Fig. 7: Biochemical measurements indicate a long-lived paused state at the HIV-1 promoter.

A Residency time of RNA polymerase II at the HIV-1 promoter. The graph depicts the RNA polymerase II ChIP signals at the HIV-1 and GAPDH promoters during a Triptolide time course experiment, for the High Tat and No Tat cell lines. GAPDH TSS: transcription start site of the human GAPDH gene; HIV-1 TSS: transcription start site of the HIV-1 promoter; Control DNA: a non-transcribed genomic locus. ChIP signals were measure by qPCR and values are expressed as percent of input and normalized to the zero time point. For the control genomic regions (Control DNA), values are normalized to that of GAPDH TSS at time zero. Values are averaged from two independent experiments (+/- standard deviation) and source data are provided as a Source Data file. B Effect of pTEFb inhibition on the residency time of RNA polymerase II at the GAPDH promoter. Legend as in panel A, except that the KM sample was pretreated with the Cdk9 inhibitor KM05382 for 2 h before triptolide addition. Values are averaged from two independent experiments (±standard deviation) and source data are provided as a Source Data file. C Model depicting the dynamics of the HIV-1 promoter and highlighting the positive and negative effects of Tat. The numbers are from the facultative pausing model fitted to the High Tat and No Tat data (see Fig. 6C and S4; Supplementary Notes Table S4). The model with facultative pausing has two symmetrical branches (see model M2 in the Supplementary Notes Figure S5), and each branch of the model could correspond to the paused state. The values indicated attribute the pause state to the branch that is most affected by the presence of Tat.