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.

EPB41L2-encoded candidate novel microRNA during HIV infection. In addition to annotated microRNAs, we also detected changes in other types of small RNAs, including piRNAs at 24 hpi. piRNA expression was previously detected in HIV-infected Jurkat cells (8) . In our study, we detected piRNA expression in an additional T lymphoblast cell line, SUP-T1 cells, providing support for the expression of piRNAs in non-germ-line cells. HIV infection resulted in changes in the expression of 21 piRNAs. piRNAs are hypothesized to function in epigenetic regulatory mechanisms; however, due to a lack of consensus about their function in nongerm-line cells, we report these changes for completeness only (34) . We also detected changes in several candidate novel micro-RNAs. In particular, one candidate encoded in the first intron of EPB41L2 was highly expressed in uninfected cells and strongly downregulated in infected cells. Multiple lines of evidence supported the existence of this microRNA, including ENCODE small RNA-Seq data on multiple immune cell types. Interestingly, Yeung et al. detected a sequence identical to this candidate novel microRNA in the context of HIV infection (8) . This small RNA was found to have RNA interference activity toward the HIV-1 RNA primer-binding site where tRNA binds to initiate reverse transcription, and antagomirs directed toward the small RNA resulted in increased HIV-1 replication (8). We find a deeper investigation into the connection between this microRNA and HIV to be outside the scope of the present work. However, in the future it would be interesting to determine whether more direct evidence of the association between this microRNA and HIV-1 RNA could be obtained, such as through immunoprecipitation of the two RNA species in complex.