151
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Coley W, Van Duyne R, Carpio L, Guendel I, Kehn-Hall K, Chevalier S, Narayanan A, Luu T, Lee N, Klase Z, Kashanchi F. Absence of DICER in monocytes and its regulation by HIV-1. J Biol Chem 2010; 285:31930-43. [PMID: 20584909 DOI: 10.1074/jbc.m110.101709] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small RNA molecules that function to control gene expression and restrict viral replication in host cells. The production of miRNAs is believed to be dependent upon the DICER enzyme. Available evidence suggests that in T lymphocytes, HIV-1 can both suppress and co-opt the host's miRNA pathway for its own benefit. In this study, we examined the state of miRNA production in monocytes and macrophages as well as the consequences of viral infection upon the production of miRNA. Monocytes in general express low amounts of miRNA-related proteins, and DICER in particular could not be detected until after monocytes were differentiated into macrophages. In the case where HIV-1 was present prior to differentiation, the expression of DICER was suppressed. MicroRNA chip results for RNA isolated from transfected and treated cells indicated that a drop in miRNA production coincided with DICER protein suppression in macrophages. We found that the expression of DICER in monocytes is restricted by miR-106a, but HIV-1 suppressed DICER expression via the viral gene Vpr. Additionally, analysis of miRNA expression in monocytes and macrophages revealed evidence that some miRNAs can be processed by both DICER and PIWIL4. Results presented here have implications for both the pathology of viral infections in macrophages and the biogenesis of miRNAs. First, HIV-1 suppresses the expression and function of DICER in macrophages via a previously unknown mechanism. Second, the presence of miRNAs in monocytes lacking DICER indicates that some miRNAs can be generated by proteins other than DICER.
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Affiliation(s)
- William Coley
- National Center for Biodefense and Infectious Diseases, Department of Molecular and Microbiology, George Mason University, Manassas, Virginia 20110, USA
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152
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Liu Q, Tuo W, Gao H, Zhu XQ. MicroRNAs of parasites: current status and future perspectives. Parasitol Res 2010; 107:501-7. [DOI: 10.1007/s00436-010-1927-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 05/18/2010] [Indexed: 12/26/2022]
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153
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HIV-miR-H1 evolvability during HIV pathogenesis. Biosystems 2010; 101:88-96. [PMID: 20546828 DOI: 10.1016/j.biosystems.2010.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 05/16/2010] [Accepted: 05/17/2010] [Indexed: 12/12/2022]
Abstract
The discovery of microRNAs (miRNAs) in viruses has generated considerable attention into their functional relevance in processes such as cell death, viral proliferation, and oncogenesis. Two early studies found no detectable miRNAs expressed within HIV; however, several studies have verified the existence and function of three HIV miRNAs, most notably HIV-miR-TAR, thus making the earlier results controversial. Although miRNAs are highly conserved within most species, HIV is known to have a high mutation rate, which could contribute to the opposing experimental findings and raises questions about whether all HIV miRNAs are robust enough to maintain their integrity, especially in viral regions prone to insertions and deletions. In addition, could the evolvability of HIV miRNAs contribute to the diversity in HIV disease pathogenesis? To address this question, we examined mutations in 1293 sequences in a suspect HIV miRNA, called miR-H1, derived from a large variety of tissues from seven patients. We found considerable diversity within the structures, including a patient-specific deletion and the potential for the development of new miRNAs as a result of deletions. We also note a potential disease association between a less stable miR-H1 and the development of AIDS-related lymphoma (ARL).
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154
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Carpio L, Klase Z, Coley W, Guendel I, Choi S, Van Duyne R, Narayanan A, Kehn-Hall K, Meijer L, Kashanchi F. microRNA machinery is an integral component of drug-induced transcription inhibition in HIV-1 infection. JOURNAL OF RNAI AND GENE SILENCING : AN INTERNATIONAL JOURNAL OF RNA AND GENE TARGETING RESEARCH 2010; 6:386-400. [PMID: 20628499 PMCID: PMC2902143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2010] [Revised: 05/21/2010] [Accepted: 05/24/2010] [Indexed: 11/17/2022]
Abstract
RNA interference plays a significant role in manipulating cellular and viral mechanisms to maintain latency during HIV-1 infection. HIV-1 produces several microRNAs including one from the TAR element which alter the host's response to infection. Since cyclin/cdk complexes are important for viral transcription, these studies focus on the possible cdk inhibitors that inhibit viral transcription, without affecting normal cellular mechanisms. Roscovitine and Flavopiridol are well-studied cdk inhibitors that are effective at suppressing their target cdks at a low IC50. These cdk inhibitors and possibly future generations of drugs are affected by microRNA mechanisms. From our studies, we developed a third generation derivative called CR8#13. In cells that lack Dicer there was a higher level of basal viral LTR-reporter transcription. When drugs, specifically Flavopiridol and CR8#13 were added, the transcriptional inhibition of the LTR was less potent in cells that lacked Dicer. Also, after transfection with HIV-1 clone (pNL4.3), CR8 and CR8#13 derivatives were shown to be more effective viral transcription inhibitors in cell lines that contained Dicer (T-cells) as compared to Dicer deficient lines (monocytes). We next asked whether the addition of CR8 or CR8#13 could possibly increase levels of TAR microRNA in HIV-1 LTR containing cells. We demonstrate that the 3'TAR microRNA is produced in higher amounts after drug treatment, resulting in microRNA recruitment to the LTR. MicroRNA recruitment results in chromatin alteration, changes in Pol II phosphorylation and viral transcription inhibition. In conclusion, our results indicate that viral microRNA, specifically the TAR microRNA produced from the HIV-1 LTR is responsible for maintaining latent infections by manipulating host cell mechanisms to limit transcription from the viral LTR promoter. With the microRNA machinery present, cdk inhibitors are able to significantly increase the amount of TAR microRNA, leading to downregulation of viral LTR transcription.
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Affiliation(s)
- Lawrence Carpio
- National Center for Biodefense and Infectious Disease, 10900 University Blvd MS 1H8, George Mason University, Manassas, VA 20110, USA
| | - Zachary Klase
- Laboratory of Molecular Microbiology, NIAID, National Institutes of Health, Bethesda, MD 20892, USA
| | - William Coley
- The Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine, Washington, DC 20037, USA
| | - Irene Guendel
- National Center for Biodefense and Infectious Disease, 10900 University Blvd MS 1H8, George Mason University, Manassas, VA 20110, USA
| | - Sarah Choi
- National Center for Biodefense and Infectious Disease, 10900 University Blvd MS 1H8, George Mason University, Manassas, VA 20110, USA
| | - Rachel Van Duyne
- National Center for Biodefense and Infectious Disease, 10900 University Blvd MS 1H8, George Mason University, Manassas, VA 20110, USA
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Disease, 10900 University Blvd MS 1H8, George Mason University, Manassas, VA 20110, USA
| | - Kylene Kehn-Hall
- National Center for Biodefense and Infectious Disease, 10900 University Blvd MS 1H8, George Mason University, Manassas, VA 20110, USA
| | - Laurent Meijer
- National Center for Biodefense and Infectious Disease, 10900 University Blvd MS 1H8, George Mason University, Manassas, VA 20110, USA
| | - Fatah Kashanchi
- National Center for Biodefense and Infectious Disease, 10900 University Blvd MS 1H8, George Mason University, Manassas, VA 20110, USA,Correspondence to: Fatah Kashanchi, , Tel: +703 993 9160, Fax: +703 993 7022
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155
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Luers AJ, Loudig OD, Berman JW. MicroRNAs are expressed and processed by human primary macrophages. Cell Immunol 2010; 263:1-8. [PMID: 20403586 DOI: 10.1016/j.cellimm.2010.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 02/24/2010] [Accepted: 03/18/2010] [Indexed: 12/21/2022]
Abstract
Macrophages are crucial to host defense, functioning in innate and cell-mediated immunity. MicroRNAs (miRNAs) are small non-coding RNA molecules that repress transcription and protein production. Little is known about miRNA expression in primary human macrophages, or about how macrophage miRNAs contribute to both normal macrophage function and to the pathogenesis of disease in humans. Using Western blot analyses, we demonstrated the production of miRNA machinery proteins by human primary macrophages. Using two different miRNA array techniques, we identified 119 miRNAs expressed by human primary macrophages, including hsa-let-7a, miR-16, -23a, 30b, -103, -146a, -212, and -378 and validated them by quantitative RT-PCR. Our findings provide a knowledge base to which macrophage miRNA expression in organ-specific macrophages or disease processes may be compared in humans.
