Antiviral RNA Interference in Mammalian Cells

TLDR

Antiviral RNA interference involves DICER processing viral dsRNA into siRNAs that guide ARGONAUTE proteins to silence viral RNA, but its existence in mammals remains unproven despite viral suppressors of RNAi counteracting this pathway. We demonstrate that undifferentiated mouse cells infected with EMCV or NoV generate ~22‑nt siRNAs from viral dsRNA, which load into AGO2, depend on DICER, diminish upon differentiation, and whose reduction by a NoV VSR knockout lowers viral load, confirming antiviral RNAi in mammals.

Abstract

In antiviral RNA interference (RNAi), the DICER enzyme processes virus-derived double-stranded RNA (dsRNA) into small interfering RNAs (siRNAs) that guide ARGONAUTE proteins to silence complementary viral RNA. As a counterdefense, viruses deploy viral suppressors of RNAi (VSRs). Well-established in plants and invertebrates, the existence of antiviral RNAi remains unknown in mammals. Here, we show that undifferentiated mouse cells infected with encephalomyocarditis virus (EMCV) or Nodamura virus (NoV) accumulate ~22-nucleotide RNAs with all the signature features of siRNAs. These derive from viral dsRNA replication intermediates, incorporate into AGO2, are eliminated in Dicer knockout cells, and decrease in abundance upon cell differentiation. Furthermore, genetically ablating a NoV-encoded VSR that antagonizes DICER during authentic infections reduces NoV accumulation, which is rescued in RNAi-deficient mouse cells. We conclude that antiviral RNAi operates in mammalian cells.