Analysis of the roles of HIV-derived microRNAs

Bibliography

• Bartel DP. MicroRNAs: genomics, biogenesis, mechanism and function. Cell 2004;116(2):281-97
   PubMed Web of Science ®Google Scholar
• Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993;75(5):843-54
   PubMed Web of Science ®Google Scholar
• Reinhart BJ, Slack FJ, Basson M, The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000;403(6772):901-6
   PubMed Web of Science ®Google Scholar
• Fabian MR, Sundermeier TR, Sonenberg N. Understanding how miRNAs post-transcriptionally regulate gene expression. Prog Mol Subcell Biol 2010;50:1-20
   PubMedGoogle Scholar
• Fabian MR, Sonenberg N, Filipowicz W. Regulation of mRNA translation and stability by microRNAs. Annu Rev Biochem 2010;79:351-79
   PubMed Web of Science ®Google Scholar
• Inui M, Martello G, Piccolo S. MicroRNA control of signal transduction. Nat Rev Mol cell Biol 2010;11(4):252-63
   PubMed Web of Science ®Google Scholar
• Cai Y, Yu X, Hu S, Yu J. A brief review on the mechanisms of miRNA regulation. Genomics Proteomics Bioinformatics 2009;7(4):147-54
   PubMedGoogle Scholar
• Subramanian S, Steer CJ. MicroRNAs as gatekeepers of apoptosis. J Cell Physiol 2010;223(2):289-98
   PubMed Web of Science ®Google Scholar
• Zhang C. Novel functions of small RNA molecules. Curr Opin Mol Ther 2009;11(6):641-51
   PubMed Web of Science ®Google Scholar
• Chua JH, Armugam A, Jeyaseelan K. MicroRNAs: biogenesis, function and applications. Curr Opin Mol Ther 2009;11(2):189-99
   PubMed Web of Science ®Google Scholar
• Ying SY, Lin SL. Intron-mediated RNA interference and microRNA biogenesis. Methods Mol Biol 2009;487:387-413
   PubMedGoogle Scholar
• Perron MP, Provost P. Protein components of the microRNA pathway and human diseases. Methods Mol Biol 2009;487:369-85
   PubMedGoogle Scholar
• Winter J, Jung S, Keller S, Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 2009;11(3):228-34
   PubMed Web of Science ®Google Scholar
• Faller M, Guo F. MicroRNA biogenesis: there's more than one way to skin a cat. Biochim Biophys Acta 2008;1779(11):663-7
   PubMed Web of Science ®Google Scholar
• Perron MP, Provost P. Protein interactions and complexes in human microRNA biogenesis and function. Front Biosci 2008;13:2537-47
   PubMed Web of Science ®Google Scholar
• Cai X, Hagedorn CH, Cullen BR. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 2004;10(12):1957-66
   PubMed Web of Science ®Google Scholar
• Lee Y, Ahn C, Han J, The nuclear RNase III drosha initiates microRNA processing. Nature 2003;425(6956):415-19
   PubMed Web of Science ®Google Scholar
• Han J, Lee Y, Yeom KH, The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 2004;18(24):3016-27
   PubMed Web of Science ®Google Scholar
• Yi R, Qin Y, Macara IG, Cullen BR. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 2003;17(24):3011-16
   PubMed Web of Science ®Google Scholar
• Kim VN. MicroRNA precursors in motion: exportin-5 mediates their nuclear export. Trends Cell Biol 2004;14(4):156-9
   PubMed Web of Science ®Google Scholar
• Chendrimada TP, Gregory RI, Kumaraswamy E, TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 2005;436:740-41
   PubMed Web of Science ®Google Scholar
• Haase AD, Jaskiewicz L, Zhang H, TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep 2005;6(10):961-7
   PubMed Web of Science ®Google Scholar
• Kawamata T, Tomari Y. Making RISC. Trends Biochem Sci 2010;35(7):368-76
   PubMed Web of Science ®Google Scholar
