The major emphasis of this research is to understand the molecular mechanisms that govern gene expression in animal cells and viruses, focusing specifically on the transcriptional controls on the AIDS retrovirus long terminal repeat (LTR) and HSV-1 Immediate-Early (IE) promoters. Recent studies have revealed the existence of a class of sequence-specific DNA binding proteins that confer transcriptional specificity to RNA polymerase II. The mechanisms through which these proteins work with other components of the transcriptional machinery to initiate RNA synthesis remains a major question which can be best addressed through biochemcial studies on individual cellular transcription factors. One goal is to identify, isolate and characterize the biochemical properties of promoter and enhancer binding proteins, as well as cellular transcription factors that interact with the downstream trans-activation regulatory sequences located in the AIDS virus leader and with the far-upstream activation elements of the IE genes. In particular, we hope to define both the cis-acting elements and the important protein-protein and protein-DNA interactions that mediate promoter utilization and regulation. Purification of the proteins that recognize important viral promoter elements by sequence-specific DNA affinity chromatography will allow detailed biochemica studies on their mode of action and interaction with other transcription factors, and with cellular genes that are the normal targets for these proteins. Isolation of these factors from virus-infected cell extracts, or from cell lines that contain integrated copies of the viral regulatory proteins, will allow us to examine any biochemical changes in the activity or levels of the cellular factors that mediate viral activation, and to develop an in vitro transcription system that responds to virus trans-activator proteins. Experimental approaches developed to study the relatively simple control circuits of viruses can then be applied to more complex cellular gene families that utilize common transcription factors and may therefore respond to viral regulation in the infected cell.
