RNA interference (RNAi) is a double-stranded RNA (dsRNA) guided mechanism that mediates sequence specific degradation of RNA. The recent demonstration that RNA interference can be used to inhibit virus replication has initiated an exciting field of research. First, it provides a novel antiviral therapeutic approach and, second, it may constitute a hitherto unrecognized natural antiviral defense mechanism. The long-term goal of this proposal is to gain a better understanding of the significance and therapeutic potential of RNA interference (RNAi) in the inhibition of viral infections. To this end we propose three specific aims to: (1) understand the determinants of siRNA-based viral inhibition;(2) investigate RNAi as a natural antiviral defense mechanism;and (3) identify and characterize novel components of the RNAi machinery. We will employ well-characterized positive stranded RNA viruses (picornaviruses,alphaviruses, and flaviviruses) as model viruses, and employ Drosophila and mammalian cells as model hosts. (1) To understand the determinants of siRNA-based viral inhibition, we will define the genome regions of RNA viruses that are susceptible to RNAi, and explore the efficiency of different siRNA design approaches. We will also investigate the ability of viruses to escape RNAi. (2) To investigate RNAi as a natural antiviral defense mechanism, we examine whether viral infection of animal cells produces siRNAs and analyze whether inhibiting components of the RNAi machinery enhances viral replication in mammalian cells. We will also determine whether viral infection induces changes in the RNAi machinery. (3) To identify and characterize novel components of the RNAi machinery, we carry out genome-wide screens in Drosophila cells. We will then employ cell biology and biochemistry to characterize the mechanism of entry and the role of the genes identified in our screens, and isolate the mammalian orthologs of RNAi entry components identified in our screens and explore their role in RNAi entry in mammalian systems.
