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Transient-mediated fate determination in a transcriptional circuit of HIV

Abstract

Steady-state behavior and bistability have been proposed as mechanisms for decision making in gene circuits1,2,3. However, transient gene expression has also been proposed to control cell fate4,5, with the decision arbitrated by the duration of a transient gene expression pulse. Here, using an HIV-1 model system, we directly quantify transcriptional feedback strength and its effects on both the duration of HIV-1 Tat transcriptional pulses and the fate of HIV-infected cells. By measuring shifts in the autocorrelation of noise inherent to gene expression, we found that transcriptional positive feedback extends the single-cell Tat expression lifetime two- to sixfold for both minimal Tat circuits and full length, actively replicating HIV-1. Notably, artificial weakening of Tat positive feedback shortened the duration of Tat expression transients and biased the probability in favor of latency. Thus, transcriptional positive feedback can modulate transient expression lifetime to a greater extent than protein half-life modulation, and it has a critical role in the cell-fate decision in HIV.

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Figure 1: Positive feedback extends the lifetime of gene expression transients.
Figure 2: Measuring positive-feedback strength by exploiting inherent gene expression noise.
Figure 3: Positive-feedback strength drives an extended Tat expression transient in both minimal Tat circuits and full-length HIV-1.
Figure 4: SirT1 overexpression in full-length HIV-1 decreases positive-feedback strength and increases the probability of latency.

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Acknowledgements

We thank D. Botstein, T. Shenk, T. Cox, N. Wingreen, A. Caudy, D. Spector, M. Doktycz, J. Cooke and P. Cummings for helpful comments and S. Werner for technical expertise. The J-lat clonal cell line (J-lat full-length clone 10.6) was obtained through the US National Institutes of Health AIDS Research and Reference Reagent Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, US National Institutes of Health from E. Verdin. L.S.W. acknowledges support from the University of California San Diego and the Lewis Thomas Fellowship (Princeton University). R.D.D. and M.L.S. acknowledge support from the Center for Nanophase Materials Sciences, which is sponsored by the Division of Scientific User Facilities, Office of Basic Energy Sciences, US Department of Energy.

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Authors and Affiliations

Authors

Contributions

L.S.W., R.D.D. and M.L.S. conceived and designed this study; L.S.W. carried out the single-cell imaging; R.D.D. analyzed the cell images and did the simulations; M.L.S. carried out the analytical derivations; and L.S.W., R.D.D. and M.L.S. wrote the paper.

Corresponding authors

Correspondence to Leor S Weinberger or Michael L Simpson.

Supplementary information

Supplementary Text and Figures

Supplementary Methods and Supplementary Figures 1–6, Supplementary Table 1 (PDF 2084 kb)

Supplementary Movie 1

Sample movie of quantitative single cell tracking .zip file) (AVI 19533 kb)

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Weinberger, L., Dar, R. & Simpson, M. Transient-mediated fate determination in a transcriptional circuit of HIV. Nat Genet 40, 466–470 (2008). https://doi.org/10.1038/ng.116

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