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.

In the small RNA-Seq data set, we detected several classes of small RNAs, including piwi-interacting RNAs (piRNAs) and mi-croRNAs (see Fig. S1A in the supplemental material). After filtering by a minimum criterion for expression, we found that 155 piRNAs were expressed in the small RNA data set at 12 and 24 hpi; of these, none were DE at 12 hpi, and 21 were DE at 24 hpi, with the majority being upregulated (see Table S1 in the supplemental material). We also found that 531 annotated microRNAs were expressed in the small RNA data set. Levels of expression varied broadly. In particular, a small number of microRNAs were highly expressed. Four microRNAs constituted over half of all microRNA-mapped reads, and 10 microRNAs accounted for over 70% of all microRNA-mapped reads (see Fig. S1B ). Among the most highly expressed were several members of the miR-181 family (miR-181a-1, -181b-1, -181d) and let-7 family (let-7a-1, -7f-1) (see Fig. S1B ). In contrast, a large number of microRNAs were detected at low levels. Two hundred sixty-three microRNAs had normalized mean read counts of less than 100 in each sample.