HIV, the retrovirus that causes AIDS, can establish rare, latent infections of cells, and the resulting latent pools of virus represent the most significant barrier to elimination of virus from a patient since they persist for decades and can reactivate at any time. After HIV enters a cell, it integrates its genetic material into the host genome and then utilizes the transcriptional machinery from the host cell to regulate its gene expression. Furthermore, efficient HIV transcriptional regulation also requires the viral protein Tat, a protein encoded within in the HIV genome. Since the viral protein Tat helps catalyze the transcription of HIV genome, this constitutes a strong positive feedback circuit. Genetic positive feedback circuits can often attain two distinct states (active and inactive), and the state of circuit may be susceptible to genetic noise which can lead to switching between states. Such sources of noise become increasingly important in systems with low concentrations of regulatory factors, such as an HIV infected cell with very low numbers of Tat molecules. We have previously reported that stochastic fluctuations in Tat lead to phenotypic diversity in HIV gene expression, a phenomenon that can be observed experimentally and predicted computationally with stochastic modeling [1]. We have hypothesized that stochastic delays in the onset of viral gene expression can contribute to the formation of latent viral infections.

The HIV viral promoter, a primary determinant of viral gene expression dynamics, is regulated by the cellular signaling state, the chromatin environment of the viral integration site, and the level of viral protein Tat. Computational studies predict that transcription factor binding sites in the viral promoter, as well as the surrounding chromatin state, can exert a strong influence on the dynamic behavior of the feedback loop. The viral promoter contains numerous binding sites for cis-acting cellular transcription factors including well-conserved sites for NFkappaB and Sp complexes. Recruitment of cellular transcription factors NFkappaB and Sp regulates HIV transcription by active transcription initiation, recruitment of histone modifying proteins which remodel chromatin structure, and direct and indirect interactions with Tat protein.

Using both experimental and computational approaches, we are building on our previous discovery that stochastic fluctuations in Tat lead to phenotypic diversity in a small, but significant, portion of HIV infected cells possessing native NFkappaB and Sp complexes [1]; however, we examining the effects of such cis-acting cellular transcription complexes on the stochastic effects in transcriptional regulation of HIV. With further computational analyses, we aim to understand and predict stochastic fluctuations of Tat, which regulate the establishment of latency or the transactivation of viral gene expression.

1. Weinberger, L.S., Burnett, J.C., Toettcher, J.E., Arkin, A.P., and Schaffer, D.V. (2005) Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell, 122, 169-82.

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