Characterization of RNA interference in the cnidarian Nematostella vectensis reveals partial target silencing but lack of small RNA amplification

RNA interference (RNAi) is a sequence-specific mRNA degradation mechanism, in which short interfering RNAs (siRNAs) guide Argonaute proteins to complementary targets, resulting in their degradation. In many organisms, RNAi also serves antiviral roles by processing viral double-stranded RNA (dsRNA) into siRNAs that prevent viral replication. Antiviral RNAi is considered an ancestral mechanism which invertebrates rely on for defense against viruses, whereas vertebrates have evolved instead the interferon pathway. Recent studies suggest that sea anemones, members of the basally-branching phylum Cnidaria, might possess an innate immune response with more vertebrate characteristics than previously thought; however, it is unknown whether cnidarians also employ RNAi as an antiviral response similarly to nematodes and insects. Here, we characterize the response of the model cnidarian Nematostella vectensis to simulated viral infection. We injected dsRNA with eGFP sequence into eGFP-expressing transgenic zygotes and show that siRNAs mapping to the eGFP sequence are generated and induce a moderate but significant knockdown of eGFP expression. Interestingly, we detected no evidence for secondary siRNA production, despite their crucial role in the amplification of antiviral response in other organisms. Notably, siRNA pathway components are specifically upregulated upon dsRNA injection, while microRNA pathway components are downregulated. Furthermore, injection of mRNA coding for self-replicating viral gene fused to eGFP, also induced upregulation of siRNA-related genes and a mild decrease in transgene expression. Overall, we propose that N. vectensis possesses an siRNA-mediated response that lacks secondary amplification and likely functions as a short-term antiviral mechanism.