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

In this study, we generated small RNA libraries from two different mammalian cell lines infected with SINV. Although the percentage of sequences mapping to the viral genome was significant (~1.7 to~8% in HEK293 and Vero cells, respectively), we were unable to detect either siRNA or piRNA signatures. On the contrary, the viral reads displayed a highly biased strand distribution. Although antigenomic (negative) strand-derived sequences represented a very small percentage of the total viral reads, they showed properties distinct from the genomic (positive) strand reads: their size distribution peaked at 22 nt, and their localization on the viral genome is restricted to the promoters required for the synthesis of both the genomic and subgenomic RNA. Although the cloned 22-nt sequences were not visible by Northern blot analysis, we could detect the accumulation of an~44-nt product that in our knowledge has never been observed before. We hypothesize that these RNA species could be critical for viral replication, similarly to what has been previously reported for influenza virus (44) .