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

We selected 14 candidates among the most abundant peaks obtained in both cell types for validation by Northern blot analysis (see Fig. S3A in the supplemental material). We could detect several SINV-derived viral small RNAs (SvsRNAs) of 20 to 30 nt in length that were derived from all along the viral genome (Fig. S3B ). Among them, SvsRNA-1, -2, and -3 were detected in both HEK293 and Vero cells (Fig. S3C) . The presence of abundant larger bands accumulating between 40 and 100 nt was also evidenced. Of note, the expression of both larger and smaller viral RNAs increased proportionally to the accumulation of the viral genome during a time course of infection ( Fig. 1D and E) . The identification of SINV-derived small RNAs prompted us to analyze more closely their origin and biochemical properties.