Investigation of an Evolutionarily Conserved Staufen-mediated mRNA Decay Pathway that Involves SINEs and lncRNAs

Abstract

Thesis (Ph.D.)--University of Rochester. School of Medicine & Dentistry. Dept. of Biochemistry and Biophysics, 2014.The mammalian double stranded (ds)RNA-binding protein Staufen (STAU)1, is a multi-functional protein that regulates gene expression at different levels. One example is STAU1-mediated mRNA decay (SMD). STAU1, when bound to a STAU1-binding site (SBS) in the 3'-untranslated region (3'UTR) of mRNAs, functions in complex with UPF1 to elicit the decay of targeted mRNAs in a way that depends on mRNA translation. Human SBSs can be formed by intramolecular or intermolecular base-paring, the latter of which is between an mRNA 3'UTR Alu element and a partially complementary Alu element within long noncoding RNAs (lncRNAs) called ½-sbsRNAs. Alu elements are a type of short interspersed element (SINE). Even though Alu elements are confined to primates, I have shown that SINE-dependent intermolecular SBS formation is not. My computational analyses demonstrated that 13.2% of annotated mouse mRNAs contain a single 3'UTR SINE, and 28.4% of known mouse lncRNAs contain one or more SINEs. Further experiments provide evidence that SMD occurs in mouse cells via partially complementary mRNA−lncRNA base-pairing. I have shown the physiological relevance of these interactions by demonstrating that mouse (m)½-sbsRNA-triggered SMD regulates C2C12-cell myogenesis. I undertook a series of computational analyses to pursue the mechanistic similarity between SINE- and ½-sbsRNA-dependent SMD in human and mouse cells despite the distinct evolutionary origins of their SINEs. These analyses demonstrate that 4.3% of the orthologous genes in human and mouse contain at least one 3'UTR SINE, a commonality of which indicates that SINEs have been positively selected for after integration. Subsequent deep sequencing of RNA in human and mouse skeletal muscle cell lines identified mRNA orthologs whose levels are elevated upon downregulation of STAU1 and, independently UPF1. Statistical analyses confirmed that the percentage of 3'UTR SINE-containing transcripts in orthologous SMD target pairs is significantly higher than that in the sum total of orthologous mRNA pairs. This indicates that SMD contributes, at least in part, to the selection and/or maintenance of SINEs in mRNA 3'UTRs. We speculate that such a selection was favored due to its involvement in conserved functions, which implies a convergent evolution of 3'UTR SINEs mediated by SMD