• Schwartz DS, Hutvagner G, Du T, Asymmetry in the assembly of the RNAi enzyme complex. Cell 2003;115(2):199-208
   PubMed Web of Science ®Google Scholar
• Parker JS, Parizotto EA, Wang M, Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Mol Cell 2009;33(2):204-14
   PubMed Web of Science ®Google Scholar
• Parker JS, Roe SM, Barford D. Molecular mechanism of target RNA transcript recognition by Argonaute-guide complexes. Cold Spring Harb Symp Quant Biol 2006;71:45-50
   PubMedGoogle Scholar
• Kulkarni M, Ozgur S, Stoecklin G. On track with P-bodies. Biochem Soc Trans 2010;38(pt 1):242-51
   PubMedGoogle Scholar
• Zofall M, Grewal SI. RNAi-mediated heterochromatin assembly in fission yeast. Cold Spring Harb Symp Quant Biol 2006;71:487-96
   PubMedGoogle Scholar
• Verdel A, Jia S, Gerber S, RNAi-mediated targeting of heterochromatin by the RITS complex. Science 2004;303(5658):672-6
   PubMed Web of Science ®Google Scholar
• Buhler M, Moazed D. Transcription and RNAi in heterochromatic gene silencing. Nat Struct Mol Biol 2007;14:1041-8
   PubMed Web of Science ®Google Scholar
• Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005;120(1):15-20
   PubMed Web of Science ®Google Scholar
• Pfeffer S, Zavolan M, Grasser FA, Identification of virus-encoded MicroRNAs. Science 2004;304(5671):734-6
   PubMed Web of Science ®Google Scholar
• Cai X, Schafer A, Lu S, Epstein-Barr Virus microRNAs are evolutionarily conserved and differentially expressed. PLoS Pathog 2006;2:e23
   PubMed Web of Science ®Google Scholar
• Grundhoff A, Sullivan CS, Ganem D. A combined computational and microarray based approach identifies novel microRNAs encoded by human gamma-herpesviruses. RNA 2006;12:733-50
   PubMed Web of Science ®Google Scholar
• Zhu JY, Pfuhl T, Motsch N, Identification of novel Epstein-barr virus microRNA genes from nasopharyngeal carcinomas. J Virol 2009;83(7):3333-41
   PubMed Web of Science ®Google Scholar
• Ganem D, Ziegelbauer J. MicroRNAs of Kaposi's sarcoma associated herpes virus. Semin Cancer Biol 2008;18(6):437-40
   PubMed Web of Science ®Google Scholar
• Dolken L, Pfeffer S, Koszinowski UH. Cytomegalovirus microRNAs. Virus Genes 2009;38(3):355-64
   PubMed Web of Science ®Google Scholar
• Boss IW, Plaisance KB, Renne R. Role of virus-encoded microRNAs in herpesvirus biology. Trends Microbiol 2009;17(12):544-53
   PubMed Web of Science ®Google Scholar
• Pfeffer S, Sewer A, Lagos-Quintana M, Identification of microRNAs of the herpesvirus family. Nat Methods 2005;2(4):269-76
   PubMed Web of Science ®Google Scholar
• Lin J, Cullen BR. Analysis of the interaction of primate retroviruses with the human RNA interference machinery. J Virol 2007;81(22):12218-26
   PubMed Web of Science ®Google Scholar
• Kaul D, Ahlawat A, Gupta SD. HIV-1 genome encoded hiv1-mir-H1 impairs cellular responses to infection. Mol Cell Biochem 2009;323:143-8
   PubMed Web of Science ®Google Scholar
• Yeung ML, Bennasser Y, Le SY, Jeang KT. Si RNA, miRNA and HIV: promises and challenges. Cell Res 2005;15(11-12):935-46
   PubMed Web of Science ®Google Scholar
• Yeung ML, Bennasser Y, Watasgu K, 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(19):6575-86
   PubMed Web of Science ®Google Scholar
• Perez JT, Varble A, Sachidanandam R, Influenza A virus-generated small RNAs regulate the switch from transcription to replication. Proc Natl Acad Sci USA 2010;107(25):11525-30
   PubMed Web of Science ®Google Scholar
• Pumfery A, Deng L, Maddukuri A, Chromatin remodeling and modification during HIV-1 Tat-activated transcription. Curr HIV Res 2003;1:261-2741