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Affiliation(s)
- Aimée J Luers
- Department of Pathology, The Albert Einstein College of Medicine (Einstein), Bronx, NY 10461, USA
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156
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[Viral noncoding RNAs]. Uirusu 2010; 59:179-87. [PMID: 20218326 DOI: 10.2222/jsv.59.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Many lines of recent evidence indicate that non-coding RNAs including micro RNAs (miRNAs) and small interfering RNAs (siRNAs) play an important role in the control of gene expression in diverse cellular processes and in defense responses against molecular parasites such as viruses and transposons. Viruses also use many different types of non-coding RNAs for regulating expression of their own genome or host genome temporally and spatially to ensure efficient virus proliferation and/or latency in the host cell. Here, we introduce the generation mechanisms and functions of novel non-coding RNAs generated from both animal and plant RNA viruses, after a brief review of non-coding RNAs of DNA viruses.
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157
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Epigenetic regulation of Kaposi's sarcoma-associated herpesvirus latency by virus-encoded microRNAs that target Rta and the cellular Rbl2-DNMT pathway. J Virol 2010; 84:2697-706. [PMID: 20071580 DOI: 10.1128/jvi.01997-09] [Citation(s) in RCA: 178] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) encodes a cluster of 12 microRNAs (miRNAs) that are processed from a transcript that is embedded within the major latency control region. We have generated a deletion mutation that eliminates 10 of the 12 viral miRNAs from the KSHV bacmid by using recombineering methods. The KSHV miRNA deletion mutant (BAC36 DeltamiR) behaved similarly to wild-type (wt) BAC36 in viral production, latency gene transcription, and viral DNA copy number in 293 and dermal microvascular endothelial cells (DMVECs). However, BAC36 DeltamiR consistently expressed elevated levels of viral lytic genes, including the immediate-early transcriptional activator Rta (ORF50). At least one KSHV microRNA (miRK12-5) was capable of suppressing ORF50 mRNA, but poor seed sequence alignments suggest that these targets may be indirect. Comparison of epigenetic marks in DeltamiR KSHV genomes revealed decreases in histone H3 K9 methylation, increases in histone H3 acetylation, and a striking loss of DNA methylation throughout the viral and cellular genome. One viral miRNA, K12-4-5p, was found to have a sequence targeting retinoblastoma (Rb)-like protein 2 (Rbl2), which is a known repressor of DNA methyl transferase 3a and 3b mRNA transcription. We show that ectopic expression of miR-K12-4-5p reduces Rbl2 protein expression and increases DNMT1, -3a, and -3b mRNA levels relative to the levels for control cells. We conclude that KSHV miRNA targets multiple pathways to maintain the latent state of the KSHV genome, including repression of the viral immediate-early protein Rta and a cellular factor, Rbl2, that regulates global epigenetic reprogramming.
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158
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Ouellet DL, Provost P. Current knowledge of MicroRNAs and noncoding RNAs in virus-infected cells. Methods Mol Biol 2010; 623:35-65. [PMID: 20217543 DOI: 10.1007/978-1-60761-588-0_3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Within the past few years, microRNAs (miRNAs) and other noncoding RNAs (ncRNAs) have emerged as elements with critically high importance in posttranscriptional control of cellular and, more recently, viral processes. Endogenously produced by a component of the miRNA-guided RNA silencing machinery known as Dicer, miRNAs are known to control messenger RNA (mRNA) translation through recognition of specific binding sites usually located in their 3' untranslated region. Recent evidences indicate that the host miRNA pathway may represent an adapted antiviral defense mechanism that can act either by direct miRNA-mediated modulation of viral gene expression or through recognition and inactivation of structured viral RNA species by the protein components of the RNA silencing machinery such as Dicer. This latter process, however, is a double-edge sword, as it may yield viral miRNAs exerting gene regulatory properties on both host and viral mRNAs. Our knowledge of the interaction between viruses and host RNA silencing machineries, and how this influences the course of infection, is becoming increasingly complex. This chapter aims to summarize our current knowledge about viral miRNAs/ncRNAs and their targets, as well as cellular miRNAs that are modulated by viruses upon infection.
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Affiliation(s)
- Dominique L Ouellet
- Centre de Recherche en Rhumatologie et Immunologie, CHUL Research Center/CHUQ, Quebec, QC, Canada
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159
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Abstract
One of the most significant recent advances in biomedical research has been the discovery of the approximately 22-nt-long class of noncoding RNAs designated microRNAs (miRNAs). These regulatory RNAs provide a unique level of posttranscriptional gene regulation that modulates a range of fundamental cellular processes. Several viruses, especially herpesviruses, also encode miRNAs, and over 200 viral miRNAs have now been identified. Current evidence indicates that viruses use these miRNAs to manipulate both cellular and viral gene expression. Furthermore, viral infection can exert a profound impact on the cellular miRNA expression profile, and several RNA viruses have been reported to interact directly with cellular miRNAs and/or to use these miRNAs to augment their replication potential. Here we discuss our current knowledge of viral miRNAs and virally influenced cellular miRNAs and their relationship to viral infection.
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Affiliation(s)
- Rebecca L Skalsky
- Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA.
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160
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Coley W, Kehn-Hall K, Van Duyne R, Kashanchi F. Novel HIV-1 therapeutics through targeting altered host cell pathways. Expert Opin Biol Ther 2009; 9:1369-82. [PMID: 19732026 DOI: 10.1517/14712590903257781] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The emergence of drug-resistant HIV-1 strains presents a challenge for the design of new drugs. Anti-HIV compounds currently in use are the subject of advanced clinical trials using either HIV-1 reverse transcriptase, viral protease or integrase inhibitors. Recent studies show an increase in the number of HIV-1 variants resistant to anti-retroviral agents in newly infected individuals. Targeting host cell factors involved in the regulation of HIV-1 replication might be one way to combat HIV-1 resistance to the currently available anti-viral agents. A specific inhibition of HIV-1 gene expression could be expected from the development of compounds targeting host cell factors that participate in the activation of the HIV-1 LTR promoter. Here we discuss how targeting the host can be accomplished either by using small molecules to alter the function of the host's proteins such as p53 or cdk9, or by utilizing new advances in siRNA therapies to knock down essential host factors such as CCR5 and CXCR4. Finally, we will discuss how the viral protein interactomes should be used to better design therapeutics against HIV-1.
