Host-virus genome interactions: Macro roles for microRNAs

Cellular Microbiology

Volumn 9, Issue 12, 2007, Pages 2784-2794

  Scaria, Vinod ^a   Hariharan, Manoj ^a   Pillai, Beena ^a   Maiti, Souvik ^a   Brahmachari, Samir K ^a  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOVIRUS VECTOR; AMINO ACID TRANSPORTER; DNA; MICRORNA; PEPTIDE NUCLEIC ACID; RETROVIRUS VECTOR; RNA INDUCED SILENCING COMPLEX; RNA POLYMERASE; SHORT HAIRPIN RNA; SMALL INTERFERING RNA; UNTRANSLATED RNA;

CARCINOGENESIS; EPSTEIN BARR VIRUS; EUKARYOTE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE SILENCING; GENETIC ENGINEERING; HEPATITIS C VIRUS; HERPES SIMPLEX VIRUS; HUMAN IMMUNODEFICIENCY VIRUS; INFLUENZA VIRUS A H5N1; MOLECULAR MECHANICS; NONHUMAN; PATHOGENESIS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROCESSING; RNA INTERFERENCE; SHORT SURVEY; SIMIAN VIRUS 40; SPUMA VIRUS; TISSUE SPECIFICITY; VIRAL GENE DELIVERY SYSTEM; VIRUS CELL INTERACTION; VIRUS IMMUNITY;

GENE EXPRESSION REGULATION; HOST-PATHOGEN INTERACTIONS; MICRORNAS; VIRULENCE FACTORS; VIRUS DISEASES;

EUKARYOTA;

EID: 35948938551     PISSN: 14625814     EISSN: 14625822     Source Type: Journal    
DOI: 10.1111/j.1462-5822.2007.01050.x     Document Type: Short Survey

References (95)

