Characterization of three novel RNAi machinery components in C. elegans

Abstract

RNA interference (RNAi) is a homology-based and antisense small RNA-dependent gene silencing mechanism found in most eukaryotes. This dissertation describes identification and characterization of three novel RNAi pathway components in nematode Caenorhabditis elegans: rde-10, rde-11 and rde-12. We demonstrated that they are required for targeted mRNA degradation and the subsequent secondary siRNA biogenesis. The molecular mechanisms for targeted mRNA degradation in C. elegans undergoing RNA interference (RNAi) are not fully understood. Using a combination of genetic, proteomic and biochemical approaches, we have identified a divergent RDE-10/RDE-11 complex that is required for RNAi in C. elegans. Genetic analysis indicates that the RDE-10/RDE-11 complex acts in parallel to nuclear RNAi. Association of the complex with target mRNA is dependent on RDE-1 but not RRF-1, suggesting that target mRNA recognition depends on primary but not secondary short interfering RNA (siRNA). Furthermore, RDE-11 is required for mRNA degradation subsequent to target engagement. Results of deep sequencing analyses reveal a 5-fold decrease in secondary siRNA abundance in rde-10 and rde-11 mutant animals, despite normal primary siRNA and micro-RNA biogenesis. Therefore, the RDE-10/RDE-11 complex is critical for amplifying the exogenous RNAi response. Our work uncovers an essential output of the RNAi pathway in C. elegans. RDE-12, a putative DEAD-box RNA helicase, was identified from the same genetic screen. A GFP