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HIV Long Terminal Repeat (1):
Recent article
HIV Long Terminal Repeat
Nucleic Acids Research (38)11 2010
Abstract
We investigated how the D1 domain and two peptides encompassing the D1 basic clusters chaperoned the annealing of complementary canonical nucleic acids that correspond to the DNA sequences of the HIV-1 transactivation response element TAR and its complementary cTAR. The core peptides were found to a...
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PMID: 20167640
PDF is available here.
PDF is available here.
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Abstract
We previously described the polymorphism in the interferon regulatory factor-1 (IRF-1) gene as a novel correlate of resistance to HIV-1 infection in a Kenyan female sex worker cohort. However, the underlying mechanisms likely mediating this association remained to be elucidated. The initiation of HI...
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PMID: 20100115
PDF is available here.
PDF is available here.
Biophysical Journal (98)8 2010
Abstract
We analyze noise in gene-expression from HIV-1's long terminal repeat (LTR) promoter at different HIV-1 integration sites across the human genome. Flow cytometry analysis of GFP expression from the HIV-1 LTR shows high variability (noise) at each integration site. Notably, the measured noise levels...
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PMID: 20409455
PDF is available here.
PDF is available here.
Abstract
We tested several siRNAs directed against the human VEGF promoter. Of these, siVFp(-992) exhibited > or =50% suppression of VEGF production in two human cell lines. To determine the specificity of this siRNA-mediated suppression, plasmids were prepared to express a luciferase reporter under the cont...
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PMID: 20026621
PDF is available here.
PDF is available here.
Abstract
Since the discovery and synthesis of a novel DNA mimic, peptide nucleic acid (PNA) in 1991, PNAs have attracted tremendous interest and have shown great promise as potential antisense drugs. They have been used extensively as tools for specific modulation of gene expression by targeting translation...
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PMID: 19534584
PDF is available here.
PDF is available here.
Journal of Molecular Biology (390)2 2009
Abstract
We investigated the mechanism of PKR activation by an RNA hairpin with a number of base pairs intermediate between these 15- to 30-bp limits: human immunodeficiency virus type 1 transactivation-responsive region (TAR) RNA, a 23-bp hairpin with three bulges that is known to dimerize. TAR monomers and...
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PMID: 19445956
PDF is available here.
PDF is available here.
Abstract
Due to its highly conserved zinc fingers and its nucleic acid chaperone properties which are critical for HIV-1 replication, the nucleocapsid protein (NC) constitutes a major target in AIDS therapy. Different families of molecules targeting NC zinc fingers and/or inhibiting the bindi...
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PMID: 19401213
PDF is available here.
PDF is available here.
Abstract
A small but significant number of HIV-2 cases have been reported from India. Although all HIV-2 viruses identified belong to subtype A, there are no studies on the diversity of the HIV-2 envelope and other genomic regions from India. Furthermore, HIV-2 envelope quasispecies in infected individuals h...
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PMID: 19327056
PDF is available here.
PDF is available here.
Abstract
A peptide nucleic acid (PNA) oligomer and a series of PNA conjugates featuring covalently attached pendant 1,4,7,10-tetraazacyclododecane (cyclen) or bis((pyridin-2-yl)methyl)amine (DPA) moieties have been synthesized that are complementary to regions of the HIV-1 TAR messenger RNA stem-loop. Therma...
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PMID: 19015900
PDF is available here.
PDF is available here.
Abstract
The aptamer technology has been introduced in the early 1990s. With this technique ligands for organic dyes and proteins have been identified in many research field, providing various inhibitory molecules that allow functional interference in biological systems. Aptamers can therefore be employed fo...
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PMID: 19377996
PDF is available here.
PDF is available here.
Abstract
A number of aminoglycoside antibiotics, and in particular neomycin B, are demonstrated to promote strand cleavage of RNA oligonucleotides (minimised HIV-1 TAR element and prokaryotic ribosomal A-site), by binding and causing sufficient distortion to the RNA backbone to render it more susceptible to...
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PMID: 19081939
PDF is available here.
PDF is available here.
Abstract
We describe here a genomic SELEX approach and its application to the recognition of stem-loop structures prone to the formation of kissing complexes. We also provide technical details for running a procedure termed 2D-SELEX that takes advantage of both in vitro selection and dynamic combinatorial ch...
