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.

HIV-1 induces large-scale changes in transcription by 24 hpi. By 24 hpi, large-scale changes in the transcriptomes of HIVinfected cells were evident (Table 1 ; see the heatmap in Fig. S5A in the supplemental material). Consistent with the large number of DE genes at 24 hpi, we found that a wide range of biological processes was affected as determined by further analysis using DAVID ( Fig. 2B ; complete listing in Table S3 in the supplemental material). T cell activation and differentiation continued to be overrepresented and were associated with an increased number of DE genes (as lymphocyte differentiation [ Fig. 2B] ). Other fundamental cellular functions associated with DE genes at 24 hpi included DNA metabolism, transcription, mRNA processing and splicing, translation, protein degradation, and cell cycle control (Fig. 2B ). This breadth of functional regulation suggests that HIV-1 infection resulted in the effective transcriptional reprogramming of SUP-T1 cells by 24 hpi.