Fig. 8: Bursting of the HIV-1 promoter in latently infected HeLa cells.
From: Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting
A Schematic of the HIV-1 reporter construct used to generate latent cells. SD1: major HIV-1 splice site donor; SA7: last HIV-1 splice site acceptor; ψ: packaging signal; RRE: Rev-responsive element; LTR: long terminal repeat; IRES: internal ribosome entry site; Hygro: hygromycin selectable marker; TK: herpes simplex thymidine kinase counter selectable marker. B Expression of HIV-1 in three latently infected HeLa clones. The histograms represent the distribution of the number of released HIV-1 128xMS2 pre-mRNAs per cell, in each of the three clones. Experimental RNA distributions are from smFISH data. x-axis: number of HIV-1 pre-mRNA molecules per cell; y-axis: number of cells. Red bars: untreated cells; blue bars cells incubated with TNFα (50 ng/ml for 30 min); inset: cell treatment, with the mean number of HIV-1 pre-mRNAs per cell indicated in parenthesis. Source data are provided as a Source Data file. C Active and inactive periods of the HIV-1 promoter, for the indicated cell lines. Each line is a cell and the activity of the HIV-1 promoter is color-coded (green: active; red: inactive), using the threshold shown in Fig. S4. x-axis: time in hours. D, E Fluctuations of HIV-1 transcription over 15–30 min periods, with one image stack recorded every 3 s in cells from the clone 12. D each graph is a single transcription site; the x-axis represents the time (in minutes) and y-axis represents the intensity of transcription sites, expressed in equivalent numbers of full-length pre-mRNA molecules. E Each line is a cell and the transcription site intensity is color-coded (scale on the right). Source data are provided as a Source Data file. F Model scores. The graph depicts the score of each model (inverse of the minimal value of the fitted Objective Function), for clone 12 and for each of the model of Fig. 6A. G pausing characteristics predicted by the model of facultative pausing for the clone 12. The two indicated values come from the two branches of the model that could each correspond to the paused state (see Fig. S4).
