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

基本信息

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
项目类别：
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&apos 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

项目摘要

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 剪接是一种额外的方法。遗传变异与复杂疾病之间的主要联系。因此，了解遗传如何以及哪些内容影响 RNA 剪接的变异可以极大地帮助我们了解非编码变异的影响。尽管 RNA 剪接在调节疾病遗传风险中的重要性，这是确定 mRNA 的主要检测方法细胞或组织中的内容，聚腺苷酸化 mRNA 的 RNA-seq，主要捕获稳态 mRNA 亚型，这不仅反映了 RNA 剪接，还反映了其他过程，例如 RNA 衰变。此外，RNA-seq 还提供关于 RNA 同工型生物发生途径的信息很少。然而，除 RNA-seq 之外的其他检测报告 RNA 剪接的途径及其独立于衰变的方式非常缺乏，显着损害了我们解释基因变异如何影响以及哪些基因变异影响 RNA 剪接的能力。我们建议首先开发一系列新颖的基因组检测方法来监测剪接途径，然后利用这些检测方法定义遗传变异对剪接的影响。我们将优化此类方法以产生用于研究的数据集以前所未有的细节了解遗传变异影响 mRNA 剪接的机制。具体来说，要实现我们的目标是，i) 开发全基因组检测，以新颖的方式监测剪接，ii) 寻找使用这些测定法剪接定量轨迹基因座，以及 iii) 通过综合方法来解释遗传变异影响剪接的功能机制。在这个项目结束时，我们将拥有开发的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联系起来并最终与疾病联系起来的机制。