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Affiliation(s)
- William Coley
- George Washington University, School of Medicine, Department of Microbiology, Immunology and Tropical Medicine, Washington, DC 20037, USA
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161
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Colin L, Van Lint C. Molecular control of HIV-1 postintegration latency: implications for the development of new therapeutic strategies. Retrovirology 2009; 6:111. [PMID: 19961595 PMCID: PMC2797771 DOI: 10.1186/1742-4690-6-111] [Citation(s) in RCA: 172] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Accepted: 12/04/2009] [Indexed: 02/07/2023] Open
Abstract
The persistence of HIV-1 latent reservoirs represents a major barrier to virus eradication in infected patients under HAART since interruption of the treatment inevitably leads to a rebound of plasma viremia. Latency establishes early after infection notably (but not only) in resting memory CD4+ T cells and involves numerous host and viral trans-acting proteins, as well as processes such as transcriptional interference, RNA silencing, epigenetic modifications and chromatin organization. In order to eliminate latent reservoirs, new strategies are envisaged and consist of reactivating HIV-1 transcription in latently-infected cells, while maintaining HAART in order to prevent de novo infection. The difficulty lies in the fact that a single residual latently-infected cell can in theory rekindle the infection. Here, we review our current understanding of the molecular mechanisms involved in the establishment and maintenance of HIV-1 latency and in the transcriptional reactivation from latency. We highlight the potential of new therapeutic strategies based on this understanding of latency. Combinations of various compounds used simultaneously allow for the targeting of transcriptional repression at multiple levels and can facilitate the escape from latency and the clearance of viral reservoirs. We describe the current advantages and limitations of immune T-cell activators, inducers of the NF-κB signaling pathway, and inhibitors of deacetylases and histone- and DNA- methyltransferases, used alone or in combinations. While a solution will not be achieved by tomorrow, the battle against HIV-1 latent reservoirs is well- underway.
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Affiliation(s)
- Laurence Colin
- Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium.
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162
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Morris KV. RNA-directed transcriptional gene silencing and activation in human cells. Oligonucleotides 2009; 19:299-306. [PMID: 19943804 PMCID: PMC2861411 DOI: 10.1089/oli.2009.0212] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 09/01/2009] [Indexed: 11/13/2022]
Abstract
The overt loss or uncontrolled gain of gene expression is found at some level in virtually every malady afflicting humans. From cancer to HIV-1, the uncontrolled expression or loss of gene expression is prevalent in human diseases. Approaches toward the specific control of gene expression at the transcriptional level could have the potential to revert or reduce disease pathologies. Over the last several years, researchers have developed methodologies that utilize small antisense non-coding RNAs to specifically silence transcription. Only recently has the endogenous molecular pathway usurped by the introduction of these small RNAs to regulate transcription in human cells been defined. Observations suggest that long antisense non-coding RNAs function as the endogenous epigenetic regulators of transcription in human cells, thus explaining why small antisense RNAs were observed early on to silence transcription via directed epigenetic changes at the target loci. The mechanism of action whereby small regulatory RNAs can either turn gene transcription on or off will be discussed as evidence that one day it may be possible to develop therapeutics to regulate gene transcription and ameliorate particular disease conditions.
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Affiliation(s)
- Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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163
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A synonymous variant in scavenger receptor, class B, type I gene is associated with lower SR-BI protein expression and function. Atherosclerosis 2009; 210:177-82. [PMID: 20060115 DOI: 10.1016/j.atherosclerosis.2009.11.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 11/16/2009] [Accepted: 11/19/2009] [Indexed: 11/22/2022]
Abstract
OBJECTIVE A synonymous variant within scavenger receptor class B type I gene (SCARB1), exon 8 rs5888, has been associated with altered lipid levels and cardiovascular risk in humans. The objective was to determine if rs5888 decreased SR-BI protein expression and function in vitro. METHODS SR-BI RNA secondary structure, turnover, polysomal distribution and protein expression were examined in COS cells transfected with wild-type or rs5888-SR-BI plasmids by selective 2'-hydroxyl acylation and primer extension assays, actinomycin D inhibition, polysomal profiling, and western blotting. SR-BI function in murine macrophages stably expressing wild-type or rs5888-SR-BI was assessed by measuring the specific cell association of (125)I,(3)H-cholesteryl ester (CE) radiolabeled HDL. RESULTS Rs5888 changed RNA secondary structure and led to marked differences in the polysomal profiles compared with wild-type transcript (p<0.02). As compared to wild-type cells, COS cells expressing rs5888 had significantly lower SR-BI protein expression (p<0.04), but no difference in total RNA transcript levels. There were no differences in SR-BI RNA turnover in murine macrophages, whereas specific cell association of (125)I (p<0.0001) or (3)H-CE (p<0.00001) was significantly lower in rs5888 cells. CONCLUSIONS The rs5888 variant affected SR-BI RNA secondary structure, protein translation, and was significantly associated with reduced SR-BI protein expression and function in vitro.
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164
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Dahl V, Josefsson L, Palmer S. HIV reservoirs, latency, and reactivation: prospects for eradication. Antiviral Res 2009; 85:286-94. [PMID: 19808057 DOI: 10.1016/j.antiviral.2009.09.016] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 09/24/2009] [Accepted: 09/30/2009] [Indexed: 12/11/2022]
Abstract
Current antiretroviral therapy effectively suppresses but does not eradicate HIV-1 infection. During therapy patients maintain a persistent low-level viremia requiring lifelong adherence to antiretroviral therapies. This viremia may arise from latently infected reservoirs such as resting memory CD4+ T-cells or sanctuary sites where drug penetration is suboptimal. Understanding the mechanisms of HIV latency will help efforts to eradicate the infection. This review examines the dynamics of persistent viremia, viral reservoirs, the mechanisms behind viral latency, and methods to purge the viral reservoirs. This article forms part of a special issue of Antiviral Research marking the 25th anniversary of antiretroviral drug discovery and development, vol. 85, issue 1, 2010.
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Affiliation(s)
- Viktor Dahl
- Swedish Institute for Infectious Disease Control, Karolinska Institutet, Nobels väg 18, SE-171 82 Solna, Sweden
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165
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Strebel K, Luban J, Jeang KT. Human cellular restriction factors that target HIV-1 replication. BMC Med 2009; 7:48. [PMID: 19758442 PMCID: PMC2759957 DOI: 10.1186/1741-7015-7-48] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 09/16/2009] [Indexed: 01/23/2023] Open
Abstract
Recent findings have highlighted roles played by innate cellular factors in restricting intracellular viral replication. In this review, we discuss in brief the activities of apolipoprotein B mRNA-editing enzyme 3G (APOBEC3G), bone marrow stromal cell antigen 2 (BST-2), cyclophilin A, tripartite motif protein 5 alpha (Trim5alpha), and cellular microRNAs as examples of host restriction factors that target HIV-1. We point to countermeasures encoded by HIV-1 for moderating the potency of these cellular restriction functions.
