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.

To further characterize the EPB41L2-encoded candidate novel microRNA, we generated predictions using the TargetScan algorithm and performed a correlation analysis to identify possible mRNA targets. The novel microRNA was predicted to target a total of 365 mRNAs by TargetScan. Out of these, 53 were significantly, negatively correlated in their expression levels (see Table S4 in the supplemental material). No individual annotation was found to be enriched among these host targets (with adjusted P values of Ͻ0.05; data not shown). However, we noted that an identical 18-nucleotide RNA was identified by Yeung et al. in the context of HIV infection, and this RNA was found perfectly complementary to the primer-binding site of HIV RNA (5) .