Identification of RNase L-Dependent, 3'-End-Modified, Viral Small RNAs in Sindbis Virus-Infected Mammalian Cells

Girardi, Erika; Chane-Woon-Ming, Béatrice; Messmer, Mélanie; Kaukinen, Pasi; Pfeffer, Sébastien

Although extensive deep sequencing analyses have been performed to identify siRNAs in mammalian cells infected with several RNA viruses, there is so far no good evidence for a possible antiviral role of RNAi in mammalian somatic cells (7) . Nevertheless, another class of small noncoding RNAs, microRNAs (miRNAs), has been shown to play an important role during viral infection in mammals. miRNAs are evolutionarily conserved small RNAs derived from large primary transcripts, which are sequentially processed by the respective nuclear and cytoplasmic RNase III enzymes, Drosha and Dicer, to generate mature single-stranded~21-or 22-nucleotide (nt) RNAs (8, 9) . Similar to siRNAs, they are incorporated into an effector Ago-containing RNA-induced silencing complex (RISC), whereby they mediate posttranscriptional regulation of target mRNAs via partially complementary sites (10) . On one hand, miRNAs of cellular origin can directly or indirectly regulate viral infections (11, 12) . On the other hand, some viruses have evolved the capacity to encode their own miRNAs, which represent an ideal tool to stealthily modulate the cellular environment. To date, viral miRNAs have been almost exclusively identified in the genomes of DNA viruses, mostly herpesviruses (13) (14) (15) (16) (17) , with the notable exception of bovine leukemia virus, a retrovirus with an RNA genome (18) . It has been commonly assumed that cytoplasmic RNA viruses cannot encode miRNAs, not only because they do not have access to the nuclear biogenesis machinery but also because their genomic integrity would be destabilized by miRNA processing (19) . Nevertheless, it has recently been demonstrated that the insertion of a cellular miRNA precursor into the 3=-end nontranslated region (NTR) of Sindbis virus (SINV) genomic RNA leads to its cytoplasmic processing without affecting the viral replication (20, 21) .