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Affiliation(s)
- Klaus Strebel
- Laboratory of Molecular Microbiology, NIAID, the National Institutes of Health, Bethesda, Maryland, USA
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166
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Charles S, Ammosova T, Cardenas J, Foster A, Rotimi J, Jerebtsova M, Ayodeji AA, Niu X, Ray PE, Gordeuk VR, Kashanchi F, Nekhai S. Regulation of HIV-1 transcription at 3% versus 21% oxygen concentration. J Cell Physiol 2009; 221:469-79. [PMID: 19626680 DOI: 10.1002/jcp.21882] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
HIV transcription is induced by the HIV-1 Tat protein, in concert with cellular co-factors including CDK9, CDK2, NF-kappaB, and others. The cells of most of the body's organs are exposed to approximately 3-6% oxygen, but most in vitro studies of HIV replication are conducted at 21% oxygen. We hypothesized that activities of host cell factors involved in HIV-1 replication may differ at 3% versus 21% O(2), and that such differences may affect HIV-1 replication. Here we show that Tat-induced HIV-1 transcription was reduced at 3% O(2) compared to 21% O(2). HIV-1 replication was also reduced in acutely or chronically infected cells cultured at 3% O(2) compared to 21% O(2). This reduction was not due the decreased cell growth or increased cellular toxicity and also not due to the induction of hypoxic response. At 3% O(2), the activity of CDK9/cyclin T1 was inhibited and Sp1 activity was reduced, whereas the activity of other host cell factors such as CDK2 or NF-kappaB was not affected. CDK9-specific inhibitor ARC was much less efficient at 3% compared to 21% O(2) and also expression of CDK9/cyclin T1-dependent IkappaB inhibitor alpha was repressed. Our results suggest that lower HIV-1 transcription at 3% O(2) compared to 21% O(2) may be mediated by lower activity of CDK9/cyclin T1 and Sp1 at 3% O(2) and that additional host cell factors such as CDK2 and NF-kappaB might be major regulators of HIV-1 transcription at low O(2) concentrations.
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Affiliation(s)
- Sharroya Charles
- Center for Sickle Cell Disease, Howard University, Washington, DC 20001, USA
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167
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Yeung ML, Bennasser Y, Watashi K, Le SY, Houzet L, Jeang KT. Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid. Nucleic Acids Res 2009; 37:6575-86. [PMID: 19729508 PMCID: PMC2770672 DOI: 10.1093/nar/gkp707] [Citation(s) in RCA: 191] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Small non-coding RNAs of 18-25 nt in length can regulate gene expression through the RNA interference (RNAi) pathway. To characterize small RNAs in HIV-1-infected cells, we performed linker-ligated cloning followed by high-throughput pyrosequencing. Here, we report the composition of small RNAs in HIV-1 productively infected MT4 T-cells. We identified several HIV-1 small RNA clones and a highly abundant small 18-nt RNA that is antisense to the HIV-1 primer-binding site (PBS). This 18-nt RNA apparently originated from the dsRNA hybrid formed by the HIV-1 PBS and the 3' end of the human cellular tRNAlys3. It was found to associate with the Ago2 protein, suggesting its possible function in the cellular RNAi machinery for targeting HIV-1.
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Affiliation(s)
- Man Lung Yeung
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-0460, USA
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168
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Easley R, Van Duyne R, Coley W, Guendel I, Dadgar S, Kehn-Hall K, Kashanchi F. Chromatin dynamics associated with HIV-1 Tat-activated transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1799:275-85. [PMID: 19716452 DOI: 10.1016/j.bbagrm.2009.08.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 08/14/2009] [Accepted: 08/20/2009] [Indexed: 02/07/2023]
Abstract
Chromatin remodeling is an essential event for HIV-1 transcription. Over the last two decades this field of research has come to the forefront, as silencing of the HIV-1 provirus through chromatin modifications has been linked to latency. Here, we focus on chromatin remodeling, especially in relation to the transactivator Tat, and review the most important and newly emerging studies that investigate remodeling mechanisms. We begin by discussing covalent modifications that can alter chromatin structure including acetylation, deacetylation, and methylation, as well as topics addressing the interplay between chromatin remodeling and splicing. Next, we focus on complexes that use the energy of ATP to remove or secure nucleosomes and can additionally act to control HIV-1 transcription. Finally, we cover recent literature on viral microRNAs which have been shown to alter chromatin structure by inducing methylation or even by remodeling nucleosomes.
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Affiliation(s)
- Rebecca Easley
- The George Washington University Medical Center, Department of Microbiology, Immunology, and Tropical Medicine, Washington, DC 20037, USA
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169
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Cellular microRNA and P bodies modulate host-HIV-1 interactions. Mol Cell 2009; 34:696-709. [PMID: 19560422 DOI: 10.1016/j.molcel.2009.06.003] [Citation(s) in RCA: 302] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 11/17/2008] [Accepted: 06/08/2009] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs), approximately 22 nt noncoding RNAs, assemble into RNA-induced silencing complexes (RISCs) and localize to cytoplasmic substructures called P bodies. Dictated by base-pair complementarity between miRNA and a target mRNA, miRNAs specifically repress posttranscriptional expression of several mRNAs. Here we report that HIV-1 mRNA interacts with RISC proteins and that disrupting P body structures enhances viral production and infectivity. In HIV-1-infected human T lymphocytes, we identified a highly abundant miRNA, miR-29a, which specifically targets the HIV-1 3'UTR region. Inhibiting miR-29a enhanced HIV-1 viral production and infectivity, whereas expressing a miR-29 mimic suppressed viral replication. We also found that specific miR-29a-HIV-1 mRNA interactions enhance viral mRNA association with RISC and P body proteins. Thus we provide an example of a single host miRNA regulating HIV-1 production and infectivity. These studies highlight the significance of miRNAs and P bodies in modulating host cell interactions with HIV-1 and possibly other viruses.
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170
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Senzer N, Rao D, Nemunaitis J. Letter to the editor: Does dicer expression affect shRNA processing? GENE REGULATION AND SYSTEMS BIOLOGY 2009; 3:103-4. [PMID: 19838337 PMCID: PMC2758281 DOI: 10.4137/grsb.s2551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Elevated Dicer and Drosha mRNA levels have been documented across a range of tumor types (including ovarian carcinoma) by a number of investigators without any demonstrable correlation with patient survival nor evidence of interference with shRNA processing. A recent publication by Merritt et al. (NEJM 359(25):2641-50, 2008) reporting their findings in patients with ovarian carcinoma reach opposite conclusions. Further study will be needed to resolve this issue.
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171
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Umbach JL, Cullen BR. The role of RNAi and microRNAs in animal virus replication and antiviral immunity. Genes Dev 2009; 23:1151-64. [PMID: 19451215 DOI: 10.1101/gad.1793309] [Citation(s) in RCA: 308] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The closely related microRNA (miRNA) and RNAi pathways have emerged as important regulators of virus-host cell interactions. Although both pathways are relatively well conserved all the way from plants to invertebrates to mammals, there are important differences between these systems. A more complete understanding of these differences will be required to fully appreciate the relationship between these diverse host organisms and the various viruses that infect them. Insights derived from this research will facilitate a better understanding of viral pathogenesis and the host innate immune response to viral infection.
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Affiliation(s)
- Jennifer L Umbach
- Department of Molecular Genetics and Microbiology and Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
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172
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Silencing viral microRNA as a novel antiviral therapy? J Biomed Biotechnol 2009; 2009:419539. [PMID: 19704916 PMCID: PMC2688686 DOI: 10.1155/2009/419539] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2008] [Accepted: 03/20/2009] [Indexed: 12/16/2022] Open
Abstract
Viruses are intracellular parasites that ensure their existence by converting host cells into viral particle producing entities or into hiding places rendering the virus invisible to the host immune system. Some viruses may also survive by transforming the infected cell into an immortal tumour cell. MicroRNAs are small non-coding transcripts that function as posttranscriptional regulators of gene expression. Viruses encode miRNAs that regulate expression of both cellular and viral genes, and contribute to the pathogenic properties of viruses. Hence, neutralizing the action of viral miRNAs expression by complementary single-stranded oligonucleotides or so-called anti-miRNAs may represent a strategy to combat viral infections and viral-induced pathogenesis. This review describes the miRNAs encoded by human viruses, and discusses the possible therapeutic applications of anti-miRNAs against viral diseases.
