PROJECT SUMMARY There are fundamental gaps in our understanding of the regulatory mechanisms of nonsense- mediated mRNA decay (NMD). Originally conceived as a quality-control checkpoint to recognize and degrade aberrant transcripts, NMD has become appreciated as a post-transcriptional gene regulation mechanism to fine-tune expression of many non-aberrant endogenous mRNAs. However, despite a plethora of biochemical characterization on the NMD pathway, the mechanism of NMD regulation and the criteria for NMD target selection are poorly understood. Our long-term goal is to develop computational methods to discover the principles of gene expression regulation and explore how variations or defects in gene regulation cause phenotypic variation or disease. The overall objective of this application is to elucidate the context-dependent NMD regulation of individual genes through genetical genomics. Genetic variants associated with changes in gene expression (expression quantitative trait loci, eQTLs) are being catalogued in increasingly large-scale human studies, such as the Genotype-Tissue Expression (GTEx) project. We will take advantage of this unprecedented resource to dissect NMD control and to discover NMD regulatory rules in a systematic and unbiased manner. Traditional biochemical and molecular approaches are essential to deciphering NMD mechanism but are slow in progress with intrinsic limitations. Genetical genomics will provide a fresh view and has great promise to uncover new regulatory rules of NMD. We will develop novel statistical and computational methods tailored to the analysis of NMD regulation. These methods can also be broadly applied to studies of other regulatory variants. Our long-standing expertise in transcriptomics analysis, eQTL analysis, and NMD regulation places us in a unique position to accomplish the proposed project. The proposed methods meet the analysis challenges arising from transcriptomics, eQTL mapping, and RNA biology. The completion of this project will vertically advance and expand our understanding of how NMD regulates gene expression. Ultimately, such knowledge has the potential to develop NMD-based preventive and therapeutic interventions.