Mapping the Small RNA Content of Simian Immunodeficiency Virions (SIV)

• Published in: PloS one Vol. 8; no. 9; p. e75063
• Main Authors: Brameier, Markus, Ibing, Wiebke, Höfer, Katharina, Montag, Judith, Stahl-Hennig, Christiane, Motzkus, Dirk
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 23.09.2013; Public Library of Science (PLoS)
• Subjects: Analysis; Base Sequence; Binding sites; Cell culture; Cell Line; Deoxyribonucleic acid; DNA; Enzymes; Exosomes; Exosomes - metabolism; Gene mapping; Genomes; Genomics; Health aspects; High-Throughput Nucleotide Sequencing; HIV; Human immunodeficiency virus; Humans; Immunodeficiency; Infections; Isoacceptors; MicroRNAs; MicroRNAs - genetics; MicroRNAs - metabolism; Molecular Sequence Data; Nucleoli; Nucleotide sequence; Packaging; Physiology; Polyethylene glycol; Ribonucleic acid; RNA; RNA polymerase; RNA, Ribosomal - genetics; RNA, Ribosomal - metabolism; RNA, Small Cytoplasmic - genetics; RNA, Small Cytoplasmic - metabolism; RNA, Small Nucleolar - genetics; RNA, Small Nucleolar - metabolism; RNA, Transfer, Lys - genetics; RNA, Transfer, Lys - metabolism; RNA, Untranslated - metabolism; RNA, Viral - genetics; RNA, Viral - metabolism; Sequences; Signal Recognition Particle - genetics; Signal Recognition Particle - metabolism; Simian immunodeficiency virus; Simian Immunodeficiency Virus - genetics; Stem cells; Virion - genetics; Virions; Viruses; Germany
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0075063

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), which were compared to mock-control preparations. Our analysis revealed that more than 428,000 sequence reads matched the SIV mac239 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, tRNA(Lys3) and tRNA(Lys) isoacceptors, we also identified defined fragments derived from small ILF3/NF90-associated RNA snaR-A14, that were enriched more than 50 fold 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, which gives novel insights into viral packaging.