Title: Genetic analysis of small RNA-mediated gene silencing in Caenorhabditis elegans
Description: Small RNA-mediated gene silencing is a recently discovered set of related gene regulatory pathways found from fungi to humans that are integral to cell biology, development, and the pathology and treatment of disease. Small RNA silencing pathways include microRNA repression, exogenous and endogenous RNA interference (RNAi), and piwi-associated RNA. While many classes of small RNAs have been characterized, and an array of RNA silencing protein cofactors have been described, there is still much to be learned about the genes in these pathways and the mechanisms by which they act. In this dissertation, I present studies in the nematode Caenorhabditis elegans that identify novel genes in small RNA silencing pathways, and describe the substrates and mechanism of the RNAi pathway exonuclease ERI-1. I present two genome-wide RNAi screens utilizing GFP reporter strains to identify components of the RNAi pathway. In the-first screen, 90 candidate genes are identified, including 11 known RNAi factors, as well as an array of predicted RNA binding and processing components, chromatin modifying enzymes that may act in transcriptional gene silencing, and proteins involved in transcription and translation. Secondary analyses of these genes indicate that some are likely to act in related small RNA silencing pathways.

The second screen employs an enhanced RNAi strain to more sensitively identify candidate RNAi genes. Integration of the genes identified in these screens with other RNAi screens and proteomic analysis for components of RNA silencing pathways in C. elegans generates a high-confidence list of shared small RNA pathway candidates. Loss-of-function analysis in mutants for some of the genes identified confirms their activity in RNAi. The exonuclease ERI-1 negatively regulates some RNAi pathways in worms and fungi and is required for the production of endogenous, small-interfering RNA (siRNA) in worms. I present data demonstrating that ERI-1 is a conserved rRNA processing component that mediates 3' end maturation of the 5.8S ribosomal RNA (rRNA) in both C. elegans and S. pombe. I show that one ERI-1 protein isoform, ERI-1b, mediates endogenous siRNA production and the association of the C. elegans Dicer ortholog, DCR-1, with a large complex that co-fractionates with the ribosome, Lastly, I identify the 7SL RNA as a second structural RNA substrate of ERI-1. Together these results indicate that ERI-1 plays a conserved dual role in the RNAi and structural RNA processing pathways.