1. Alvarez-Garcia, I., and Miska, E.A. (2005) MicroRNA functions in animal development and human disease. Development 132: 4653-4662.
2. Bennasser, Y., Le, S.Y., Yeung, M.L., and Jeang, K.T. (2004) HIV-1 encoded candidate micro-RNAs and their cellular targets. Retrovirology 1: 43.
3. Bentwich, I. (2005) Prediction and validation of microRNAs and their targets. FEBS Lett 579: 5904-5910.
4. Bhattacharyya, S.N., Habermacher, R., Martine, U., Closs, E.I., and Filipowicz, W. (2006) Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 125: 1111-1124.
5. Borchert, G.M., Lanier, W., and Davidson, B.L. (2006) RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol 13: 1097-1101.
6. Browne, E.P., Li, J., Chong, M., and Littman, D.R. (2005) Virus-host interactions: New insights from the small RNA world. Genome Biol 6: 238.
7. Brummelkamp, T.R., Bernards, R., and Agami, R. (2002) Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell 2: 243-247.
8. Burnside, J., Bernberg, E., Anderson, A., Lu, C., Meyers, B.C., Green, P.J., et al. (2006) Marek's disease virus encodes MicroRNAs that map to meq and the latency-associated transcript. J Virol 80: 8778-8786.
9. Cai, X., and Cullen, B.R. (2006) Transcriptional origin of Kaposi's sarcoma-associated herpesvirus microRNAs. J Virol 80: 2234-2242.
10. Cai, X., Lu, S., Zhang, Z., Gonzalez, C.M., Damania, B., and Cullen, B.R. (2005) Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proc Natl Acad Sci USA 102: 5570-5575.
11. Cai, X., Schafer, A., Lu, S., Bilello, J.P., Desrosiers, R.C., Edwards, R., et al. (2006) Epstein-Barr virus microRNAs are evolutionarily conserved and differentially expressed. PLoS Pathog 2: E23.
12. Caldas, C., and Brenton, J.D. (2005) Sizing up miRNAs as cancer genes. Nat Med 11: 712-714.
13. Calin, G.A., Liu, C.G., Sevignani, C., Ferracin, M., Felli, N., Dumitru, C.D., et al. (2004) MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci USA 101: 11755-11760.
14. Calin, G.A., Ferracin, M., Cimmino, A., Di, L.G., Shimizu, M., Wojcik, S.E., et al. (2005) A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 353: 1793-1801.
15. Castoldi, M., Schmidt, S., Benes, V., Noerholm, M., Kulozik, A.E., Hentze, M.W., et al. (2006) A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA 12: 913-920.
16. Chang, K., Elledge, S.J., and Hannon, G.J. (2006) Lessons from nature: microRNA-based shRNA libraries. Nat Methods 3: 707-714.
17. Cheng, L.C., Tavazoie, M., and Doetsch, F. (2005) Stem cells: From epigenetics to microRNAs. Neuron 46: 363-367.
18. Ciafre, S.A., Galardi, S., Mangiola, A., Ferracin, M., Liu, C.G., Sabatino, G., et al. (2005) Extensive modulation of a set of microRNAs in primary glioblastoma. Biochem Biophys Res Commun 334: 1351-1358.
19. Couturier, J.P., and Root-Bernstein, R.S. (2005) HIV may produce inhibitory microRNAs (miRNAs) that block production of CD28, CD4 and some interleukins. J Theor Biol 235: 169-184.
20. Croce, C.M., and Calin, G.A. (2005) miRNAs, cancer, and stem cell division. Cell 122: 6-7.
21. Crooke, S.T., and Bennett, C.F. (1996) Progress in antisense oligonucleotide therapeutics. Annu Rev Pharmacol Toxicol 36: 107-129.
22. Cui, C., Griffiths, A., Li, G., Silva, L.M., Kramer, M.F., Gaasterland, T., et al. (2006) Prediction and identification of herpes simplex virus 1-encoded microRNAs. J Virol 80: 5499-5508.
23. Cummins, J.M., and Velculescu, V.E. (2006) Implications of micro-RNA profiling for cancer diagnosis. Oncogene 25: 6220-6227.
24. Dias, N., and Stein, C.A. (2002) Antisense oligonucleotides: Basic concepts and mechanisms. Mol Cancer Ther 1: 347-355.
25. Du, T., and Zamore, P.D. (2005) microPrimer: The biogenesis and function of microRNA. Development 132: 4645-4652.
26. Eder, M., and Scherr, M. (2005) MicroRNA and lung cancer. N Engl J Med 352: 2446-2448.
27. Elayadi, A.N., and Corey, D.R. (2001) Application of PNA and LNA oligomers to chemotherapy. Curr Opin Investig Drugs 2: 558-561.
28. Esquela-Kerscher, A., and Slack, F.J. (2006) Oncomirs -microRNAs with a role in cancer. Nat Rev Cancer 6: 259-269.
