La Jolla Institute for Immunology, La Jolla, CA, USA.
Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA.
Nat Genet. 2021 Jan;53(1):110-119. doi: 10.1038/s41588-020-00745-3. Epub 2020 Dec 21.
Expression quantitative trait loci (eQTLs) studies provide associations of genetic variants with gene expression but fall short of pinpointing functionally important eQTLs. Here, using H3K27ac HiChIP assays, we mapped eQTLs overlapping active cis-regulatory elements that interact with their target gene promoters (promoter-interacting eQTLs, pieQTLs) in five common immune cell types (Database of Immune Cell Expression, Expression quantitative trait loci and Epigenomics (DICE) cis-interactome project). This approach allowed us to identify functionally important eQTLs and show mechanisms that explain their cell-type restriction. We also devised an approach to eQTL discovery that relies on HiChIP-based promoter interaction maps as a structural framework for deciding which SNPs to test for association with gene expression, and observe ultra-long-distance pieQTLs (>1 megabase away), including several disease-risk variants. We validated the functional role of pieQTLs using reporter assays, CRISPRi, dCas9-tiling guides and Cas9-mediated base-pair editing. In this article we present a method for functional eQTL discovery and provide insights into relevance of noncoding variants for cell-specific gene regulation and for disease association beyond conventional eQTL mapping.
表达数量性状基因座 (eQTL) 研究提供了遗传变异与基因表达之间的关联，但未能确定功能重要的 eQTL。在这里，我们使用 H3K27ac HiChIP 检测，在五个常见免疫细胞类型中（免疫细胞表达数据库、表达数量性状基因座和表观基因组学 (DICE) 顺式互作组计划），绘制了与它们的靶基因启动子相互作用的活性顺式调控元件重叠的 eQTL（启动子相互作用 eQTL，pieQTL）。这种方法使我们能够识别功能重要的 eQTL，并展示解释其细胞类型限制的机制。我们还设计了一种依赖于基于 HiChIP 的启动子相互作用图谱的 eQTL 发现方法，作为决定要测试哪些 SNP 与基因表达相关联的结构框架，并观察到超长距离 pieQTL（> 1 Mb 远），包括几个疾病风险变异。我们使用报告基因检测、CRISPRi、dCas9 平铺引导和 Cas9 介导的碱基对编辑来验证 pieQTL 的功能作用。在本文中，我们提出了一种用于功能 eQTL 发现的方法，并提供了对非编码变异在细胞特异性基因调控和疾病关联中的相关性的见解，超越了传统的 eQTL 映射。
