The utility of siRNA transcripts produced by RNA polymerase I in down regulating viral gene expression and replication of negative- and positive-strand RNA viruses

Virology

Volumn 313, Issue 2, 2003, Pages 514-524

  McCown, Matthew ^a   Diamond, Michael S ^a   Pekosz, Andrew ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Antivirals; Gene expression; Influenza A virus; RNA interference; West Nile virus

Indexed keywords

DNA DIRECTED RNA POLYMERASE; GENOMIC RNA;

ARTICLE; CONTROLLED STUDY; DOWN REGULATION; GENE EXPRESSION; GENE REPLICATION; GENE TARGETING; INFLUENZA VIRUS A; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; RNA TRANSCRIPTION; RNA VIRUS; VIRUS GENE; WEST NILE FLAVIVIRUS;

INFLUENZA A VIRUS; RNA VIRUSES; WEST NILE VIRUS;

EID: 0041920922     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0042-6822(03)00341-6     Document Type: Article

References (65)

1. Abbas-Terki T., Blanco-Bose W., Deglon N., Pralong W., Aebischer P. Lentiviral-mediated RNA interference. Hum. Gene Ther. 13:2002;2197-2201.
2. Alexopoulou L., Holt A.C., Medzhitov R., Flavell R.A. Recognition of double-stranded RNA and activation of NF-kappaB by Toll-like receptor 3. Nature. 413:2001;732-738.
3. Arteaga H.J., Hinkula J., Van Dijk-Hard I., Dilber M.S., Wahren B., Christensson B., Mohamed A.J., Edvard Smith C.I. Choosing CCR5 or Rev siRNA in HIV-1. Nat. Biotechnol. 21:2003;230-231.
4. Barton G.M., Medzhitov R. Retroviral delivery of small interfering RNA into primary cells. Proc. Natl. Acad. Sci. USA. 99:2002;14943-14945.
5. Baulcombe D. RNA silencing. Curr. Biol. 12:2002;R82-R84.
6. Bitko V., Barik S. Phenotypic silencing of cytoplasmic genes using sequence-specific double-stranded short interfering RNA and its application in the reverse genetics of wild type negative-strand RNA viruses. BMC Microbiol. 1:2001;34.
7. Brandt W.E., McCown J.M., Gentry M.K., Russell P.K. Infection enhancement of dengue type 2 virus in the U-937 human monocyte cell line by antibodies to flavivirus cross-reactive determinants. Infect. Immunol. 36:1982;1036-1041.
8. Brummelkamp T.R., Bernards R., Agami R. A system for stable expression of short interfering RNAs in mammalian cells. Science. 296:2002;550-553.
9. Carmell M.A., Zhang L., Conklin D.S., Hannon G.J., Rosenquist T.A. Germline transmission of RNAi in mice. Nat. Struct. Biol. 10:2003;91-92.
10. Castrucci M., Kawaoka Y. Reverse genetics system for generation of an influenza A virus mutant containing a deletion of the carboxyl-terminal residue of M2 protein. J. Virol. 69:1995;2725-2728.
11. Chambers T.J., Hahn C.S., Galler R., Rice C.M. Flavivirus genome organization, expression, and replication. Annu. Rev. Microbiol. 44:1990;649-688.
12. Chen W., Calvo P.A., Malide D., Gibbs J., Schubert U., Bacik I., Basta S., O'Neill R., Schickli J., Palese P., Henklein P., Bennink J.R., Yewdell J.W. A novel influenza A virus mitochondrial protein that induces cell death. Nat. Med. 7:2001;1306-1312.
13. Coburn G.A., Cullen B.R. Potent and specific inhibition of human immunodeficiency virus type 1 replication by RNA interference. J. Virol. 76:2002;9225-9231.
14. Cullen B.R. RNA interference antiviral defense and genetic tool . Nat. Immunol. 3:2002;597-599.
15. Diamond M.S., Edgil D., Roberts T.G., Lu B., Harris E. Infection of human cells by dengue virus is modulated by different cell types and viral strains. J. Virol. 74:2000;7814-7823.
16. Diamond M.S., Roberts T.G., Edgil D., Lu B., Ernst J., Harris E. Modulation of Dengue virus infection in human cells by alpha, beta, and gamma interferons. J. Virol. 74:2000;4957-4966.
17. Ebel G.D., Dupuis A.P. 2nd, Ngo K., Nicholas D., Kauffman E., Jones S.A., Young D., Maffei J., Shi P.Y., Bernard K., Kramer L.D. Partial genetic characterization of West Nile virus strains, New York State, 2000. Emerg. Infect. Dis. 7:2001;650-653.
18. Elbashir S.M., Harborth J., Lendeckel W., Yalcin A., Weber K., Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature. 411:2001;494-498.
19. Elbashir S.M., Lendeckel W., Tuschl T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15:2001;188-200.
