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：
10772507
负责人：
Yang Li
金额：
$ 12万
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 2025-02-28
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10772507
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 Maps Measurement Measures Mediating Messenger RNA Methods Monitor Nature Nucleotides Pathway interactions Play Polyadenylation Pathway 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 Transcription Process Treatment Efficacy Untranslated RNA Variant data integration 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无编码的。许多非编码疾病风险变体会影响基因表达的幅度。但是，我们已经将mRNA剪接确定为附加遗传变异与复杂疾病之间的主要联系。因此，了解如何以及哪个遗传变体影响RNA剪接可以极大地帮助我们理解非编码变体的影响。尽管有 RNA剪接在介导疾病遗传风险中的重要性，这是确定mRNA的主要测定在细胞或组织中的含量，聚腺苷酸化mRNA的RNA-SEQ，主要捕获稳态mRNA同工型，它不仅反映了RNA剪接，还反映了其他过程，例如RNA衰减。此外，RNA-seq提供关于RNA同工型生物发生途径的信息很少。然而，除了RNA-seq之外的其他测定 RNA剪接的途径和独立于衰减的方式非常缺乏损害了我们考虑如何以及哪些遗传变异影响RNA剪接的能力。我们建议首先开发一系列新型的基因组测定，以监测剪接途径，然后利用这些测定定义遗传变异对剪接的影响。我们将优化此类方法，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，要实现我们的目标，我们建议i）开发全基因组测定法，以新颖的方式监测剪接，ii）搜索使用这些测定法进行拼接定量跟踪基因座，以及iii），以通过集成方法来考虑遗传变异影响剪接的功能机制。在这个项目的结论下，我们将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化与剪接变化以及最终与疾病的变化联系起来的机制。