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.

RNA transport. The importance of host regulation of RNA fate was underscored by another cluster of gene sets related to RNA transport (Fig. 2B) . Host factors for RNA transport are known to be coopted by HIV-1 to allow the export of unspliced, partially spliced, or fully spliced viral mRNAs out of the nucleus (18) . In particular, the host factors Crm1 (exportin 1) and Ran GTPase are used for the export of unspliced viral mRNA, while the host factor NXF1 (nuclear RNA export factor 1) facilitates the export of fully spliced viral mRNA in a Ran-independent manner (19) . In our data set, we observed no change in the expression of the Crm1-encoding gene XPO1, but several members of the Ran signaling pathway were downregulated, suggesting that the overall export of unspliced viral RNA was suppressed (see Fig. S5B in the supplemental material; data not shown for XPO1). However, in contrast to other RNA transport-related genes, NXF1 and NXF3 were expressed more highly in infected cells, suggesting that HIV infection may have selectively enhanced the export of fully spliced viral RNA (Fig. S5B) .