Virus-Activated siRNAs (vasiRNAs) - A Novel Class of Arabidopsis Endogenous siRNAs Induced by Virus Infection

Genetic studies and deep sequencing have identified distinct classes of Arabidopsis endogenous siRNAs that require either RNA-dependent RNA polymerase 2 (RDR2) or RDR6 for biogenesis. However, it remains unknown if Arabidopsis RDR1 also produces endogenous siRNAs in addition to its known role in the biogenesis of secondary virus-derived siRNAs (vsiRNAs). Here we describe a novel class of Arabidopsis endogenous siRNAs produced in response to virus infection, designated as virus-activated siRNAs (vasiRNAs). vasiRNAs are predominantly 21 nucleotides long with an approximately equal ratio of sense and antisense strands and are mapped to the exon regions of more than 1,000 host genes and rRNA. Genetically, vasiRNAs are distinct from the known plant endogenous siRNAs characterized to date and instead resemble secondary vsiRNAs by requiring Dicer-like 4 (DCL4) and RDR1 for biogenesis. However, loss of Exoribonuclease4(XRN4)/Ethylene-insensitive5 (EIN5) enhances vasiRNA biogenesis and virus resistance without altering the biogenesis of vsiRNAs. We show that vasiRNAs are active in directing widespread silencing of the target host genes and that Argonaute-2 binds to and is essential for the silencing activity of vasiRNAs. Production of vasiRNAs is readily detectable in Arabidopsis plants after infection by viruses from two distinct supergroups of plant RNA virus families and is targeted for inhibition by the silencing suppressor protein 2b of Cucumber mosaic virus. We propose that production of vasiRNAs is a conserved host response to virus infection and that widespread silencing of host genes directed by vasiRNAs confers broad-spectrum antiviral activity.