   PubMedGoogle Scholar
• Berkhout B, Gatignol A, Rabson AB, Jeang KT. TAR-independent activation of the HIV-1 LTR: evidence that tat requires specific regions of the promoter. Cell 1990;62:757-67
   PubMed Web of Science ®Google Scholar
• Das AT, Klaver B, Berkhout B. The 5′ and 3′ TAR elements of human immunodeficiency virus exert effects at several points in the virus life cycle. J Virol 1998;72(11):9217-23
   PubMed Web of Science ®Google Scholar
• Bennasser Y, Le SY, Yeung ML, Jeang KT. HIV-1 encoded candidate micro-RNAs and their cellular targets. Retrovirology 2004;1:43
   PubMedGoogle Scholar
• Purzycka KJ, Adamiak RW. The HIV-2 TAR RNA domain as a potential source of viral-encoded miRNA. A reconnaissance study. Nucleic Acids Symp Ser (Oxf) 2008;(52):511-12
   PubMedGoogle Scholar
• Gatignol A, Buckler-White A, Berkhout B, Jeang KT. Characterization of a human TAR RNA-binding protein that activates the HIV-1 LTR. Science 1991;251(5001):1597-600
   PubMed Web of Science ®Google Scholar
• Klase Z, Kale P, Winograd R, HIV-1 TAR element is processed by Dicer to yield a viral micro-RNA involved in chromatin remodeling of the viral LTR. BMC Mol Biol 2007;8:63
   PubMed Web of Science ®Google Scholar
• Klase Z, Winograd R, Davis J, HIV-1 TAR miRNA protects against apoptosis by altering cellular gene expression. Retrovirology 2009;6:18
   PubMed Web of Science ®Google Scholar
• Ouellet DL, Plante I, Landry P, Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element. Nucleic Acids Res 2008;36(7):2353-65
   PubMed Web of Science ®Google Scholar
• Joseph AM, Kumar M, Mitra D. Nef: “necessary and enforcing factor” in HIV infection. Curr HIV Res 2005;3(1):87-94
   PubMed Web of Science ®Google Scholar
• Foster JL, Garcia JV. HIV-1 Nef: at the crossroads. Retrovirology 2008;5:84
   PubMed Web of Science ®Google Scholar
• Yamamoto T, Omoto S, Mizuguchi M, Double-stranded nef RNA interferes with human immunodeficiency virus type 1 replication. Microbiol Immunol 2002;46(11):809-17
   PubMed Web of Science ®Google Scholar
• Olivetta E, Pugliese K, Bona R, Cis expression of the F12 human immunodeficiency virus (HIV) Nef allele transforms the highly productive NL4-3 HIV type 1 to a replication-defective strain: involvement of both Env gp41 and CD4 intracytoplasmic tails. J Virol 2000;74(1):483-92
   PubMed Web of Science ®Google Scholar
• Omoto S, Ito M, Tsutsumi Y, HIV-1 nef suppression by virally encoded microRNA. Retrovirology 2004;1:44
   PubMedGoogle Scholar
• Lamers SL, Fogel GB, McGrath MS. HIV-miR-H1 evolvability during HIV pathogenesis. Biosystems 2010;101(2):88-96
   PubMed Web of Science ®Google Scholar
• Bennasser Y, Le SY, Benkirane M, Jeang KT. Evidence that HIV-1 encodes an siRNA and a suppressor of RNA silencing. Immunity 2005;22(5):607-19
   PubMed Web of Science ®Google Scholar
• Perez JT, Varble A, Sachidanandam R, Influenza A virus-generated small RNAs regulate the switch from transcription to replication. Proc Natl Acad Sci USA 2010;107(25):11525-30
   PubMed Web of Science ®Google Scholar
• Karjee S, Minhas A, Sood V, The 7a accessory protein of severe acute respiratory syndrome coronavirus acts as an RNA silencing suppressor. J Virol 2010;84(19):10395-401
   PubMed Web of Science ®Google Scholar
• Andersson MG, Haasnoot PC, Xu N, Suppression of RNA interference by adenovirus virus-associated RNA. J Virol 2005;79(15):9556-65
   PubMed Web of Science ®Google Scholar
