Next-Generation Sequencing of Small RNAs from HIV-Infected Cells Identifies Phased microRNA Expression Patterns and Candidate Novel microRNAs Differentially Expressed upon Infection

Chang, Stewart T.; Thomas, Matthew J.; Sova, Pavel; Green, Richard R.; Palermo, Robert E.; Katze, Michael G.

To determine the effect of HIV infection on cellular small-RNA expression, we infected human lymphoblastoid SUP-T1 cells with HIV-1 strain LAI and determined small RNA expression at three different time points: 5, 12, and 24 h postinfection (hpi). In a previous study (1) , we found that levels of virus were nearly undetectable at 4 hpi, increasing at 12 hpi and peaking at 24 hpi. Our choice of timing parallels these time points. For controls, we also mock-infected cells using cell culture medium or alternatively infected cells with UV-inactivated HIV-1 (HIV UV ). Small RNAs were then size selected, and cDNA libraries were generated and then sequenced by NGS. To analyze the resulting small RNA-Seq data set, we employed a workflow that included mapping sequences to different small RNA annotations, identifying DE mi-croRNAs based on the mapped data, and determining the mRNA targets of the DE microRNAs (Fig. 1) .