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.

Additional data supported the existence of an EPB41L2encoded microRNA. mRNA-Seq reads mapped to EPB41L2 exons in the same experimental samples, indicating transcriptional activity at this locus (see Fig. S4 in the supplemental material) (1). However, EPB41L2 mRNA expression was found unchanged in HIV-infected cells at 12 and 24 hpi (1), suggesting that while the putative microRNA may have been derived from the EPB41L2 pre-mRNA, regulation occurred at the level of the excised intron, pre-microRNA, or mature microRNA, rather than at the level of the primary transcript. Interestingly, for the other two candidate novel microRNAs encoded within mRNA-encoding transcripts, a similar lack of concordance between microRNA and mRNA levels was observed (Table 3; see Table S4 ).