• Haasnoot J, de Vries W, Geutjes EJ, The Ebola virus VP35 protein is a suppressor of RNA silencing. PLoS Pathog 2007;3(6):e86
   PubMedGoogle Scholar
• de Vries W, Haasnoot J, Fouchier R, Differential RNA silencing suppression activity of NS1 proteins from different influenza A virus strains. J Gen Virol 2009;90(Pt 8):1916-22
   PubMedGoogle Scholar
• Schnettler E, de Vries W, Hemmes H, The NS3 protein of rice hoja blanca virus complements the RNAi suppressor function of HIV-1 Tat. EMBO Rep 2009;10(3):258-63
   PubMed Web of Science ®Google Scholar
• Coley W, Van Duyne R, Carpio L, Absence of Dicer in monocytes and its regulation by HIV-1. J Biol Chem 2010;285(42):31930-43
   PubMed Web of Science ®Google Scholar
• Kolber MA. Development of drug resistance mutations in patients on highly active antiretroviral therapy: does competitive advantage drive evolution. AIDS Rev 2007;9(2):68-74
   PubMed Web of Science ®Google Scholar
• Siliciano JD, Siliciano RF. A long-term latent reservoir for HIV-1: discovery and clinical implications. J Antimicrob Chemother 2004;54(1):6-9
   PubMed Web of Science ®Google Scholar
• Baba M. Inhibitors of HIV-1 gene expression and transcription. Curr Top Med Chem 2004;4(9):871-82
   PubMed Web of Science ®Google Scholar
• Vrolijk MM, Harwig A, Berkhout B, Das AT. Destrabilization of the TAR hairpin leads to extension of the polyA hairpin and inhibition of HIV-1 polyadenylation. Retrovirology 2009;6:13
   PubMed Web of Science ®Google Scholar
• Berkhout B. Structural features in TAR RNA of human and simian immunodeficiency viruses: a phylogenetic analysis. Nucleic Acids Res 1992;20(1):27-31
   PubMed Web of Science ®Google Scholar
• Klaver B, Berkhout B. Evolution of a disrupted TAR RNA hairpin structure in the HIV-1 virus. EMBO J 1994;13(11):2650-9
   PubMed Web of Science ®Google Scholar
• Das AT, Brummelkamp TR, Westerhout EM, Human immunodeficiency virus type 1 escapes from RNA interference-mediated inhibition. J Virol 2004;78(5):2601-5
   PubMed Web of Science ®Google Scholar
• 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(5):484-94
   PubMed Web of Science ®Google Scholar
• Berkhout B. A new Houdini act: multiple routes for HIV-1 escape from RNAi-mediated inhibition. Future Microbiol 2009;4(2):151-4
   PubMed Web of Science ®Google Scholar
• Nathans R, Chu CY, Serquina AK, Cellular microRNA and P bodies modulate host-HIV-1 interactions. Mol Cell 2009;34(6):696-709
   PubMed Web of Science ®Google Scholar
• Triboulet R, Mari B, Lin YL, Suppression of microRNA-silencing pathway by HIV-1 during virus replication. Science 2007;315(5818):1579-82
   PubMed Web of Science ®Google Scholar
• Sung TL, Rice AP. miR-198 inhibits HIV-1 gene expression and replication in monocytes and its mechanism of action appears to involve repression of cyclin T1. PLoS Pathog 2009;5(1):e1000263
   PubMedGoogle Scholar
• Ahluwalia JK, Khan SZ, Soni K, Human cellular microRNA has-miR-29a interferes with viral nef protein expression and HIV-1 replication. Retrovirology 2008;5:117
   PubMedGoogle Scholar
• Wang X, Ye L, Hou W, Cellular microRNA expression correlates with susceptibility of monocytes/macrophages to HIV-1 infection. Blood 2009;113(3):671-4
   PubMed Web of Science ®Google Scholar
• Huang J, Wang F, Argyris E, Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes. Nat Med 2007;13(10):1241-7
   PubMed Web of Science ®Google Scholar
• Son J, Uchil PD, Kim YB, Effective suppression of HIV-1 by artificial bispecific miRNA targeting conserved sequences with tolerance for wobble base-pairing. Biochem Biophys Res Commun 2008;374(2):214-18
