Mapping the small RNA content of simian immunodeficiency virions (SIV)

Recent evidence indicates that regulatory small non-coding RNAs are not only components of eukaryotic cells and vesicles, but also reside within a number of different viruses including retroviral particles. Using ultra-deep sequencing we have comprehensively analyzed the content of simian immunodeficiency virions (SIV), that were compared to mock-control preparations. Our analysis revealed that more than 428,000 sequence reads matched the SIVmac239 genome sequence. Among these we could identify 12 virus-derived small RNAs (vsRNAs) that were highly abundant. Beside known retrovirus enriched small RNAs, like 7SL-RNA, tRNALys3 and tRNALys isoacceptors, we also identified virion-enriched tRNA-derived fragments (tRFs) from tRNAThr, tRNAArg, and tRNAMet, that have not been previously described. Furthermore, we detected defined fragments derived from small ILF3/NF90-associated RNA snaR-A14, that were enriched more than 50fold in SIV. We also found evidence that small nucleolar RNAs U2 and U12 were underrepresented in the SIV preparation, indicating that the relative number or the content of co-isolated exosomes was changed upon infection. Our comprehensive atlas of SIV-incorporated small RNAs provides a refined picture of the composition of retrovirions, that gives novel insights into viral packaging.