Naturally Occurring Human Immunodeficiency Virus Type 1 Long Terminal Repeats Have a Frequently Observed Duplication That Binds RBF-2 and Represses Transcription

Abstract

Approximately 38% of human immunodeficiency virus type 1 (HIV-1)-infected patients within the Vancouver Lymphadenopathy-AIDS Study have proviruses bearing partial 15- to 34-nucleotide duplications upstream of the NF-κB binding sites within the 5′ long terminal repeat (LTR). This most frequent naturally occurring length polymorphism (MFNLP) of the HIV-1 5′ LTR encompasses potential binding sites for several candidate transcription factors, including TCF-1α/hLEF, c-Ets, AP-4, and Ras-responsive binding factor 2 (RBF-2) (M. C. Estable et al., J. Virol. 70:4053–4062, 1996). RBF-2 and an apparently related factor, RBF-1, bind to at least fourcis elements within the LTR which are required for full transcriptional responsiveness to protein-tyrosine kinases and v-Ras (B. Bell and I. Sadowski, Oncogene 13:2687–2697, 1996). Here we demonstrate that representative MFNLPs from two patients specifically bind RBF-2. In both cases, deletion of the MFNLP caused elevated LTR-directed transcription in cells expressing RBF-2 but not in cells with undetectable RBF-2. RBF-1, but not RBF-2, appears to contain the Ets transcription factor family member GABPα/GABPβ1. Taken together with the fact that every MFNLP from a comparative study of over 500 LTR sequences from 42 patients contains a predicted binding site for RBF-2, our data suggest that the MFNLP is selected in vivo because it provides a duplicated RBF-2 cis element, which may limit transcription in monocytes and activated T cells.

Distinctive variation in the U3R region of the 5' Long Terminal Repeat from diverse HIV-1 strains

“…Besides the most frequent variant CA predominant in sequences from non-B, D, G and non-CRF01_AE isolates, the AP-1-like sequence displayed some strains distinctive motifs ( Fig 1D ). It was followed by the MFNLP which in accordance with previous reports [ 21 , 22 ], was displayed by about 33% of the LTRs in our study. Commonly observed in LTRs from CRF22_01A1 specimens as well as in LTRs subtyped as F2, CRF12_BF (80%) and CRF02_AG (67%), this insert was less frequent (≤ 40%) in clades A1, G, C and D. It was scarcely found in LTRs subtyped as B, and was totally absent in the LTRs from CRF01_AE isolates.…”

Specific interaction of TFII‐I with an upstream element on the HIV‐1 LTR regulates induction of latent provirus

“…Unincorporated label was removed, and the probes digested with Xbal and gel purified to minimize signal from non‐specific end‐labeling. DNasel footprinting reactions were performed as previously described [8] Chromatin immunopreciptation assays with USF1, USF2 and TFII‐I antibodies were as in previous experiments [2,3].…”

Regulation of HIV-1 gene transcription: from lymphocytes to microglial cells

“…A representative subtype D virus circulating in Uganda harbors a duplication of the LEF-1/TCF-1␣-binding sequence, which results in high infectivity [181]. This LEF-1binding site duplication also occurs in ϳ38% of HIV-infected patients within the Vancouver Lymphadenopathy-AIDS Study [182]. Sequence variations in the ATF/CREB-binding site also impact transcription factor recruitment and result in more active isolates [183].…”