29. Fu, H., Tie, Y., Xu, C., Zhang, Z., Zhu, J., Shi, Y., et al. (2005) Identification of human fetal liver miRNAs by a novel method. FEBS Lett 579: 3849-3854.
30. Giraldez, A.J., Mishima, Y., Rihel, J., Grocock, R.J., van Dongen, S., Inoue, K., et al. (2006) Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312: 75-79.
31. Gregory, R.I., and Shiekhattar, R. (2005) MicroRNA biogenesis and cancer. Cancer Res 65: 3509-3512.
32. Griffiths-Jones, S. (2006) miRBase: The microRNA sequence database. Methods Mol Biol 342: 129-138.
33. Grundhoff, A., Sullivan, C.S., and Ganem, D. (2006) A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses. RNA 12: 733-750.
34. Gupta, A., Gartner, J.J., Sethupathy, P., Hatzigeorgiou, A.G., and Fraser, N.W. (2006) Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. Nature 442: 82-85.
35. Haasnoot, J., and Berkhout, B. (2006) RNA interference: Its use as antiviral therapy. Handb Exp Pharmacol 173: 117-150.
36. Hamilton, H., Gomos, J., Berns, K.I., and Falck-Pedersen, E. (2004) Adeno-associated virus site-specific integration and AAVS1 disruption. J Virol 78: 7874-7882.
37. Han, J., Lee, Y., Yeom, K.H., Nam, J.W., Heo, I., Rhee, J.K., et al. (2006) Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125: 887-901.
38. Hariharan, M., Scaria, V., Pillai, B., and Brahmachari, S.K. (2005) Targets for human encoded microRNAs in HIV genes. Biochem Biophys Res Commun 337: 1214-1218.
39. He, H., Jazdzewski, K., Li, W., Liyanarachchi, S., Nagy, R., Volinia, S., et al. (2005) The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci USA 102: 19075-19080.
40. Hertel, J., and Stadler, P.F. (2006) Hairpins in a Haystack: Recognizing microRNA precursors in comparative genomics data. Bioinformatics 22: e197-e202.
41. Hsu, P.W., Lin, L.Z., Hsu, S.D., Hsu, J.B., and Huang, H.D. (2007) ViTa: prediction of host microRNAs targets on viruses. Nucleic Acids Res 35: D381-D385.
42. Iorio, M.V., Ferracin, M., Liu, C.G., Veronese, A., Spizzo, R., Sabbioni, S., et al. (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65: 7065-7070.
43. Jopling, C.L., Yi, M., Lancaster, A.M., Lemon, S.M., and Sarnow, P. (2005) Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science 309: 1577-1581.
44. Joseph, A.M., Kumar, M., and Mitra, D. (2005) Nef: 'necessary and enforcing factor' in HIV infection. Curr HIV Res 3: 87-94.
45. Karkare, S., and Bhatnagar, D. (2006) Promising nucleic acid analogs and mimics: Characteristic features and applications of PNA, LNA, and morpholino. Appl Microbiol Biotechnol 71: 575-586.
46. Kauppinen, S., Vester, B., and Wengel, J. (2006) Locked nucleic acid: high-affinity targeting of complementary RNA for RNomics. Handb Exp Pharmacol 173: 405-422.
47. Kim, V.N. (2004) MicroRNA precursors in motion: Exportin-5 mediates their nuclear export. Trends Cell Biol 14: 156-159.
48. Kim, T.W., Chung, H., Kwon, I.C., Sung, H.C., Shin, B.C., and Jeong, S.Y. (2005) Airway gene transfer using cationic emulsion as a mucosal gene carrier. J Gene Med 7: 749-758.
49. Kirchhoff, F., Greenough, T.C., Brettler, D.B., Sullivan, J.L., and Desrosiers, R.C. (1995) Brief report: Absence of intact nef sequences in a long-term survivor with nonprogressive HIV-1 infection. N Engl J Med 332: 228-232.
50. Kluiver, J., Haralambieva, E., de Jong, D., Blokzijl, T., Jacobs, S., Kroesen, B.J., et al. (2006) Lack of BIC and microRNA miR-155 expression in primary cases of Burkitt lymphoma. Genes Chromosomes Cancer 45: 147-153.
51. Konstantinova, P., ter Brake, O., Haasnoot, J., de Haan, P., and Berkhout, B. (2007) Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome. Retrovirology 4: 15.
52. Krol, J., Sobczak, K., Wilczynska, U., Drath, M., Jasinska, A., Kaczynska, D., et al. (2004) Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design. J Biol Chem 279: 42230-42239.
53. Krutzfeldt, J., Rajewsky, N., Braich, R., Rajeev, K.G., Tuschl, T., Manoharan, M., et al. (2005) Silencing of microRNAs in vivo with 'antagomirs'. Nature 438: 685-689.
54. Kumar, A. (2007) The silent defense: Micro-RNA directed defense against HIV-1 replication. Retrovirology 4: 26.
