HIV-1 core promoter lacks a simple initiator element but contains a bipartite activator at the transcription start site

Abstract

The human immunodeficiency virus type 1 (HIV-1) core promoter region, extending approximately from nucleotides -40 to +80 relative to the transcription start site, contains a complex array of putative regulatory elements, including a TATA box, an initiator element, an element between the TATA box and start site, binding sites for LBP/UBP, the TAR element, and others. However, because of this elaborate architecture, the precise boundaries and functional roles for the individual regulatory elements have not been defined. To facilitate a detailed analysis of the HIV-1 core promoter, we employed in vitro transcription assays to identify the simplest control elements that activate RNA synthesis in the context of a synthetic, heterologous promoter. Because mutations at the start site previously were shown to diminish transcription, we anticipated finding an initiator as a basic regulator. However, we have demonstrated that the HIV-1 core promoter lacks an initiator that is functionally analogous to those found in the terminal transferase and adenovirus major late promoters. In its place, we identified two elements between -6 and +30, both of which appear to be necessary for significant transcriptional activation. Unlike a strong initiator, the activity of these elements was dependent on the presence of a TATA box and on their position relative to TATA. We have called the region containing these two elements the HIV-1 SSR to distinguish it from the simple transcriptional initiator elements found in other genes.