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.

Following this protocol, we identified a large number of anticorrelated interactions between DE microRNAs and expressed mRNAs. In total, we identified 5,023 anticorrelated interactions involving 46 DE microRNAs and 1,917 detected mRNAs (see Table S2 in the supplemental material). Out of these 1,917 mRNAs, 1,900 were previously detected as DE by mRNA-Seq (1), indicating that DE mRNAs were overrepresented among anticorrelated target mRNAs (P Ͻ 10 Ϫ15 by Fisher's exact test). MicroRNAs and mRNAs varied widely in the number of predicted interactions, and individual microRNAs were predicted to target as many as 518 mRNAs, and individual mRNAs were predicted to be targeted by as many as 15 microRNAs (see Table S2 ).