Mapping enhancer-gene regulation in single cells to connect genetic variants to target genes and cell types

项目摘要 人类基因组编码超过200万个称为增强子的DNA调节元件， 控制特定细胞类型和状态的基因表达。强化者体内有成千上万的 影响常见疾病和特征风险的遗传变异。这些增强剂中的每一种 变异可以揭示人类疾病的分子机制。然而， 缺乏工具来系统地绘制每个基因中哪些增强子调节哪些基因， 人体内有数千种细胞类型。 为了应对这一挑战，我们最近开发了CRISPR工具， 数以千计的增强子，并发现了一个简单的计算模型，可以预测 从染色质状态的增强子基因调控。这些新兴技术表明， 这是一种在许多细胞类型中映射增强子以将非编码变体连接到靶基因的策略。 在这里，我们将发展和扩展这些新技术，以映射和预测增强子基因 单细胞分辨率的连接。首先，我们将描述增强子功能如何变化 通过将我们的CRISPR工具与新的单细胞读数相结合， 方法来调查成千上万的增强子基因连接分化血管细胞。 其次，我们将开发一个计算模型，可以预测增强子基因的调控， 染色质可及性的单细胞测量。第三，我们将应用这些工具来构建地图 增强子基因调控在成人心脏，并证明这些地图的实用性 通过表征与冠状动脉疾病相关的遗传变异。 这些技术将能够在许多细胞类型中绘制增强子基因调控图， 将非编码遗传变异与其分子功能联系起来的基础资源。这 这种方法将广泛适用于任何常见的复杂疾病。该提案基于 PI在基因组学和团队科学方面与ENCODE联盟和变体的经验- 功能倡议。这个R35基因组创新奖将帮助PI在 人类基因组学和心血管疾病的接口，将包括重大贡献 科学团队的努力。斯坦福大学遗传学系的环境 儿童心脏中心是支持这些科学和领导角色的理想场所。

Project Summary The human genome encodes over 2 million DNA regulatory elements called enhancers that control gene expression in specific cell types and states. Enhancers harbor tens of thousands of genetic variants that influence risk for common diseases and traits. Each of these enhancer variants could reveal insights into the molecular mechanisms of human diseases. Yet, we have lacked tools to systematically map which enhancers regulate which genes in each of the thousands of cell types in the human body. To address this challenge, we have recently developed CRISPR tools to experimentally test thousands of enhancers in parallel, and discovered a simple computational model that can predict enhancer-gene regulation from chromatin state. These nascent technologies suggest a new strategy to map enhancers across many cell types to connect noncoding variants to target genes. Here we will develop and extend these new technologies to map and predict enhancer-gene connections at single-cell resolution. First, we will characterize how enhancer function changes across developmental trajectories, by combining our CRISPR tool with a new single-cell readout method to survey thousands of enhancer-gene connections in differentiating vascular cells. Second, we will develop a computational model that can predict enhancer-gene regulation from single-cell measurements of chromatin accessibility. Third, we will apply these tools to build maps of enhancer-gene regulation in the adult human heart, and demonstrate the utility of these maps by characterizing genetic variants associated with coronary artery disease. These technologies will enable mapping enhancer-gene regulation in many cell types, building a foundational resource for connecting noncoding genetic variants to their molecular functions. This approach will be broadly applicable to any common, complex disease. This proposal builds on the PI’s experiences in genomics and team science with the ENCODE Consortium and Variant- to-Function Initiative. This R35 Genomic Innovator Award will help the PI launch a career at the interface of human genomics and cardiovascular disease that will include significant contributions to team science efforts. The environment at Stanford University in the Department of Genetics and Children’s Heart Center is ideal for supporting these scientific and leadership roles.