20. Elbashir S.M., Martinez J., Patkaniowska A., Lendeckel W., Tuschl T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20:2001;6877-6888.
21. Flick R., Neumann G., Hoffmann E., Neumeier E., Hobom G. Promoter elements in the influenza vRNA terminal structure. RNA. 2:1996;1046-1057.
22. Flick R., Pettersson R.F. Reverse genetics system for Uukuniemi virus (Bunyaviridae) RNA polymerase I-catalyzed expression of chimeric viral RNAs . J. Virol. 75:2001;1643-1655.
23. Garrus J.E., von Schwedler U.K., Pornillos O.W., Morham S.G., Zavitz K.H., Wang H.E., Wettstein D.A., Stray K.M., Cote M., Rich R.L., Myszka D.G., Sundquist W.I. Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding. Cell. 107:2001;55-65.
24. Ge Q., McManus M.T., Nguyen T., Shen C.H., Sharp P.A., Eisen H.N., Chen J. RNA interference of influenza virus production by directly targeting mRNA for degradation and indirectly inhibiting all viral RNA transcription. Proc. Natl. Acad. Sci. USA. 100:2003;2718-2723.
25. Gitlin L., Karelsky S., Andino R. Short interfering RNA confers intracellular antiviral immunity in human cells. Nature. 418:2002;430-434.
26. Harborth J., Elbashir S.M., Bechert K., Tuschl T., Weber K. Identification of essential genes in cultured mammalian cells using small interfering RNAs. J. Cell Sci. 114:2001;4557-4565.
27. Houng H.S., Chung-Ming Chen R., Vaughn D.W., Kanesa-thasan N. Development of a fluorogenic RT-PCR system for quantitative identification of dengue virus serotypes 1-4 using conserved and serotype-specific 3′ noncoding sequences. J. Virol. Methods. 95:2001;19-32.
28. Hutvagner G., Zamore P.D. RNAi nature abhors a double-strand . Curr. Opin. Genet. Dev. 12:2002;225-232.
29. Jacque J.M., Triques K., Stevenson M. Modulation of HIV-1 replication by RNA interference. Nature. 418:2002;435-438.
30. Kapadia S.B., Brideau-Andersen A., Chisari F.V. Interference of hepatitis C virus RNA replication by short interfering RNAs. Proc. Natl. Acad. Sci. USA. 100:2003;2014-2018.
31. Kawasaki H., Taira K. Short hairpin type of dsRNAs that are controlled by tRNA(Val) promoter significantly induce RNAi-mediated gene silencing in the cytoplasm of human cells. Nucleic Acids Res. 31:2003;700-707.
32. Lamb R.A., Krug R.M. Orthomyxoviridae the viruses and their replication . Knipe D.M., Howley P.M. Fields Virology. 2001;1487-1532 Lippincott, Williams, & Wilkins, Philadelphia.
33. Lanciotti R.S., Kerst A.J., Nasci R.S., Godsey M.S., Mitchell C.J., Savage H.M., Komar N., Panella N.A., Allen B.C., Volpe K.E., Davis B.S., Roehrig J.T. Rapid detection of West Nile virus from human clinical specimens, field-collected mosquitoes, and avian samples by a TaqMan reverse transcriptase-PCR assay. J. Clin. Microbiol. 38:2000;4066-4071.
34. Lanciotti R.S., Roehrig J.T., Deubel V., Smith J., Parker M., Steele K., Crise B., Volpe K.E., Crabtree M.B., Scherret J.H., Hall R.A., MacKenzie J.S., Cropp C.B., Panigrahy B., Ostlund E., Schmitt B., Malkinson M., Banet C., Weissman J., Komar N., Savage H.M., Stone W., McNamara T., Gubler D.J. Origin of the West Nile virus responsible for an outbreak of encephalitis in the northeastern United States. Science. 286:1999;2333-2337.
35. Li H., Li W.X., Ding S.W. Induction and suppression of RNA silencing by an animal virus. Science. 296:2002;1319-1321.
36. Lindenbach B.D., Rice C.M. RNAi targeting an animal virus news from the front . Mol. Cell. 9:2002;925-927.
37. Martinez M.A., Gutierrez A., Armand-Ugon M., Blanco J., Parera M., Gomez J., Clotet B., Este J.A. Suppression of chemokine receptor expression by RNA interference allows for inhibition of HIV-1 replication. AIDS. 16:2002;2385-2390.
38. Neumann G., Watanabe T., Ito H., Watanabe S., Goto H., Gao P., Hughes M., Perez D.R., Donis R., Hoffmann E., Hobom G., Kawaoka Y. Generation of influenza A viruses entirely from cloned cDNAs. Proc. Natl. Acad. Sci. USA. 96:1999;9345-9350.
39. Neumann G., Zobel A., Hobom G. RNA polymerase I-mediated expression of influenza viral RNA molecules. Virology. 202:1994;477-479.
40. Niwa H., Yamamura K., Miyazaki J. Efficient selection for high-expression transfectants with a novel eukaryotic vector. Gene. 108:1991;193-199.
