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.

Our finding that this candidate microRNA was downregulated at 24 hpi, despite largely unchanged expression in mRNA from the same locus, suggests that the candidate microRNA may have been selectively inhibited during HIV infection. Our examination of NGS data from another experimental infection system, HCMV in human fibroblasts, both validated the existence of the candidate microRNA and showed it to be downregulated during a different infection, suggesting this microRNA may function more generally during the immune response to viral infection. Finally, we note that this microRNA displays strong specificity to higher primates, and its presence may reflect a response unique to primates and viruses that target them, such as HIV-1 and HCMV. Unlike known microRNAs, this and other candidate novel microRNAs may represent entirely novel targets for intervention or diagnosis during HIV-1 infection and demonstrate a distinct benefit of applying NGS to the profiling of small RNAs.