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.

In this study, we also detected several noncoding RNA species in HIV-infected cells that were differentially expressed (DE). In most cases, the functions of these noncoding RNAs and their relevance to infection remains unknown. One noncoding RNA of interest, the microRNA host gene MIR17HG, encoded a cluster of microRNAs and was strongly downregulated during infection. While our method of RNA library preparation precluded direct detection of mature microRNAs, the NGS data set allowed the expression of both regulators and targets of microRNAs to also be observed. For example, we observed a concurrent upregulation of the known target host gene PCAF, a cellular factor required for HIV replication (25) . In contrast to Triboulet et al. (25) who observed that PCAF was upregulated at the protein level but not the mRNA levels in infected peripheral blood mononuclear cells (PB-MCs), we found that PCAF was upregulated at the mRNA level in infected SUP-T1 cells. This may indicate alternative modes of PCAF regulation in different cell types. In addition, MIR17HGencoded microRNAs have hundreds of other candidate targets in the TargetScan database (26) . Several of these candidates were found to be coexpressed with PCAF in our data set, including KLF3 (unpublished data). KLF3 encodes a zinc finger transcription factor whose precise function is unknown but whose sequence is located proximally to a single-nucleotide polymorphism strongly associated with HIV-1 plasma levels (27) . We also observed differential expression of factors that may have mediated MIR17HG downregulation. For example, O'Donnell et al. (28) found that c-Myc regulates expression of MIR17HG. Consistent with that study, we observed that MYC and MIR17HG were concordantly expressed, as MYC was downregulated at 12 and 24 hpi (Fig. 1) . MYC suppression by HIV-1 may therefore underlie a number of subsequent of transcriptional events.