Novel methods to detect and interpret splicing quantitative trait loci - Renewal

Predicting the effects of noncoding sequence on gene regulation and complex traits remains one of the most important problems in genomics. Many expression quantitative trait loci do not overlap enhancers or promoters. Our previous work showed that about one third of all expression quantitative trait loci likely function after transcription initiation. Further, we have implicated a deep contribution of pre-mRNA splicing to human variation. 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 have been developing genome-wide assays that explicitly target pre-mRNA splicing. By one assay, we uncovered an under-appreciated mechanism contributing to gene expression and human phenotypic variation: unproductive splicing, which results in transcripts subject to cytoplasmic nonsense- mediated decay. By another assay, we have defined the timing of splicing genome-wide and in doing so discovered an unexpected degree of non-canonical splicing that competes with canonical splicing. In this grant, we propose novel assays to explicitly and efficiently measure canonical and non-canonical splicing. We will develop analytical methods to measure inter-individual variation in these processes and use this variation to study the mechanisms and impact of these regulatory phenotypes. At the end of this project, we will have developed innovative genomic assays that will illuminate novel RNA splicing biology and will have tested hypotheses regarding the function and regulatory mechanisms of RNA splicing. Our work will help improve our understanding of functional gene regulatory variation.