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PMID: 19377979
PDF is available here.
PDF is available here.
Abstract
Our results demonstrate that in cells, TRBP controls PACT activation of PKR, an activity that is reversed by stress....
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PMID: 18936160
PDF is available here.
PDF is available here.
Biochemistry (Washington) (47)51 2008
Abstract
Specific HIV integrase strand transfer inhibitors are thought to bind to the integrase active site, positioned to coordinate with two catalytic magnesium atoms in a pocket flanked by the end of the viral LTR. A structural role for the 3' terminus of the viral LTR in the inhibitor-bound state has not...
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PMID: 18991395
PDF is available here.
PDF is available here.
Abstract
We demonstrate the optimization of an intron encoding three endogenous miRNAs for the ectopic expression of heterologous anti-HIV-1 small interfering RNAs (siRNAs) processed from a single RNA polymerase II primary miRNA. Our expression system, designated as MCM7, is engineered from the intron-embedd...
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PMID: 18800151
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)22 2008
Abstract
We describe here the crystal structure of TAR bound to a high-affinity RNA aptamer. The two hairpins form a kissing complex and interact through six Watson-Crick base pairs. The complex adopts an overall conformation with an inter-helix angle of 28.1 degrees , thus contrasting with previously report...
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PMID: 18996893
PDF is available here.
PDF is available here.
Abstract
We show that expression of FOXP3 in primary human CD4 T-cells significantly inhibits HIV-1 infection. Since FOXP3 inhibits NFAT activity, and NFAT proteins contribute to HIV-1 transcription, we explore a transcriptional repressive function of HIV-1 LTR by FOXP3. Over-expression of FOXP3 in primary C...
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PMID: 18829063
PDF is available here.
PDF is available here.
Abstract
We assessed HIV-1 and HIV-2 2-long terminal repeat (LTR) circular DNA production in peripheral blood mononuclear cells, MT4-CXCR4 cells and HeLa-CXCR4-CCR5 cells in vitro, relative to the respective total amounts of HIV DNA. Whatever the cell type, HIV-2 produced a smaller total amount of DNA than H...
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PMID: 19005280
PDF is available here.
PDF is available here.
Abstract
A new laser-based mass spectrometry method, called laser induced liquid bead ion desorption (LILBID), was applied to investigate RNA:ligand interactions. As model system the HIV Tat:TAR transactivation complex and its binding behavior were analyzed. TARwt of HIV Type 1 and Type 2 and different artif...
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PMID: 18693035
PDF is available here.
PDF is available here.
Abstract
We demonstrate that primer sets for HIV late reverse transcripts and 2-LTR circles have similar sensitivity and accuracy with either universal or fast QPCR methods. However, both cost and time are reduced with fast QPCR....
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PMID: 18762215
PDF is available here.
PDF is available here.
Abstract
We provide evidence that the transcription factor BCL11B represses expression from the HIV-1 long terminal repeat (LTR) in T lymphocytes through direct association with the HIV-1 LTR. We also demonstrate that the NuRD corepressor complex mediates BCL11B transcriptional repression of the HIV-1 LTR. I...
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PMID: 18768194
PDF is available here.
PDF is available here.
Abstract
We determined the mechanism that regulates HIV-1 activation via prostaglandin J(2) (PGJ(2)) in Caco-2 cells. We showed that treatment of Caco-2 cells with PGJ(2) decreased the infectivity of a luciferase reporter virus, pHXB-luc, as well as HIV production following infection of cells with a X4-tropi...
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PMID: 18755491
PDF is available here.
PDF is available here.
Abstract
Twenty-four purine derivatives bearing aryl groups at N9 position were designed and synthesized as HIV-1 Tat-TAR interaction inhibitors. All the compounds showed high antiviral activities in inhibiting the formation of SIV-induced syncytium in CEM174 cells. Ten of them with low cytotoxicities were e...
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PMID: 18693018
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)16 2008
Abstract
We describe a two-step ligation method for enzymatic joining of dsRNA adaptors to any dsRNA molecule in its duplex form without a need for prior sequence or termini information. The method is specific for dsRNA and can ligate various adaptors to label, map or amplify dsRNA sequences. When combined w...
