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.

We detected no DE candidate novel microRNAs at 5 or 12 hpi and six DE candidate novel microRNAs at the 24 hpi time point (with nonzero read counts in both mock-and HIV-infected samples; Table 3 ). The most significantly DE candidate novel mi-croRNA was an 18-mer encoded in the first intron of the EPB41L2 (erythrocyte membrane protein band 4.1-like 2, transcript variant 3) gene (Table 3 ; Fig. 4 ). This putative microRNA was found highly expressed in uninfected cells and downregulated by 90% at 24 hpi, a change specific to infection with live virus (Table 3 and data not shown). Other DE candidate novel microRNAs were expressed at lower levels overall or associated with smaller fold changes, leading us to focus on the EPB41L2-encoded candidate microRNA in further analysis.