41. Paddison P.J., Caudy A.A., Bernstein E., Hannon G.J., Conklin D.S. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16:2002;948-958.
42. Paddison P.J., Caudy A.A., Hannon G.J. Stable suppression of gene expression by RNAi in mammalian cells. Proc. Natl. Acad. Sci. USA. 99:2002;1443-1448.
43. Paterson, R.G., Lamb, R.A., 1993. The molecular biology of influenza viruses and paramyxoviruses, in: Molecular Virology: A Practical Approach, Oxford University Press, Oxford, UK, pp. 35-73.
44. Pekosz A., Lamb R.A. The CM2 protein of influenza C virus is an oligomeric integral membrane glycoprotein structurally analogous to influenza A virus M2 and influenza B virus NB proteins. Virology. 237:1997;439-451.
45. Pekosz A., Lamb R.A. Cell surface expression of biologically active influenza C virus HEF glycoprotein expressed from cDNA. J. Virol. 73:1999;8808-8812.
46. Qin X.F., An D.S., Chen I.S., Baltimore D. Inhibiting HIV-1 infection in human T cells by lentiviral-mediated delivery of small interfering RNA against CCR5. Proc. Natl. Acad. Sci. USA. 100:2003;183-188.
47. Randall G., Grakoui A., Rice C.M. Clearance of replicating hepatitis C virus replicon RNAs in cell culture by small interfering RNAs. Proc. Natl. Acad. Sci. USA. 100:2003;235-240.
48. Roberts P.C., Lamb R.A., Compans R.W. The M1 and M2 proteins of influenza A virus are important determinants in filamentous particle formation. Virology. 240:1998;127-137.
49. Russell P.K., Nisalak A. Dengue virus identification by the plaque reduction neutralization test. J. Immunol. 99:1967;291-296.
50. Samuel C.E. Antiviral actions of interferons. Clin. Microbiol. Rev. 14:2001;778-809.
51. Seo M.Y., Abrignani S., Houghton M., Han J.H. Small interfering RNA-mediated inhibition of hepatitis C virus replication in the human hepatoma cell line Huh-7. J. Virol. 77:2003;810-812.
52. Silva J.M., Hammond S.M., Hannon G.J. RNA interference a promising approach to antiviral therapy? Trends Mol. Med. 8:2002;505-508.
53. Sui G., Soohoo C., Affar E.B., Gay F., Shi Y., Forrester W.C., Shi Y. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. USA. 99:2002;5515-5520.
54. 2 ion channel activity is essential for efficient replication in tissue culture. J. Virol. 76:2002;1391-1399.
55. Tiscornia G., Singer O., Ikawa M., Verma I.M. A general method for gene knockdown in mice by using lentiviral vectors expressing small interfering RNA. Proc. Natl. Acad. Sci. USA. 100:2003;1844-1848.
56. Watanabe T., Watanabe S., Ito H., Kida H., Kawaoka Y. Influenza A virus can undergo multiple cycles of replication without M2 ion channel activity. J. Virol. 75:2001;5656-5662.
57. Wilson J.A., Jayasena S., Khvorova A., Sabatinos S., Rodrigue-Gervais I.G., Arya S., Sarangi F., Harris-Brandts M., Beaulieu S., Richardson C.D. RNA interference blocks gene expression and RNA synthesis from hepatitis C replicons propagated in human liver cells. Proc. Natl. Acad. Sci. USA. 100:2003;2783-2788.
58. Xia H., Mao Q., Paulson H.L., Davidson B.L. siRNA-mediated gene silencing in vitro and in vivo. Nat. Biotechnol. 20:2002;1006-1010.
59. Yamshchikov V.F., Wengler G., Perelygin A.A., Brinton M.A., Compans R.W. An infectious clone of the West Nile flavivirus. Virology. 281:2001;294-304.
60. Yewdell J.W., Frank E., Gerhard W. Expression of influenza A virus internal antigens on the surface of infected P815 cells. J. Immunol. 126:1981;1814-1819.
61. Zebedee S.L., Lamb R.A. Influenza A virus M2 protein monoclonal antibody restriction of virus growth and detection of M2 in virions . J. Virol. 62:1988;2762-2772.
62. Zebedee S.L., Lamb R.A. Growth restriction of influenza A virus by M2 protein antibody is genetically linked to the M1 protein. Proc. Natl. Acad. Sci. USA. 86:1989;1061-1065.
63. Zeng Y., Wagner E.J., Cullen B.R. Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. Mol. Cell. 9:2002;1327-1333.
64. Zhang J., Leser G.P., Pekosz A., Lamb R.A. The cytoplasmic tails of the influenza virus spike glycoproteins are required for normal genome packaging. Virology. 269:2000;325-334.
65. Zobel A., Neumann G., Hobom G. RNA polymerase I catalysed transcription of insert viral cDNA. Nucleic Acids Res. 21:1993;3607-3614.