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PMID: 18628292
PDF is available here.
PDF is available here.
Journal of Virology (82)18 2008
Abstract
We recently constructed an SIVmac variant that does not require the Tat-TAR interaction for transcription. We used this variant to study additional roles of TAR in SIVmac replication and generated mutants with a truncated TAR structure. We demonstrate that partial or nearly complete removal of TAR d...
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PMID: 18596090
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)35 2008
Abstract
In this study, eight different HIV-1 integrase proteins containing mutations observed in strand transfer inhibitor-resistant viruses were expressed, purified, and used for detailed enzymatic analyses. All the variants examined were impaired for strand transfer activity compared with the wild type en...
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PMID: 18577511
PDF is available here.
PDF is available here.
Abstract
Treatment with rosiglitazone caused a significant decrease of virus infection in macrophages. PPARgamma stimulation inhibited virus replication by modulating NF-kappaB activation in a receptor-dependent manner, leading to downregulation of HIV-1 long terminal repeat (LTR) promoter activity and suppr...
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PMID: 18670212
PDF is available here.
PDF is available here.
Cell Host & Microbe (4)2 2008
Abstract
We found that viral integration into the actively transcribed host genes led to transcriptional interference (TI) caused by the elongating RNA polymerase II (RNAPII) transcribing through the viral promoter. The resulting physical exclusion of preinitiation complex formation on the 5' long terminal r...
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PMID: 18692772
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)13 2008
Abstract
We previously constructed an HIV-1 variant in which the TAR-Tat transcription control mechanism is replaced by the components of the Tet-ON regulatory system. In this context, the surprising finding was that TAR can be truncated or even deleted, but partial TAR deletions that destabilize the stem st...
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PMID: 18586822
PDF is available here.
PDF is available here.
Abstract
We have obtained a structural model in solution of a TAR-aptamer kissing complex with an unprecedented accuracy. This high-resolution structure reveals that the GA base pair is unilaterally shifted toward the 5' strand and is stabilized by a network of intersugar hydrogen bonds. This specific confor...
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PMID: 18607001
PDF is available here.
PDF is available here.
Abstract
We applied the transcription factor (TF) decoy approach, based on the intracellular delivery of double-stranded oligodeoxynucleotides (ODNs) causing inhibition of the binding of TF-related proteins to the different consensus sequences in the promoter of specific genes. In CF bronchial IB3-1 cells, P...
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PMID: 18258920
PDF is available here.
PDF is available here.
Virus Research (135)1 2008
Abstract
We described that HCV NS3/4A protein can activate HIV-1 transcription from its long terminal repeat (LTR) region, while the serine protease-inactive mutant of NS3/4A fails to do so. The activation effect of NS3/4A to HIV-1 transcription can be explained by its ability to enhance DNA binding activiti...
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PMID: 18433908
PDF is available here.
PDF is available here.
Abstract
We designed chimeric U5 long terminal repeat (LTR) DNA substrates by exchanging comparative sequences between human immunodeficiency virus type-1 (HIV-1) and PFV U5 LTRs, and investigated the 3'-end processing reactivity using HIV-1 and PFV INs, respectively. HIV-1 IN recognized the nucleotides pres...
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PMID: 18600045
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)10 2008
Abstract
We speculated that Tat had nucleic acid-chaperoning properties. This prompted us to examine in vitro the nucleic acid-chaperoning activities of Tat and Tat peptides made by chemical synthesis. Here we report that Tat has potent nucleic acid-chaperoning activities according to the standard DNA anneal...
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PMID: 18442994
PDF is available here.
PDF is available here.
Abstract
We demonstrate that cyclin K/CPR4-containing positive transcription elongation factor b complexes are unresponsive to Tat and HEXIM1-mediated inactivation. Enhancing expression of cyclin K/CPR4 inhibited the human and simian immunodeficiency viral replication. These data indicate that cyclin K/CPR4...
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PMID: 18520353
PDF is available here.
PDF is available here.
Abstract
Cellular APOBEC3G (A3G) protein is packaged into human immunodeficiency virus type 1 (HIV-1) virions in producer cells yet restricts viral replication in target cells. To characterize this restriction in target cells, the effect of A3G on generating various HIV-1 cDNA products was measured by quanti...