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173
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Graci JD, Colacino JM, Peltz SW, Dougherty JP, Gu Z. HIV Type-1 Latency: Targeted Induction of Proviral Reservoirs. ACTA ACUST UNITED AC 2009; 19:177-87. [DOI: 10.1177/095632020901900501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
HIV type-1 (HIV-1) can establish a state of latency in infected patients, most notably in resting CD4+ T-cells. This long-lived reservoir allows for rapid re-emergence of viraemia upon cessation of highly active antiretroviral therapy, even after extensive and seemingly effective treatment. Successful depletion of such latent reservoirs is probably essential to ‘cure’ HIV-1 infection and will require therapeutic agents that can specifically and efficiently act on cells harbouring latent HIV-1 provirus. The mechanisms underlying HIV-1 latency are not well characterized, and it is becoming clear that numerous factors, both cell- and virus-derived, are involved in the maintenance of proviral latency. The interplay of these various factors in the context of viral reactivation is still poorly understood. In this article, we review the current knowledge regarding the mechanisms underlying maintenance of HIV-1 latency, both transcriptional and post-transcriptional, with a focus on potential targets that might be exploited to therapeutically purge latent proviral reservoirs from infected patients.
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Affiliation(s)
| | | | | | - Joseph P Dougherty
- Department of Molecular Genetics, Microbiology, and Immunology, University of Medicine & Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Zhengxian Gu
- PTC Therapeutics, Inc., South Plainfield, NJ, USA
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174
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Richman DD, Margolis DM, Delaney M, Greene WC, Hazuda D, Pomerantz RJ. The challenge of finding a cure for HIV infection. Science 2009; 323:1304-7. [PMID: 19265012 DOI: 10.1126/science.1165706] [Citation(s) in RCA: 645] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although combination therapy for HIV infection represents a triumph for modern medicine, chronic suppressive therapy is required to contain persistent infection in reservoirs such as latently infected CD4+ lymphocytes and cells of the macrophage-monocyte lineage. Despite its success, chronic suppressive therapy is limited by its cost, the requirement of lifelong adherence, and the unknown effects of long-term treatment. This review discusses our current understanding of suppressive antiretroviral therapy, the latent viral reservoir, and the needs for and challenges of attacking this reservoir to achieve a cure.
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Affiliation(s)
- Douglas D Richman
- San Diego VA Healthcare System and University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0679, USA.
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175
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PENG JJ. Progress of studies on Dicer structure and function. YI CHUAN = HEREDITAS 2009; 30:1550-6. [DOI: 10.3724/sp.j.1005.2008.01550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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176
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Klase Z, Winograd R, Davis J, Carpio L, Hildreth R, Heydarian M, Fu S, McCaffrey T, Meiri E, Ayash-Rashkovsky M, Gilad S, Bentwich Z, Kashanchi F. HIV-1 TAR miRNA protects against apoptosis by altering cellular gene expression. Retrovirology 2009; 6:18. [PMID: 19220914 PMCID: PMC2654423 DOI: 10.1186/1742-4690-6-18] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 02/16/2009] [Indexed: 12/23/2022] Open
Abstract
Background RNA interference is a gene regulatory mechanism that employs small RNA molecules such as microRNA. Previous work has shown that HIV-1 produces TAR viral microRNA. Here we describe the effects of the HIV-1 TAR derived microRNA on cellular gene expression. Results Using a variation of standard techniques we have cloned and sequenced both the 5' and 3' arms of the TAR miRNA. We show that expression of the TAR microRNA protects infected cells from apoptosis and acts by down-regulating cellular genes involved in apoptosis. Specifically, the microRNA down-regulates ERCC1 and IER3, protecting the cell from apoptosis. Comparison to our cloned sequence reveals possible target sites for the TAR miRNA as well. Conclusion The TAR microRNA is expressed in all stages of the viral life cycle, can be detected in latently infected cells, and represents a mechanism wherein the virus extends the life of the infected cell for the purpose of increasing viral replication.
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Affiliation(s)
- Zachary Klase
- The Department of Microbiology, Immunology and Tropical Medicine program, The George Washington University School of Medicine, Washington, District of Columbia 20037, USA.
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177
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Vrolijk MM, Harwig A, Berkhout B, Das AT. Destabilization of the TAR hairpin leads to extension of the polyA hairpin and inhibition of HIV-1 polyadenylation. Retrovirology 2009; 6:13. [PMID: 19210761 PMCID: PMC2645353 DOI: 10.1186/1742-4690-6-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 02/11/2009] [Indexed: 11/24/2022] Open
Abstract
Background Two hairpin structures that are present at both the 5' and 3' end of the HIV-1 RNA genome have important functions in the viral life cycle. The TAR hairpin binds the viral Tat protein and is essential for Tat-mediated activation of transcription. The adjacent polyA hairpin encompasses the polyadenylation signal AAUAAA and is important for the regulation of polyadenylation. Specifically, this RNA structure represses polyadenylation at the 5' side, and enhancer elements on the 3' side overcome this suppression. We recently described that the replication of an HIV-1 variant that does not need TAR for transcription was severely impaired by destabilization of the TAR hairpin, even though a complete TAR deletion was acceptable. Results In this study, we show that the TAR-destabilizing mutations result in reduced 3' polyadenylation of the viral transcripts due to an extension of the adjacent polyA hairpin. Thus, although the TAR hairpin is not directly involved in polyadenylation, mutations in TAR can affect this process. Conclusion The stability of the HIV-1 TAR hairpin structure is important for the proper folding of the viral RNA transcripts. This study illustrates how mutations that are designed to study the function of a specific RNA structure can change the structural presentation of other RNA domains and thus affect viral replication in an indirect way.
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Affiliation(s)
- Martine M Vrolijk
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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178
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Park J, Nadeau PE, Mergia A. Activity of TAR in inducible inhibition of HIV replication by foamy virus vector expressing siRNAs under the control of HIV LTR. Virus Res 2009; 140:112-20. [PMID: 19110017 DOI: 10.1016/j.virusres.2008.11.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 11/12/2008] [Accepted: 11/17/2008] [Indexed: 12/22/2022]
Abstract
In this report we describe foamy virus vectors with conditional expression of short interfering RNAs (siRNAs) in HIV infected cells. Short hairpin RNAs (shRNAs) based on two targets in the 5' end of the untranslated region and one in the rev gene flanked with 5' and 3' microRNA 30 (miR30) sequences were synthesized and placed under the control of an HIV promoter for Tat-mediated expression. HIV permissive cells were transduced with foamy virus vectors containing each hybrid shRNA expression cassette and tested for their efficacy on the inhibition of HIV replication. Effective Tat dependent expression of the shRNAs, as well as GFP placed downstream each shRNA was evident. In addition the results show inhibition of HIV replication by greater than 98%. Interestingly, transduction of cells with a vector lacking an shRNA also revealed GFP expression in the presence of Tat with similar levels of inhibition of virus replication. When the TAR region was removed from this vector there was neither reduction in virus replication nor Tat-induced GFP expression. These results suggest that TAR in the vector, which Tat interacts to promote expression of the shRNA, is a potent inhibitor of virus replication. Previous studies with TAR regulated expression of antiviral genes ignore the contribution of TAR in the repression of virus replication. Interpretation of effective inhibition of HIV replication by antiviral genes located downstream of TAR while neglecting the efficacy of a potent repression by TAR is misleading.
