UC Riverside

We are reporting a novel WAGO small RNA pathway which specifically targets the 3’ UTR of hundreds of functionally important genes. In C.elegans, endogenous small RNAs, 22G-RNAs, bind Argonautes to regulate almost all germline genes. There are two major 22G-RNA-mediated pathways in C.elegans germline cells. One is mediated by Argonaute CSR-1 and plays important roles in chromosome segregation and embryonic development; the other is mediated by multiple Argonautes, WAGOs, and play critical roles in silencing transposons, pseudogenes, viruses, and some functional genes. In all these small RNA pathways, 22G-RNAs are generated by RNA-dependent RNA polymerases (RdRPs) using mRNAs and other RNAs as templates. Usually, these 22G-RNAs are generated from both coding regions and UTRs of RNAs. Here we are reporting a novel small RNA pathway which specifically targets the 3’ UTRs of hundreds of genes, many of which have been well studied and play important roles in germline and embryonic development. Our preliminary results indicated that these genes are targeted both by CSR-1 and WAGO Argonautes. However, CSR-1 targets the 5’ UTRs, coding regions and 3' UTRs, while the WAGO Argonautes only target the 3’ UTRs. Interestingly, the WAGO-22Gs are not dependent on rde-3, which is usually required for generating 22Gs in other WAGO-dependent pathways including exogenous RNAi pathways. Our RNA-seq results suggest that the CSR-1 22G-RNAs may be involved in silencing the target RNAs. We are currently using genetics, high-throughput sequencing, and ribosome profiling to investigate why WAGO 22Gs are only generated from the 3’ UTR regions and if these small RNAs are involved in regulating mRNA and/or translation. We are also analyzing if these 22G-RNAs affects miRNA-mediated gene regulation at the 3’UTR of RNAs, In all, we are reporting a novel WAGO-mediated 22G pathway which specifically targeting the 3’UTR of hundreds of functional genes and this pathway is different from the canonical WAGO pathway since RDE-3 is not required for the 22G biogenesis and this pathway regulates CSR-1 targets.