Vault RNAs aid viral infection by facilitating nuclear export of hnRNP C and ELAVL1

Vault RNAs (vtRNAs) are a family of four small non-coding RNAs (ncRNAs) that are ubiquitously expressed in many eukaryotes and that regulate multiple cellular pathways. Their expression is increased upon infection with various DNA and RNA viruses. This suggests they are either co-opted by the virus to aid replication or function as an antiviral restriction factor. However, their precise molecular function remains unclear. Here, we show that replication of picornaviruses, alphaviruses, and beta-coronaviruses broadly enhances vtRNA expression. We find that genetic loss of vtRNAs inhibits replication of Sindbis virus (SINV) and encephalomyocarditis virus (EMCV), independent of the antiviral type I interferon (IFN) response. A proteomic screen uncovered the vtRNA interactome and revealed that vtRNAs associate with RNA binding proteins ELAVL1 and hnRNP C in uninfected and infected cells. VtRNAs facilitate the translocation of ELAVL1 and hnRNP C from the nucleus to the cytoplasm in infected cells, an event that is required for efficient viral replication. Moreover, hnRNP C and ELAVL1 fail to associate with viral RNA in the cytosol of SINV-infected cells in the absence of vtRNAs. Together, our findings reveal a novel molecular mechanism by which vtRNAs exert proviral activity during the course of SINV and EMCV infection, which opens up new avenues for therapeutic targeting to fight infectious diseases.