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Affiliation(s)
- Jeonghae Park
- Department of Infectious Disease and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
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179
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Ouellet DL, Plante I, Barat C, Tremblay MJ, Provost P. Emergence of a complex relationship between HIV-1 and the microRNA pathway. Methods Mol Biol 2009; 487:415-33. [PMID: 19301659 DOI: 10.1007/978-1-60327-547-7_20] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Recent experimental evidences support the existence of an increasingly complex and multifaceted interaction between viruses and the microRNA-guided RNA silencing machinery of human cells. The discovery of small interfering RNAs (siRNAs), which are designed to mediate cleavage of specific messenger RNAs (mRNAs), prompted virologists to establish therapeutic strategies based on siRNAs with the aim to suppress replication of several viruses, including human immunodeficiency virus type 1 (HIV-1). It has been appreciated only recently that viral RNAs can also be processed endogenously by the microRNA-generating enzyme Dicer or recognized by cellular miRNAs, in processes that could be viewed as an adapted antiviral defense mechanism. Known to repress mRNA translation through recognition of specific binding sites usually located in their 3' untranslated region, miRNAs of host or viral origin may exert regulatory effects towards host and/or viral genes and influence viral replication and/or the host response to viral infection. This article summarizes our current state of knowledge on the relationship between HIV-1 and miRNA-guided RNA silencing, and discusses the different aspects of their interaction.
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Affiliation(s)
- Dominique L Ouellet
- Centre de Recherche en Rhumatologie et Immunologie, CHUL Research Center, Quebec, Canada
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180
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He S, Yang Z, Skogerbo G, Ren F, Cui H, Zhao H, Chen R, Zhao Y. The properties and functions of virus encoded microRNA, siRNA, and other small noncoding RNAs. Crit Rev Microbiol 2008; 34:175-88. [PMID: 18972284 DOI: 10.1080/10408410802482008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
microRNAs (miRNAs) represent a class of noncoding RNA species, believed to be regulating gene expression by binding to complementary sites in the 3'UTRs of target mRNAs. They play important regulatory roles in various metabolic pathways in most eukaryotes. The recent discovery of virus encoded miRNAs suggests that viruses may be using them to regulate host and viral gene expression. Another class of closely related small interfering RNAs (siRNAs) also has been found within the HIV-1 genome and shown to be exerting a limited impact on virus reproduction. Additionally, an additional type of viral noncoding RNAs named small noncoding RNAs (sncRNAs) ranging from a few tens to a few hundred nucleotides in length, has also been identified. sncRNAs have a wide phylogenesis and high levels of expression, suggesting they may play an important roles in different species. Here we discuss the genomic organization, expression, conservation as well as potential function of virally encoded miRNA, siRNA, and sncRNAs.
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Affiliation(s)
- Shunmin He
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science, CAMS & PUMC, Chinese Academy of Science, Beijing, China
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181
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182
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Saraiya AA, Wang CC. snoRNA, a novel precursor of microRNA in Giardia lamblia. PLoS Pathog 2008; 4:e1000224. [PMID: 19043559 PMCID: PMC2583053 DOI: 10.1371/journal.ppat.1000224] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 10/31/2008] [Indexed: 12/05/2022] Open
Abstract
An Argonaute homolog and a functional Dicer have been identified in the ancient eukaryote Giardia lamblia, which apparently lacks the ability to perform RNA interference (RNAi). The Giardia Argonaute plays an essential role in growth and is capable of binding specifically to the m7G-cap, suggesting a potential involvement in microRNA (miRNA)-mediated translational repression. To test such a possibility, small RNAs were isolated from Giardia trophozoites, cloned, and sequenced. A 26-nucleotide (nt) small RNA (miR2) was identified as a product of Dicer-processed snoRNA GlsR17 and localized to the cytoplasm by fluorescence in situ hybridization, whereas GlsR17 was found primarily in the nucleolus of only one of the two nuclei in Giardia. Three other small RNAs were also identified as products of snoRNAs, suggesting that the latter could be novel precursors of miRNAs in Giardia. Putative miR2 target sites were identified at the 3′-untranslated regions (UTR) of 22 variant surface protein mRNAs using the miRanda program. In vivo expression of Renilla luciferase mRNA containing six identical miR2 target sites in the 3′-UTR was reduced by 40% when co-transfected with synthetic miR2, while the level of luciferase mRNA remained unaffected. Thus, miR2 likely affects translation but not mRNA stability. This repression, however, was not observed when Argonaute was knocked down in Giardia using a ribozyme-antisense RNA. Instead, an enhancement of luciferase expression was observed, suggesting a loss of endogenous miR2-mediated repression when this protein is depleted. Additionally, the level of miR2 was significantly reduced when Dicer was knocked down. In all, the evidence indicates the presence of a snoRNA-derived miRNA-mediated translational repression in Giardia. Gene regulation in Giardia lamblia, a primitive parasitic protozoan responsible for the diarrheal disease giardiasis, is poorly understood. There is no consensus promoter sequence. A simple eight–base pair AT-rich region is sufficient to initiate gene transcription in this organism. Thus, the main control of gene expression may occur after the stage of transcription. The presence of Dicer and Argonaute homologs in Giardia suggested that microRNA (miRNA)-mediated translational repression could be one mechanism of gene regulation. In this work, we characterized the presence of the miRNA pathway in Giardia as well as identified the novel use of small nucleolar RNA (snoRNA) as miRNA precursors. Potential target sites for one small RNA (miR2) were identified with the miRanda program. In vivo reporter assays confirmed the specific interaction between the target sites and miR2. A ribozyme-mediated reduction of Dicer and Argonaute in Giardia showed that the former is required for miR2 production whereas the latter functions in mediating the inhibition of reporter expression, which agrees with the roles of these two proteins. This is the first evidence of miRNA-mediated gene regulation in Giardia and the first demonstration of the use of snoRNAs as miRNA precursors.
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Affiliation(s)
- Ashesh A. Saraiya
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Ching C. Wang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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183
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Leonard JN, Shah PS, Burnett JC, Schaffer DV. HIV evades RNA interference directed at TAR by an indirect compensatory mechanism. Cell Host Microbe 2008; 4:484-94. [PMID: 18996348 DOI: 10.1016/j.chom.2008.09.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 08/11/2008] [Accepted: 09/08/2008] [Indexed: 02/06/2023]
Abstract
HIV can rapidly evolve when placed under selective pressure, including immune surveillance or the administration of antiretroviral drugs. Typically, a variant protein allows HIV to directly evade the selective pressure. Similarly, HIV has escaped suppression by RNA interference (RNAi) directed against viral RNAs by acquiring mutations at the target region that circumvent RNAi-mediated inhibition while conserving necessary viral functions. However, when we directed RNAi against the viral TAR hairpin, which plays an indispensable role in viral transcription, resistant strains were recovered, but none carried a mutation at the target site. Instead, we isolated several strains carrying promoter mutations that indirectly compensated for the RNAi by upregulating viral transcription. Combining RNAi with the application of an antiviral drug blocked replication of such mutants. Evolutionary tuning of viral transcriptional regulation may serve as a general evasion mechanism that may be targeted to improve the efficacy of antiviral therapy.
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Affiliation(s)
- Joshua N Leonard
- Department of Chemical Engineering and the Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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184
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Abstract
In this review, a quick presentation of what interfering RNA (iRNA) are—small RNA able to exert an inhibition on gene expression at a posttranscriptional level, based on sequence homology between the iRNA and the mRNA—will be given. The many faces of the interrelations between iRNA and viruses, particularly HIV, will be reviewed. Four kinds of interactions have been described: i) iRNA of viral origin blocking viral RNA, ii) iRNA of viral origin downregulating cellular mRNA, iii) iRNA of cellular origin (microRNA) targeting viral RNA, and iv) microRNA downregulating cellular mRNA encoding cell proteins used by the virus for its replication. Next, HIV strategies to manipulate these interrelations will be considered: suppression of iRNA biosynthesis by Tat, trapping by the HIV TAR sequence of a cell component, TRBP, necessary for iRNA production and action, and induction by the virus of some microRNA together with suppression of others. Then, we will discuss the putative effects of these mutual influences on viral replication as well as on viral latency, immune response, and viral cytopathogenicity. Finally, the potential consequences on the human infection of genetic polymorphisms in microRNA genes and the therapeutic potential of iRNA will be presented.
