In Vitro Techniques for Studies of HIV-1 Promoter Activity

A rather unique feature of the human immunodeficiency virus type-1 (HIV-1) is the structural complexity of the regulatory sequences located in the long-terminal repeat (LTR) promoter region and the number of cellular and viral transcription factors known to interact with these sequences and modulate HIV gene expression see ref. 1 ). The HIV-1 LTR can be schematically divided into four functional regions: (1) the negative regulatory element (NRE) encompassing nuceotides −350 to −190 with respect to the transcription start site; (2) the enhancer (−140 to−81), containing two binding sites for the transcription factor NFκB; (3) the basal promoter (located between −80 and +1), including a typical TATAA box and three binding sites for the transcription factor Sp1; and (4) the trans-activation response (TAR) element, a bulged stem-and-loop structure present in the nascent RNA (+1 to +59) transcript that provides a binding site for Tat activation of HIV-1 transcription. In addition, a novel regulatory DNA element, named IST (Initiator of Short Transcripts), has been shown to be present in the HIV-1 LTR (position ⁻ 5 to ⁺ 26), encompassing the binding site for transcription factors YY1 and late SV40 transcription factor (LSF, or CP-2, or LBP-1) (see refs. 2 and 3 ). IST directs the RNA polymerase II to synthesize short (59–61 nt), correctly initiated, nonpolyadenylated transcripts that prematurely terminate at the TAR stem-loop structure. The function of these transcripts remains unclear (see ref. 4 ).