High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes

摘要 大规模基因组注释联盟，如ENCODE、表观基因组学路线图和 其他人已经鉴定了数百万个假定的调节元件。我们现在需要集中精力 全面表征和量化这些元素的功能， 在这些区域内映射的变异，基因表达和细胞表型。我们的长期 目标是为人类的每个调节元件和非编码变体分配功能 基因组，了解功能在不同情况下如何变化，并利用这些信息， 更好地了解细胞适应性、疾病机制、细胞谱系特化和组织 体内平衡为了实现这一目标，我们开发了多种新型高通量 基于CRISPR的技术用于表征推定的基因调控的功能 通过扰乱它们在内源性、原生环境中的活动来改变元素。我们把这些 使用单细胞RNA-seq的方法来鉴定每个调控元件的靶基因。我们 还开发了dCas 9效应小鼠，以表征其体内天然 上下文此外，我们还开发了基于人群的高通量报告基因检测方法， （POP-STARR）来表征非编码遗传变异对整个 基因组本提案的目的是应用和分享我们的 互补的，强大的，可扩展的，和良好的特点的方法，通过合作， 支持IGVF联盟的目标，了解基因组和基因组变异 功能和编排复杂的表型。我们在开发、应用和 共享这些高通量的表征方法，以及提供对所有数据的访问， 支持我们将通过以下具体措施成功实现目标 目标：目标1。表征细胞存活所必需的所有基因调控元件。目标2. 表征细胞谱系特化所必需的所有基因调控元件。目标3： 表征所选eQTL区域中的所有基因调控元件。目标4。描述所有非- 小鼠模型中组织稳态所必需的编码元件。我们将使所有数据 即时可用，以及共享全面协议、试剂和分析工具 向科学界展示。总之，这个表征中心的各种方法将 在理解调控元件和非编码的作用方面取得变革性进展 许多不同表型的变异。

ABSTRACT Large scale genome annotation consortia such as ENCODE, Epigenomics Roadmap, and others have identified millions of putative regulatory elements. We now need to focus efforts on comprehensively characterizing and quantifying the function of those elements, and noncoding variants that map within these regions, on gene expression and cell phenotypes. Our long-term goal is to assign function to every regulatory element and noncoding variant in the human genome, understand how that function changes in different contexts, and use that information to better understand cell fitness, disease mechanisms, cell lineage specification, and tissue homeostasis. To accomplish this goal, we have developed multiple novel high-throughput CRISPR-based technologies for characterizing the function of putative gene regulatory elements by perturbing their activity in their endogenous, native context. We have coupled these methods with single-cell RNA-seq to identify the target gene(s) for each regulatory element. We have also developed dCas9 effector mice to characterize elements in their natural in vivo context. In addition, we have developed population-based high-throughput reporter assays (POP-STARR) to characterize the impact of noncoding genetic variation across the entire genome. The objective of this proposal is to apply and share our compendium of complementary, robust, scaleable, and well-characterized methods by working collaboratively to support the IGVF Consortium goals of understanding how genomes and genomic variation function and orchestrate complex phenotypes. Our track record in developing, applying, and sharing these high-throughput characterization methods, as well as providing access to all data, supports that we will be successful in accomplishing our objective via the following specific aims: Aim 1. Characterize all gene regulatory elements essential for cell survival. Aim 2. Characterize all gene regulatory elements essential to cell lineage specification. Aim 3. Characterize all gene regulatory elements in select eQTL regions. Aim 4. Characterize all non- coding elements essential to tissue homeostasis in a mouse model. We will make all data immediately available, as well as share comprehensive protocols, reagents, and analysis tools to the scientific community. Together, the diverse approaches of this Characterization Center will lead to transformative progress in understanding the role of regulatory elements and noncoding variants across many diverse phenotypes.