Characterization of Argonaute-related small RNA pathways in Caenorhabditis elegans

Abstract

In Small-RNA-mediated pathways, small RNAs engage a protein of the Argonaute family and utilize base-pairing interactions to identify and regulate complementary genetic information. My research has focused on understanding how diverse classes of small RNAs in the model organism Caenorhabditis elegans interact with specific members of the Argonaute protein family to carry out unique biological functions. During RNA interference (RNAi), functionally and structurally distinct Argonaute proteins act sequentially to silence target mRNAs. In the first step, the Argonaute RDE-1 interacts with primary siRNAs, and interaction of this complex with the target mRNA triggers a secondary amplification step. In this second step, RNA dependent RNA polymerases (RdRPs) use the targeted mRNA as a template to generate an abundant pool of small RNAs (22G-RNAs), which interact multiple Argonaute proteins to mediate target silencing. Several endogenous small-RNA-mediated pathways are essential for germline development. One of these pathways is required for chromosome segregation and relies exclusively on the Argonaute CSR-1, which utilizes 22G-RNAs generated from proteincoding genes to promote the proper organization of chromatin domains. A distinct 22GRNA germline pathway utilizes ‘aberrant’ RNAs as templates and is essential in maintaining genome stability. Proper germline development also requires the 21U-RNA class of small RNAs. 21U-RNAs specifically interact with the Piwi Argonaute PRG-1, thus establishing 21URNAs as members of the piRNA family, which is important for germline integrity in all metazoans. With only one known exception, 21U-RNAs fail to exhibit sequence complementarity or evidence for direct regulation of other expressed sequences. We now appreciate that the extent and means of small RNA regulation is much greater than we initially expected. My studies have contributed to the emerging theme that small RNA pathways function on a genome-wide scale, to regulate many aspects of cell biology and organismal homeostasis, from chromosome structure to gene expression.