mRNA decay is important for regulation of gene expression. The amount of a particular mRNA present at a specific time in a cell is dependent on its rate of synthesis and decay. The nonsense mediated mRNA decay pathway (NMD) is a specialized mRNA decay pathway that recognizes and rapidly degrades mRNA with premature stop codons and some wild-type mRNAs. Wild-type mRNAs degraded by NMD have been identified in Saccharomyces cerevisiae, Drosophila melanogaster and humans. 5-10% of the S. cerevisiae transcriptome is affected when NMD is inactivated. Thus NMD has a significant impact on wild-type gene expression. Long 3'-untranslated regions (3'-UTRs) target mRNAs for NMD. Normal S. cerevisiae cellular mRNAs have 3'-UTRs ranging in size from 50-350 nucleotides, with most approximately 100 nucleotides long. mRNAs containing mutations that generate aberrant extended 3'-UTRs are degraded by NMD. A subset of wild-type transcripts from S. cerevisiae have naturally extended 3'-UTRs. However, the impact of these extended 3'-UTRs on the decay of these mRNAs has not been examined. Preliminary data shows that some wild-type mRNAs with long 3'-UTRs are degraded by NMD while others are immune to NMD. The long-term goal of this project is to understand the targeting and recognition of wild-type mRNAs with long 3'-UTRs for NMD. The overall objective for this project is to determine the extent to which long 3'-UTRs target wild-type mRNAs for degradation by NMD. The central hypothesis, based on the faux 3'-UTR model, is that wild-type mRNAs with longer than normal 3'-UTR are targets for NMD. Further, additional cis-acting sequences are required to protect wild-type mRNAs with long 3'-UTRs from NMD. The central hypothesis will be tested by determining the role of longer than normal 3'-UTRs in mRNA degradation by NMD and in parallel determine why one mRNA with a longer than normal 3'-UTR is immune to NMD. This project will define the role of long 3'-UTRs in the degradation of wild-type mRNAs by NMD in S. cerevisiae. This knowledge will advance the field's understanding of the recognition and targeting of wild-type mRNAs by specialized mRNA decay pathways. The project involves a bioinformatics-based approach that will enhance the skills of the principal investigator who is African, an underrepresented minority in sciences. Furthermore the project will involve mentoring an undergraduate African American student.
