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

Consistent with the relative abundance of the positive strand compared to the negative strand, the majority of reads were derived from the plus-strand RNA and more specifically from the region corresponding to the subgenomic RNA sequence. We could detect several hot spots of small RNA accumulation, indicating that discrete SINV-derived viral small RNA species (SvsR-NAs) could be produced in infected mammalian cells. These Svs-RNAs do not display any peak in size distribution and do not map to any alphavirus conserved regions. Nonetheless, we noticed that they originate from the same viral genomic positions in both infected African green monkey and human cells. In order to confirm that this was not solely due to a bias in the small RNA cloning protocol, we performed Northern blot analyses of several small RNA candidates. For some of the candidates, we were able to detect discrete bands, which increased in intensity throughout the time course of infection.