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Affiliation(s)
- Pierre Corbeau
- Laboratoire d'Immunologie, Hôpital Carémeau, Nîmes and Institut de Génétique Humaine, CNRS UPR1142, Montpellier, France.
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185
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Ludwig LB. RNA silencing and HIV: a hypothesis for the etiology of the severe combined immunodeficiency induced by the virus. Retrovirology 2008; 5:79. [PMID: 18786256 PMCID: PMC2553099 DOI: 10.1186/1742-4690-5-79] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Accepted: 09/11/2008] [Indexed: 12/29/2022] Open
Abstract
A novel intrinsic HIV-1 antisense gene was previously described with RNA initiating from the region of an HIV-1 antisense initiator promoter element (HIVaINR). The antisense RNA is exactly complementary to HIV-1 sense RNA and capable of forming ~400 base-pair (bp) duplex RNA in the region of the long terminal repeat (LTR) spanning the beginning portion of TAR in the repeat (R) region and extending through the U3 region. Duplex or double-stranded RNA of several hundred nucleotides in length is a key initiating element of RNA interference (RNAi) in several species. This HIVaINR antisense RNA is also capable of forming multiple stem-loop or hairpin-like secondary structures by M-fold analysis, with at least one that perfectly fits the criteria for a microRNA (miRNA) precursor. MicroRNAs (miRNAs) interact in a sequence-specific manner with target messenger RNAs (mRNAs) to induce either cleavage of the message or impede translation. Human mRNA targets of the predicted HIVaINR antisense RNA (HAA) microRNAs include mRNA for the human interleukin-2 receptor gamma chain (IL-2RG), also called the common gamma (γc) receptor chain, because it is an integral part of 6 receptors mediating interleukin signalling (IL-2R, IL-4R, IL-7R, IL-9R, IL-15R and IL-21R). Other potential human mRNA targets include interleukin-15 (IL-15) mRNA, the fragile × mental retardation protein (FMRP) mRNA, and the IL-1 receptor-associated kinase 1 (IRAK1) mRNA, amongst others. Thus the proposed intrinsic HIVaINR antisense RNA microRNAs (HAAmiRNAs) of the human immunodeficiency virus form complementary targets with mRNAs of a key human gene in adaptive immunity, the IL-2Rγc, in which genetic defects are known to cause an X-linked severe combined immunodeficiency syndrome (X-SCID), as well as mRNAs of genes important in innate immunity. A new model of intrinsic RNA silencing induced by the HIVaINR antisense RNA in the absence of Tat is proposed, with elements suggestive of both small interfering RNA (siRNA) and miRNA.
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186
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Suzuki K, Juelich T, Lim H, Ishida T, Watanebe T, Cooper DA, Rao S, Kelleher AD. Closed chromatin architecture is induced by an RNA duplex targeting the HIV-1 promoter region. J Biol Chem 2008; 283:23353-63. [PMID: 18519571 PMCID: PMC2516975 DOI: 10.1074/jbc.m709651200] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 05/23/2008] [Indexed: 12/13/2022] Open
Abstract
In some mammalian systems small interfering RNAs (siRNA) targeting homologous sequences in promoter regions of genes induce transcriptional gene silencing (TGS). We have previously reported the induction of TGS by an siRNA (prom-A siRNA) targeting the tandem NF-kappaB-binding motifs within the human immunodeficiency virus, type 1 (HIV-1), promoter region. Here we report that induction of TGS by prom-A siRNA is accompanied by immediate and sustained local recruitment of Argonaute-1 (Ago1), histone deacetylase-1 (HDAC1), and induction of dimethylation of histone 3 at lysine 9 (H3K9me2), processes known to be associated with transcriptional silencing. Elevated levels of H3K9me2 and HDAC1 spread upstream of the target sequence, and elevated H3K9me2 levels also spread downstream into the coding region. Moreover, this siRNA induces an immediate change in DNA accessibility to restriction enzyme digestion in the region of the transcription initiation site of the HIV-1. This change in accessibility is because of the relocation of a nucleosome known to be associated with this region of the integrated pro-virus. Although there is a theoretical possibility that the observed viral suppression could be mediated by the PTGS mechanism with this siRNA acting at the 3 (R)-long term repeat of the virus, we demonstrate that this siRNA, and three other U3 targeted siRNAs, are inefficient inducers of PTGS. These data strongly suggest that siRNA targeting the promoter region acts predominantly at a site within the 5 (R)-long term repeat of HIV to induce transcriptional silencing and alterations to chromatin structure of the HIV promoter region that extend well beyond the immediate siRNA target site. These induced changes are consistent with those described in latent HIV-1 infection.
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Affiliation(s)
- Kazuo Suzuki
- Centre for Immunology, St. Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia.
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187
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Zhang H. Reversal of HIV-1 latency with anti-microRNA inhibitors. Int J Biochem Cell Biol 2008; 41:451-4. [PMID: 18761423 DOI: 10.1016/j.biocel.2008.07.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 07/07/2008] [Accepted: 07/08/2008] [Indexed: 10/21/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) latency is achieved when host cells contain integrated proviral DNA but do not produce viral particles. The virus remains in resting CD4 T-lymphocytes, evading host immune surveillance and antiviral drugs. When resting cells are activated, infectious viral particles are produced. Latency is critical for the survival of all HIV-1 strains in vivo. Recently, it has been reported that a cluster of cellular microRNAs (miRNAs) enriched specifically in resting CD4+ T-cells suppresses translation of most HIV-1-encoded proteins in the cytoplasm, sustaining HIV-1 escape from the host immune response. Complementary antisense miRNA inhibitors block the inhibitory effect of miRNAs and drive viral production from the resting T-lymphocytes without activating the cells. Therefore, inhibition of these HIV-1-specific cellular miRNAs is of great therapeutic significance for eliminating the HIV-1 reservoir in HIV-1-infected individuals receiving suppressive highly active antiretroviral therapy (HAART).
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Affiliation(s)
- Hui Zhang
- Center for Human Virology, Division of Infectious Diseases, Department of Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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188
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Abstract
Cellular defence mechanisms against HIV contribute to its persistence. One of the cellular defenses against virus infection is the silencing of viral gene expression. There is evidence that at least two gene-silencing mechanisms are used against the human immuno-deficiency virus (HIV). Paradoxically, this cellular defense mechanism contributes to viral latency and persistence, and we review here the relationship of viral latency to gene-silencing mechanisms.
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Affiliation(s)
- Hoi-Ping Mok
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
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189
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van Rij RP. Virus meets RNAi. Symposium on antiviral applications of RNA interference. EMBO Rep 2008; 9:725-9. [PMID: 18636088 DOI: 10.1038/embor.2008.133] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 06/17/2008] [Indexed: 11/09/2022] Open
Affiliation(s)
- Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen Centre for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
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190
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Abstract
Many viruses introduce DNA into the host-cell nucleus, where they must either embrace or confront chromatin factors as a support or obstacle to completion of their life cycle. Compared to the eukaryotic cell, viruses have compact and rapidly evolving genomes. Despite their smaller size, viruses have complex life cycles that involve dynamic changes in DNA structure. Nuclear entry, transcription, replication, genome stabilization, and virion packaging involve complex changes in chromosome organization and structure. Chromatin dynamics and epigenetic modifications play major roles in viral and host chromosome biology. In some cases, viruses may use novel or viral-specific epigenetic modifying activities, which may reflect variant pathways that distinguish their behavior from the bulk of the cellular chromosome. This review examines several recent discoveries that highlight the role of chromatin dynamics in the life cycle of DNA viruses.
