Novel methods to detect and interpret splicing quantitative trait loci

检测和解释剪接数量性状位点的新方法

• 批准号: 10358649
• 负责人: Yang Li
• 金额: $ 65.25万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2024-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10358649
• 关键词: 3' Splice Site; Accounting; Affect; Biogenesis; Biological Assay; Cell Line; Cells; Chromatin; Complex; Coupling; Data; Data Set; Disease; Event; Exons; Foundations; Gene Expression; Gene Expression Regulation; Genes; Genetic Risk; Genetic Transcription; Genetic Variation; Genome; Genomics; Goals; Human; Human Genetics; Introns; Link; Measurement; Measures; Mediating; Messenger RNA; Methods; Monitor; Nature; Nucleotides; Pathway interactions; Play; Positioning Attribute; Process; Protein Isoforms; Publishing; Quantitative Trait Loci; RNA; RNA Decay; RNA Splicing; Regulatory Element; Reporting; Resolution; Role; Site; Specificity; Statistical Methods; Terminator Codon; Time; Tissues; Treatment Efficacy; Untranslated RNA; Variant; disorder risk; genetic variant; genome-wide; genomic data; innovation; insight; novel; outcome prediction; polyadenylated messenger RNA; premature; risk variant; trait; transcriptome sequencing

Nearly all genetic variants associated with complex disease are noncoding. Many noncoding disease risk variants affect the amplitude of gene expression. However, we have identified mRNA splicing as an additional primary link between genetic variants and complex diseases. Thus, an understanding of how, and which, genetic variants affect RNA splicing can greatly aid our understanding of the impact of noncoding variants. Despite the importance of RNA splicing in mediating genetic risk for disease, the dominant assay to determine mRNA content in a cell or tissue, RNA-seq of polyadenylated mRNA, primarily captures steady-state mRNA isoforms, which reflect not only RNA splicing but also other processes such as RNA decay. Further, RNA-seq provides little information on the pathway of RNA isoform biogenesis. Yet, other assays beyond RNA-seq that report on the pathway of RNA splicing and in a manner independent of decay are sorely lacking, significantly compromising our ability to account for how, and which, genetic variants affect RNA splicing. We propose to first develop a battery of novel genomic assays to monitor the pathway of splicing and then exploit these assays to define the impact of genetic variation on splicing. We will optimize such approaches to yield datasets to study the mechanisms by which genetic variants affect mRNA splicing at unprecedented detail. Specifically, to achieve our goals, we propose i) to develop genome-wide assays to monitor splicing in novel ways, ii) to search for splicing quantitative trail loci using these assays, and iii) to account through an integrated approach for the functional mechanisms by which genetic variants affect splicing. At the conclusion of this project, we will have developed genomic assays and computational approaches that allow us to reach a deep understanding of the mechanisms that link sequence variation to variation in splicing and ultimately to disease.

几乎所有与复杂疾病相关的遗传变异都是非编码的。许多非编码疾病风险 变异影响基因表达的幅度。然而，我们已经确定mRNA剪接是一种额外的 遗传变异和复杂疾病之间的主要联系。因此，了解如何，以及哪些，遗传 变异影响RNA剪接的研究可以极大地帮助我们理解非编码变异的影响。尽管 RNA剪接在介导疾病遗传风险中的重要性，确定mRNA 多聚腺苷酸化mRNA的RNA-seq，主要捕获稳态mRNA同种型， 这不仅反映了RNA剪接，也反映了其他过程，如RNA衰变。此外，RNA-seq提供了 关于RNA异构体生物合成途径的信息很少。然而，除了RNA-seq之外的其他检测方法报告了 RNA剪接途径和不依赖于衰变的方式严重缺乏， 削弱了我们解释遗传变异如何以及哪些影响RNA剪接的能力。我们建议 首先开发一系列新的基因组检测来监测剪接途径，然后利用这些检测 来确定基因变异对剪接的影响。我们将优化这些方法，以产生数据集进行研究 遗传变异以前所未有的细节影响mRNA剪接的机制。具体来说，为了实现 我们的目标，我们建议i）开发全基因组检测，以新的方式监测剪接，ii）寻找 使用这些测定来剪接定量trail基因座，和iii）通过整合方法来解释 基因变异影响剪接的功能机制。在该项目结束时，我们将拥有 开发了基因组测定和计算方法，使我们能够深入了解 将序列变异与剪接变异并最终与疾病联系起来。