An in vitro model of HIV gene expression exhibits a distribution of integration-site-dependent phenotypes, including noise-driven Switching phenotypes.

(A) Schematic of the full-length HIV lentiviral model of the Tat-mediated positive feedback loop (sLTR-Tat-GFP). Viral proteins other than Tat were inactivated and Nef was replaced with GFP. (B–C) Flow cytometry histogram of Jurkat cells infected with a single HIV WT virus for (B) a bulk population with mixed integration positions and (C) sample Jurkat clonal populations, each containing a single (different) genomic integration of the WT HIV provirus. Representative Dim and Bright clonal histograms were chosen to span the range of fluorescence means. For Switching phenotypes, representative clonal histograms were chosen from the distribution clusters that were used to define a quantitative Switching criterion. GFP axis range is the same for all histograms. (D) Quantification of the WT Switching fraction based on a stratified sample of clones from the full range of GFP expression (“Full”), and based on a sub-sample of clones sorted from only the Mid region of the bulk fluorescence range (“Mid”). Error bars mark 95% confidence intervals, estimated by a bootstrap method.