| HIV-1 latency is the largest obstacle to the complete eradication of virus from a patient. After HIV-1 infects the target cell and integrates its genome into the host chromosome, the viral promoter coordinates a complex set of inputs to control the establishment of viral latency, the onset of viral gene expression, and the ensuing gene expression levels. Among these inputs are chromatin structure at the site of integration, host transcription factor levels, and the virally encoded transcriptional regulator Tat. We have employed a systems-level approach to measure the dynamics of HIV-1 gene expression and the sensitivity of these dynamics to changes in host and viral factors. Specifically, we have identified that stochastic fluctuations in the viral protein Tat, which regulates HIV-1 gene expression through a positive-feedback loop, may result in clonal populations of cells exhibiting two distinct viral expression levels. Moreover, we have demonstrated that these stochastic fluctuations are strongly influenced by host factors, such as histone acetyltransferases and deacetylases, which regulate transcription through chromatin modifications and physical interactions with Tat. Importantly, we observe that the conditions for such dynamics vary for different HIV-1 subtypes, and we have established a relationship between promoter genotype and transcriptional phenotype for eleven subtypes isolated from five continents. Finally, by identifying molecular mechanisms that promote the establishment and persistence of latency, we have tested an array of therapeutic agents for eleven HIV-1 subtype promoters and developed a novel strategy for the reactivation and clearance of latent reservoirs. |
