Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4(+) T Cell Line

Chang, Stewart T.; Sova, Pavel; Peng, Xinxia; Weiss, Jeffrey; Law, G. Lynn; Palermo, Robert E.; Katze, Michael G.

By mapping sequencing reads to RefSeq transcript annotation, we also observed changes in the expression of several non-protein-coding RNA species. Specifically, reads mapping to RefSeq transcripts that began with NR were considered noncoding. As before, expression of these transcripts was compared between infected and mock-infected samples. At 12 hpi, only one annotated noncoding RNA (NR_003697 encoding C7orf40) was found to be differentially expressed (Benjamini-Hochberg-adjusted P Ͻ 0.05). However, by 24 hpi, 305 annotated noncoding RNAs were found to be differentially expressed by the same criterion, with 73 changed by an average of 2-fold or greater (Fig. 4A) . Several classes of noncoding RNAs were represented, including microRNA host genes, hypothetical genes and open reading frames (ORFs), small nucleolar RNAs (snoRNAs), and pseudogenes (Fig. 4A) . DE pseudogenes often matched their protein-coding counterparts in directionality and degree of regulation, which suggests that regulatory regions were maintained and polyadenylated transcripts were produced (data not shown).