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191
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Abstract
The discovery of RNA interference (RNAi) has resulted in a new class of biological agents that can specifically downmodulate HIV-1 gene expression. Delivery of these RNAi-based agents and the emergence of viral resistance present pressing issues in the use of RNAi in a genetic-based therapy for HIV-1. Here, we discuss a potential avenue around viral resistance and a targeted delivery scheme for treating HIV-1-infected individuals involving transcriptional gene silencing. Specifically, the use of small antisense RNAs targeted to the viral promoter regions and delivery by lentiviral-based mobilization-competent vectors expressing these promoter targeted RNAs may prove therapeutically relevant in a genetic therapy-based approach to treating HIV-1 infection.
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Affiliation(s)
- Anne-Marie W Turner
- Department of Molecular & Experimental Medicine and Kellogg School of Science & Technology, The Scripps Research Institute, 10550 N. Torrey Pines Road, MEM-115, La Jolla, CA 92037, USA
| | - Kevin V Morris
- Department of Molecular & Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, MEM-115, La Jolla, CA 92037, USA
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192
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The roles of microRNAs in mammalian virus infection. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1779:706-11. [PMID: 18549828 DOI: 10.1016/j.bbagrm.2008.05.005] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2007] [Revised: 05/06/2008] [Accepted: 05/08/2008] [Indexed: 12/29/2022]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that are important for the control of a multitude of critical processes in mammalian cells. Increasing evidence supports that miRNAs also have important functions in viral replication and may be used by host cells to control viral infection. Expression of miRNAs has been reported for various groups of viruses including herpesviruses, small DNA viruses and retroviruses. The recent identification of target genes regulated by some of these viral miRNAs suggests that they may function in the control of lytic and latent viral replication, in the limitation of antiviral responses, in the inhibition of apoptosis, and in the stimulation of cellular growth. In this review, we summarize in brief recent findings on the antiviral activities of cellular miRNAs and the viral counter-responses to the cell's RNAi restriction.
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193
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Fujii YR. Formulation of New Algorithmics for miRNAs. Open Virol J 2008; 2:37-43. [PMID: 19440463 PMCID: PMC2678821 DOI: 10.2174/1874357900802010037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 04/02/2008] [Accepted: 04/07/2008] [Indexed: 12/12/2022] Open
Abstract
microRNAs (miRNAs) are a class of small RNAs, 21-25 nucleotides (nts) long with single-stranded RNA. miRNA targets the sequences of messenger RNA (mRNA) through incomplete base-pairing of the target sequence. The incomplete pairing of miRNA to mRNA triggers either translational repression or epigenetically mediated transcriptional gene silencing (TGS). miRNA and RNA silencing in mammalian cells may participate in natural ecological interactions and miRNA itself should contain the original information that is required to control viral proliferation, according to the hypothesis of RNA waves. While the hypothesis involves so-called resident and genomic miRNA as the genetic information, resident miRNAs may evolve and jump into other RNAs, and then become genomic miRNAs. Thus, the inheritable character may be acquired by both types of miRNAs. It is reasonable to believe that preparations of new algorithmics models for the flow of miRNAs may provide an opportunity to overcome the acquired immunodeficiency syndrome (AIDS) pandemic.
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194
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Ouellet DL, Plante I, Landry P, Barat C, Janelle ME, Flamand L, Tremblay MJ, Provost P. Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element. Nucleic Acids Res 2008; 36:2353-65. [PMID: 18299284 PMCID: PMC2367715 DOI: 10.1093/nar/gkn076] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The interaction between human immunodeficiency virus type 1 (HIV-1) and RNA silencing pathways is complex and multifaceted. Essential for efficient viral transcription and supporting Tat-mediated transactivation of viral gene expression, the trans-activation responsive (TAR) element is a structured RNA located at the 5′ end of all transcripts derived from HIV-1. Here, 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 transcript, namely miR-TAR-5p and miR-TAR-3p. In vitro RNase assays indicate that the lack of a free 3′ extremity at the base of TAR may contribute to its low processing reactivity in vivo. Both miR-TAR-5p and miR-TAR-3p down-regulated TAR miRNA sensor activity in a process that required an integral miRNA-guided RNA silencing machinery. miR-TAR-3p exerted superior gene downregulatory effects, probably due to its preferential release from HIV-1 TAR RNA by the RNase III Dicer. Our study suggests that the TAR element of HIV-1 transcripts releases functionally competent miRNAs upon asymmetrical processing by Dicer, thereby providing novel insights into viral miRNA biogenesis.
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Affiliation(s)
- Dominique L Ouellet
- Centre de Recherche en Rhumatologie et Immunologie, Quebec, QC, G1V 4G2, Canada
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195
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Kumar A. RNA interference: a multifaceted innate antiviral defense. Retrovirology 2008; 5:17. [PMID: 18241347 PMCID: PMC2259359 DOI: 10.1186/1742-4690-5-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Accepted: 02/01/2008] [Indexed: 11/12/2022] Open
Abstract
The RNA interference mechanism utilizes short RNA duplexes to either suppress or induce target gene expression. Post-transcriptional regulation mediated by microRNA is an integral component of innate antiviral defense. The magnitude and the efficiency of viral restriction guided by RNA-based defenses, as well as the full physiological implication of host-pathogen engagement, constitute exciting areas of investigation in the biology of non-coding RNAs.
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196
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Kumar A, Jeang KT. Insights into cellular microRNAs and human immunodeficiency virus type 1 (HIV-1). J Cell Physiol 2008; 216:327-31. [DOI: 10.1002/jcp.21488] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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197
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Scaria V, Jadhav V. microRNAs in viral oncogenesis. Retrovirology 2007; 4:82. [PMID: 18036240 PMCID: PMC2217556 DOI: 10.1186/1742-4690-4-82] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2007] [Accepted: 11/24/2007] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are a recently discovered class of small noncoding functional RNAs. These molecules mediate post-transcriptional regulation of gene expression in a sequence specific manner. MicroRNAs are now known to be key players in a variety of biological processes and have been shown to be deregulated in a number of cancers. The discovery of viral encoded microRNAs, especially from a family of oncogenic viruses, has attracted immense attention towards the possibility of microRNAs as critical modulators of viral oncogenesis. The host-virus crosstalk mediated by microRNAs, messenger RNAs and proteins, is complex and involves the different cellular regulatory layers. In this commentary, we describe models of microRNA mediated viral oncogenesis.
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198
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Yeung ML, Benkirane M, Jeang KT. Small non-coding RNAs, mammalian cells, and viruses: regulatory interactions? Retrovirology 2007; 4:74. [PMID: 17937800 PMCID: PMC2164956 DOI: 10.1186/1742-4690-4-74] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Accepted: 10/15/2007] [Indexed: 12/31/2022] Open
Abstract
Recent findings suggest that mammalian cells can use small non-coding RNAs (ncRNA) to regulate physiological viral infections. Here, we comment on several lines of evidence that support this concept. We discuss how viruses may in turn protect, suppress, evade, modulate, or adapt to the host cell's ncRNA regulatory schema.
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Affiliation(s)
- Man Lung Yeung
- Molecular Virology Section, Laboratory of Molecular Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health Bethesda, Maryland 20892-0460, USA.
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