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PMID: 18308358
PDF is available here.
PDF is available here.
Abstract
We determined the effect of mutations generated in HIV-1 LTR on viral gene expression in six mother-infant pairs following vertical transmission. We show that the functional domains critical for LTR function, the promoter (TATAA), enhancers (three SpI and two NFkappaB sites), the modulatory region (...
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PMID: 18313715
PDF is available here.
PDF is available here.
Abstract
We show that p14(ARF) inhibits transcription activation of HIV-1 LTR promoter activity by Tat protein. Tat protein is a RNA-bound transcriptional activator whose function is strictly required for HIV-1 replication. We determined that p14(ARF) inhibits Tat transactivation of HIV-1 LTR by promoting Ta...
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PMID: 18418067
PDF is available here.
PDF is available here.
Immunology Letters (117)2 2008
Abstract
We present evidence that Human immunodeficiency virus promotes interleukin-32 production at both mRNA and protein levels. Our results showed that there is a 74% increase in the serum levels of IL-32 among HIV patients as compared to healthy individuals. There was a three-fold increase in the promote...
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PMID: 18329725
PDF is available here.
PDF is available here.
Abstract
We show that the TCR-independent CD28 signals lead to the trans-activation of HIV-1 LTR in an NF-kappaB-dependent manner. In particular, we found that CD28 engagement by B7 induces the specific recruitment of RelA/NF-kappaB subunit to the HIV-1 LTR promoter both in vitro and in ex vivo infected cell...
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PMID: 18389481
PDF is available here.
PDF is available here.
Abstract
We have determined the crystal structure of the DNA binding domain of NFAT bound to the HIV-1 long terminal repeat (LTR) tandem kappaB enhancer element at 3.05 A resolution. NFAT binds as a dimer to the upstream kappaB site (Core II), but as a monomer to the 3' end of the downstream kappaB site (Cor...
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PMID: 18462673
PDF is available here.
PDF is available here.
Abstract
We studied the effects of these sex hormones on HIV-1 replication in peripheral blood mononuclear cells (PBMCs). We compared HIV-1 replication in PBMCs infected in the presence of mid-secretory (high concentrations) and mid-proliferative (low concentrations) or in the absence of sex hormones. With P...
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PMID: 18462082
PDF is available here.
PDF is available here.
Immunology Letters (117)1 2008
Abstract
We have employed our CD4(+) T cell model named HIV-1 resistance factor (HRF(+)) to study the inducible anti-HIV-1 responses mediated through novel soluble molecules. We found that exposure to the soluble products of HRF(+) cells activated CCCTC-binding factor (CTCF) mRNA expression in HIV-1 suscepti...
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PMID: 18207574
PDF is available here.
PDF is available here.
Abstract
The novel mechanism through which HMBA disrupts latent HIV-1 infection involves 2 cellular kinases that may be therapeutically exploited to induce expression of persistent proviral HIV-1....
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PMID: 18419522
PDF is available here.
PDF is available here.
Nature Genetics (40)4 2008
Abstract
We directly quantify transcriptional feedback strength and its effects on both the duration of HIV-1 Tat transcriptional pulses and the fate of HIV-infected cells. By measuring shifts in the autocorrelation of noise inherent to gene expression, we found that transcriptional positive feedback extends...
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PMID: 18344999
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)7 2008
Abstract
We report that this element is a source of microRNAs (miRNAs) in cultured HIV-1-infected cell lines and in HIV-1-infected human CD4+ T lymphocytes. Using primer extension and ribonuclease (RNase) protection assays, we delineated both strands of the TAR miRNA duplex deriving from a model HIV-1 transc...
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PMID: 18299284
PDF is available here.
PDF is available here.
Journal of Virology (82)7 2008
Abstract
We have previously shown that interferon-regulatory factor 1 (IRF-1) is stimulated early after HIV-1 infection and regulates promoter transcriptional activity even in the absence of the viral transactivator Tat. In this work we demonstrate that IRF-1 is also required for full NF-kappaB transcription...
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PMID: 18216101
PDF is available here.
PDF is available here.
