Analysis of siRNA-Suppressor of Gene Silencing Interactions

RNA silencing is an evolutionarily conserved system that functions as an antiviral mechanism in higher plants and animals. To counteract RNA silencing, viruses evolved silencing suppressors that interfere with siRNA guided RNA silencing pathway. We used the heterologous Drosophila in vitro embryo RNA to analyze the molecular mechanism of suppression of silencing suppressors. We found that different silencing suppressors inhibit the RNA silencing via binding to siRNAs. None of the suppressors affected the activity of preassembled RISC complexes. In contrast, suppressors uniformly inhibited the siRNA-initiated RISC assembly pathway by preventing RNA silencing initiator complex formation. Here, we provide the protocol for the detailed analysis of p19 silencing suppressors of tombusviruses in the heterologous Drosophila in vitro system.