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

项目摘要 全基因组关联研究已经确定了数千种与遗传相关的非编码遗传变异， 常见的血管疾病和特征。这些关联中的每一个都可以指向一个基因和血管细胞类型， 告诉我们疾病的机制。然而，很难将这些非编码变体与它们的 分子功能，在很大程度上是因为它们可以通过远距离3D接触来调节远距离基因。到 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 3D基因组影响血管细胞中的基因表达？ 我们最近的工作提出了一种新的策略，可以系统地绘制和计算预测3D基因组如何 将血管疾病变异体与其靶基因联系起来。通过收集数以千计的CRISPR数据， 我们开发了接触活动模型来描述3D特征如何 基因组控制增强子-启动子调控。通过分析体外人体血管细胞中的3D接触， 我们将一种血管疾病变异体与靶基因内皮素-1连接起来，该基因位于600 Kb以外。这些结果 提供了一个预测框架，以了解3D接触如何影响基因表达，并揭示了一种策略， 通过绘制体内3D基因组，系统地将变异与功能联系起来。 我们建议在血管细胞中绘制，建模和操纵3D增强子-启动子接触，以连接风险 血管疾病的变异体靶向基因和细胞类型。我们将：（1）产生全基因组的资源 原代人血管细胞中的3D接触图;（2）剖析3D接触如何引导增强子靶向基因 使用组合CRISPR扰动;以及（3）在计算和实验上将血管疾病 GWAS变体对3D接触和基因表达的影响 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 计算基因组学来绘制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 交叉合作研究。这项研究将为研究遗传变异提供资源， 血管生物学，阐明了由3D基因组调控基因表达的机制，并证明了 确定影响常见血管疾病和特征风险的生物学机制的一般策略。

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.