping, modeling, and manipulating 3D contacts in vascular cells to connect risk variants to disease genes

项目总结 全基因组关联研究已经确定了数千个非编码遗传变异与 常见血管疾病及其特点。这些关联中的每一个都可能指向一种基因和血管细胞类型，以 给我们讲讲疾病的机制。然而，很难将这些非编码变体与它们的 分子功能，很大程度上是因为它们可以通过远程3D接触来调节遥远的基因。至 将这些变异与靶基因联系起来，我们将需要回答：细胞类型和疾病特异性特征是如何 3D基因组对血管细胞基因表达的影响？ 我们最近的工作提出了一种新的策略，系统地绘制和计算预测3D基因组如何 将血管疾病变种与它们的目标基因联系起来。通过收集数千个CRISPR的数据 对于调节元件的扰动，我们开发了按接触活动模型来描述3D特征 基因组控制增强子-启动子调控。通过在体外分析人体血管细胞的3D接触， 我们将一个血管疾病变异体与一个目标基因--内皮素-1连接起来，该基因位于600 kb之外。这些结果 提供预测框架，以了解3D接触如何影响基因表达，并揭示策略 通过绘制体内3D基因组图，系统地连接变异以发挥功能。 我们建议对血管细胞中的3D增强子-启动子接触进行作图、建模和操作，以连接风险 血管疾病的变异体以基因和细胞类型为靶点。我们将：(1)产生一个全基因组的资源 原代人类血管细胞3D接触图谱；(2)3D接触如何引导增强子靶向基因 使用组合CRISPR扰动；以及(3)通过计算和实验将血管疾病联系起来 对3D接触和基因表达的影响的GWA型变异。 我们的团队包括人类遗传学、血管生物学、基因组工程、3D基因组图谱和 计算基因组学绘制3D接触图以确定动脉粥样硬化的靶点。斯坦福大学的环境 大学、布罗德研究所和贝勒医学院是支持这些创新和 交叉协作研究。这项研究将为研究影响 血管生物学，阐明了3D基因组调节基因表达的机制，并展示了 确定影响常见血管疾病和特征风险的生物机制的一般策略。

PROJECT SUMMARY Genome-wide association studies have identified thousands of noncoding genetic variants associated with common vascular diseases and traits. Each of these associations could point to a gene and vascular cell type to teach us about mechanisms of disease. Yet, it has been difficult to connect these noncoding variants to their molecular functions, in large part because they can act via long-range 3D contacts to regulate distant genes. To connect these variants to target genes, we will need to answer: How do cell-type and disease-specific features of the 3D genome impact gene expression in vascular cells? Our recent work suggests a new strategy to systematically map and computationally predict how the 3D genome connects vascular disease variants to their target genes. By collecting data on thousands of CRISPR perturbations of regulatory elements, we developed the Activity-by-Contact Model to describe how 3D features of the genome control enhancer-promoter regulation. By analyzing 3D contacts in human vascular cells in vitro, we connected one vascular disease variant to a target gene, endothelin-1, located >600 Kb away. These results provide a predictive framework to understand how 3D contacts impact gene expression, and reveal a strategy to systematically connect variants to function by mapping the 3D genome in vivo. We propose to map, model, and manipulate 3D enhancer-promoter contacts in vascular cells to connect risk variants for vascular diseases to target genes and cell types. We will: (1) generate a resource of genome-wide 3D contact maps in primary human vascular cells; (2) dissect how 3D contacts guide enhancers to target genes using combinatorial CRISPR perturbations; and (3) computationally and experimentally link vascular disease GWAS variants to effects on 3D contacts and gene expression. Our team includes experts in human genetics, vascular biology, genome engineering, 3D genome mapping, and computational genomics to map 3D contacts to identify targets for atherosclerosis. The environments at Stanford University, the Broad Institute, and Baylor College of Medicine are ideal for supporting these innovative and cross-collaborative studies. This study will provide a resource for studying genetic variants that influence vascular biology, illuminate a mechanism by the 3D genome regulates gene expression, and demonstrate a general strategy to identify biological mechanisms that influence risk for common vascular diseases and traits.