Figure 3

Identification of candidate genes that affect HIV-1 replication. (A) HIV-1-expressing (eGFP+) cells and (B) mean eGFP fluorescence intensities in the presence of over-expressed gene candidates at 48 h post transfection. (C) Levels of infectious HIV-1 determined by infection of TZM-bl indicator cells with the culture supernatant of transfected 293T cells. (D, E) cell-free (CF) and cell-associated (CA) p24 antigen levels from 293T cell cultures cotransfected with wt or vpr, vpu and nef defective (Δ3) HIV-1 constructs and gene candidate expression vectors. All panels provide values relative to those measured in 293T cultures cotransfected with the wt and Δ3 proviral HIV-1 constructs and the control vector expressing BFP only (100%). Each symbol represents the average value obtained from three independent experiments for each of the gene candidates analyzed. All candidates that reduced the values <50% in the FACS-based and <10% in the remaining assays are highlighted in green and selected genes that showed enhancing effect are indicated in red. (F) Unsupervised clustering of the different readouts allows inspection of similar activities across genes, and of the correlation between the various steps, for wt and Δ3 HIV-1.