The objective of this project is to define the molecular mechanism controlling the expression of HIV-1 in infected cells. Our studies focus on understanding the molecular basis for latency and the mechanism of reactivation from latency of HIV-1. We are using, as a model, several chronically infected cell lines which harbor the virus in a """"""""latent"""""""" state. Low level viral expression present in basal conditions can be activated in these cell lines after treatment with cytokines (TNF-alpha, GM-CSF) or phorbol esters. Our previous work examining the chromatin of HIV integrated in these cell lines identified several DNase I hypersensitive regions in the 5' and 3' LTR and in the pol gene. In addition, a new hypersensitive site was noted in the 5' LTR upon induction of viral expression. We have used micrococcal nuclease and restriction enzymes digestion of purified nuclei to map the boundaries of positioned nucleosomes in the 5' LTR. These studies demonstrated that the U3 region of the 5' LTR is nucleosome-free and therefore accessible for transcription factors to bind. The R-U5 region seems protected by a nucleosome which is removed following induction of viral expression. This nucleosome could play a role in the maintenance of latency and its removal could be the first step in activating transcription. Binding sites for transcription factors have been identified in this 'inducible' region and are being characterized. The intragenic DNase I hypersensitive site has also been examined at higher resolution in vivo with micrococcal nuclease and estriction enzymes identifying a 300bp nucleosome-free region. This region, which precisely maps where an enhancer was previously identified, has been studied in vitro by DNase I footprinting, methylation interference and gel retardation assays. Seven sites for DNA-binding proteins have been identified and characterized. The role of each of these sites in the activity of the enhancer is being defined by mutagenesis and transfection studies. The significance of these studies lies in the potential relevance for HIV- 1 latency and reactivation. The identification of a repressor nucleosome in the 5' LTR of HIV- 1 could open new therapeutic opportunities to suppress replication.