   PubMed Web of Science ®Google Scholar
• Liu YP, Haasnoot J, ter Brake O, Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron. Nucleic Acids Res 2008;36(9):2811-24
   PubMed Web of Science ®Google Scholar
• Zhang J, Rossi JJ. Strategies in designing multigene expression units to downregulate HIV-1. Methods Mol Biol 2010;623:123-36
   PubMedGoogle Scholar
• Murakami T, Yamamoto N. Role of CXCR4 in HIV infection and its potential as a therapeutic target. Future Microbiol 2010;5(7):1025-39
   PubMed Web of Science ®Google Scholar
• Chable-Bessia C, Meziane O, Latreille D, Suppression of HIV-1 replication by microRNA effectors. Retrovirology 2009;6:26
   Google Scholar
• Deng L, Ammosova T, Pumfery A, HIV-1 Tat interaction with RNA polymerase II C-terminal domain (CTD) and a dynamic association with CDK2 induce CTD phosphorylation and transcription from HIV-1 promoter. J Biol Chem 2002;277(37):33922-9
   PubMed Web of Science ®Google Scholar
• Romano G, Kasten M, De Falco G, Regulatory functions of Cdk9 and cyclin T1 in HIV tat transactivation pathway gene expression. J Cell Biochem 1999;75(3):357-68
   PubMed Web of Science ®Google Scholar
• Nekhai S, Jeang KT. Transcriptional and post-transcriptional regulation of HIV-1 gene expression: role of cellular factors for Tat and Rev. Future Microbiol 2006;1:417-26
   PubMed Web of Science ®Google Scholar
• Kim YK, Bourgeois CF, Isel C, Phosphorylation of the RNA polymerase II carboxyl-terminal domain by CDK9 is directly responsible for human immunodeficiency virus type 1 Tat-activated transcriptional elongation. Mol Cell Biol 2002;22(13):4622-37
   PubMed Web of Science ®Google Scholar
• De la Fuente C, Maddukuri A, Kehn K, Pharmacological cyclin-dependent kinase inhibitors as HIV-1 antiviral therapeutics. Curr HIV Res 2003;1(2):131-52
   PubMed Web of Science ®Google Scholar
• Pumfrey A, de la Fuente C, Berro R, Potential use of pharmacological cyclin-dependent kinase inhibitors as anti-HIV therapeutics. Curr Pharm Des 2006;12(16):1949-61
   PubMed Web of Science ®Google Scholar
• Ali A, Ghosh A, Nathans RS, Identification of flavopiridol analogues that selectively inhibit positive transcription elongation factor (P-TEFb) and block HIV-1 replication. Chembiochem 2009;10(12):2072-80
   PubMed Web of Science ®Google Scholar
• Chao SH, Fujinaga K, Marion JE, Flavopiridol inhibits P-TEFb and blocks HIV-1 replication. J Biol Chem 2000;275(37):28345-8
   PubMed Web of Science ®Google Scholar
• Fischer PM, Gianella-Borradori A. Recent progress in the discovery and development of cyclin-dependent kinase inhibitors. Expert Opin Investig Drugs 2005;14(4):457-77
   PubMed Web of Science ®Google Scholar
• Wang Y, Liu XY, De Clercq E. Role of the HIV-1 positive elongation factor P-TEFb and inhibitors thereof. Mini Rev Med Chem 2009;9(3):379-85
   PubMed Web of Science ®Google Scholar
• Agbottah E, de la Fuente C, Nekhai S, Antiviral activity of CYC202 in HIV-1-infected cells. J Biol Chem 2005;280(4):3029-42
   PubMed Web of Science ®Google Scholar
• Guendel I, Agbottah ET, Kehn-Hall K, Kashanchi F. Inhibition of human immunodeficiency virus type-1 by cdk inhibitors. AIDS Res Ther 2010;7(1):7
   PubMedGoogle Scholar
• Carpio L, Klase Z, Coley W, MicroRNA machinery is an integral component of drug-induced transcription inhibition in HIV-1 infection. J RNAi Gene Silencing 2010;6(1):386-400
   PubMedGoogle Scholar