Abstract
We hypothesized that one of the HIV-1 LTR proviral DNA sequence elements that binds host cell transcriptional factors is involved in this antiviral activity. To assess this possibility, we constructed full-length infectious HIV-1 molecular clones with mutations in the LTR elements NFAT, AP-1, IL-2 h...
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PMID: 18086484
PDF is available here.
PDF is available here.
Journal of Molecular Biology (377)3 2008
Abstract
We provided evidence that coactivator-associated arginine methyltransferase 1 (CARM1) is a transcriptional coactivator of NF-kappaB and functions as a promoter-specific regulator of NF-kappaB recruitment to chromatin. Here, we show that protein arginine methyltransferase 1 (PRMT1) synergistically co...
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PMID: 18280497
PDF is available here.
PDF is available here.
Abstract
Abstract
We demonstrate that motional couplings can be used to anchor NMR frames of reference onto different parts of an RNA molecule, thus extending the spatial resolution limit for dynamical characterization....
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PMID: 18246076
PDF is available here.
PDF is available here.
Journal of Virology (82)6 2008
Targets of small interfering RNA restriction during human immunodeficiency virus type 1 replication.
Abstract
Small interfering RNAs (siRNAs) have been shown to effectively inhibit human immunodeficiency virus type 1 (HIV-1) replication in vitro. The mechanism(s) for this inhibition is poorly understood, as siRNAs may interact with multiple HIV-1 RNA species during different steps of the retroviral life cyc...
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PMID: 18199654
PDF is available here.
PDF is available here.
Abstract
We have expressed two BIV IN versions that differ in their amino termini. The longer version, containing the 74-residue sequence, did not show any detectable 3'-end processing and strand transfer IN activities and performed only the IN-associated disintegration. Consequently, the shorter version, la...
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PMID: 17976681
PDF is available here.
PDF is available here.
Abstract
We have established a novel human immunodeficiency virus (HIV) tandem-reporter assay using HIV receptor-transduced NP-2 cells with long terminal repeat-controlled beta-galactosidase, inserted internal ribosome entry site, and secretary alkaline phosphatase genes. This assay allows users to detect re...
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PMID: 18094135
PDF is available here.
PDF is available here.
Abstract
We were able to identify a novel ligand disrupting the interaction between the Tat peptide and TAR RNA, which is part of the human immunodeficiency virus (HIV-1) mRNA. Using a single template structure (acetylpromazine) as reference molecule and a topological pharmacophore descriptor (CATS), new che...
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PMID: 18064402
PDF is available here.
PDF is available here.
Abstract
We analyzed the human immunodeficiency type 1 (HIV-1) viruses circulating between 1999 and 2004 in antiretroviral-naive women from a rural area of southern Mozambique. Nucleotide sequencing of the HIV-1 long terminal repeat (LTR) U3, envelope (env) C2V3C3, and protease (pr) genomic regions was perfo...
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PMID: 18271719
PDF is available here.
PDF is available here.
Abstract
We examined the 1125 base pair (bp) sequences encompassing these regions in 10 long-term survivors (LTSs) treated with KRG (total of 13,364 +/- 5364 g) for > 12 years, and in 8 LTS control patients with no or minimal (total of 1436 +/- 1027 g) KRG intake (LTS controls). In the 10 LTSs, 189 PCR produ...
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PMID: 18284321
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)3 2008
Abstract
A ribonuclease, RNase T-tat, specifically designed to hydrolyze the TAR RNA of HIV-1 virus has been engineered. The protein was made by domain swapping the TAT peptide at the loop 3 position of ribonuclease T1. The RNase T-tat maintains a guanine-specific RNA hydrolytic activity, and characteristica...
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PMID: 18086702
PDF is available here.
PDF is available here.
Journal of Immunology (180)3 2008
Abstract
We examined the binding of transcription factors to the HIV provirus long terminal repeat using chromatin immunoprecipitation. RON expression decreased basal levels of NF-kappaB and RNA polymerase II (Pol II) binding to the HIV provirus long terminal repeat but did not prevent the induction of these...
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PMID: 18209063
PDF is available here.
PDF is available here.
Molecular Cell (29)1 2008
Abstract
We demonstrate that both ongoing transcription and pre-mRNA processing are essential for gene loop formation, and predict that these structures represent a defining feature of active gene transcription....
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PMID: 18206969
PDF is available here.
PDF is available here.