55. Lagos-Quintana, M., Rauhut, R., Lendeckel, W., and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
56. Lau, N.C., Seto, A.G., Kim, J., Kuramochi-Miyagawa, S., Nakano, T., Bartel, D.P., et al. (2006) Characterization of the piRNA complex from rat testes. Science 313: 363-367.
57. Lecellier, C.H., Dunoyer, P., Arar, K., Lehmann-Che, J., Eyquem, S., Himber, C., et al. (2005) A cellular microRNA mediates antiviral defense in human cells. Science 308: 557-560.
58. Lee, R.C., Feinbaum, R.L., and Ambros, V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
59. Liu, J., Carmell, M.A., Rivas, F.V., Marsden, C.G., Thomson, J.M., Song, J.J., et al. (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437-1441.
60. Nair, V., and Zavolan, M. (2006) Virus-encoded microRNAs: Novel regulators of gene expression. Trends Microbiol 14: 169-175.
61. Nasevicius, A., and Ekker, S.C. (2000) Effective targeted gene 'knockdown' in zebrafish. Nat Genet 26: 216-220.
62. Navarro, L., Dunoyer, P., Jay, F., Arnold, B., Dharmasiri, N., Estelle, M., et al. (2006) A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 312: 436-439.
63. Nelson, P.T., Baldwin, D.A., Scearce, L.M., Oberholtzer, J.C., Tobias, J.W., and Mourelatos, Z. (2004) Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods 1: 155-161.
64. Nelson, P.T., Baldwin, D.A., Kloosterman, W.P., Kauppinen, S., Plasterk, R.H., and Mourelatos, Z. (2006) RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. RNA 12: 187-191.
65. Nielsen, P.E. (2000) Antisense peptide nucleic acids. Curr Opin Mol Ther 2: 282-287.
66. Okamura, K., Ishizuka, A., Siomi, H., and Siomi, M.C. (2004) Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev 18: 1655-1666.
67. Omoto, S., and Fujii, Y.R. (2005) Regulation of human immunodeficiency virus 1 transcription by nef microRNA. J Gen Virol 86: 751-755.
68. Omoto, S., Ito, M., Tsutsumi, Y., Ichikawa, Y., Okuyama, H., Brisibe, E.A., et al. (2004) HIV-1 nef suppression by virally encoded microRNA. Retrovirology 1: 44.
69. Palakodeti, D., Smielewska, M., and Graveley, B.R. (2006) MicroRNAs from the Planarian Schmidtea mediterranea: A model system for stem cell biology. RNA 12: 1640-1649.
70. Palliser, D., Chowdhury, D., Wang, Q.Y., Lee, S.J., Bronson, R.T., Knipe, D.M., et al. (2006) An siRNA-based microbicide protects mice from lethal herpes simplex virus 2 infection. Nature 439: 89-94.
71. Pfeffer, S., Sewer, A., Lagos-Quintana, M., Sheridan, R., Sander, C., Grasser, F.A., et al. (2005) Identification of microRNAs of the herpesvirus family. Nat Methods 2: 269-276.
72. Pillai, R.S., Bhattacharyya, S.N., and Filipowicz, W. (2007) Repression of protein synthesis by miRNAs: How many mechanisms? Trends Cell Biol 17: 118-126.
73. Porteous, D.J., Dorin, J.R., McLachlan, G., Davidson-Smith, H., Davidson, H., Stevenson, B.J., et al. (1997) Evidence for safety and efficacy of DOTAP cationic liposome mediated CFTR gene transfer to the nasal epithelium of patients with cystic fibrosis. Gene Ther 4: 210-218.
74. Rana, T.M. (2007) Illuminating the silence: Understanding the structure and function of small RNAs. Nat Rev Mol Cell Biol 8: 23-36.
75. Reinhart, B.J., Slack, F.J., Basson, M., Pasquinelli, A.E., Bettinger, J.C., Rougvie, A.E., et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906.
76. Salvi, R., Garbuglia, A.R., Di, C.A., Pulciani, S., Montella, F., and Benedetto, A. (1998) Grossly defective nef gene sequences in a human immunodeficiency virus type 1-seropositive long-term nonprogressor. J Virol 72: 3646-3657.
77. Samols, M.A., Hu, J., Skalsky, R.L., and Renne, R. (2005) Cloning and identification of a microRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus. J Virol 79: 9301-9305.
78. Sano, M., Kato, Y., and Taira, K. (2006) Sequence-specific interference by small RNAs derived from adenovirus VAI RNA. FEBS Lett 580: 1553-1564.
79. Scaria, V., Hariharan, M., Maiti, S., Pillai, B., and Brahmachari, S.K. (2006) Host-virus interaction: A new role for microRNAs. Retrovirology 3: 68.
80. Scaria, V., Hariharan, M., Brahmachari, S.K., Maiti, S., and Pillai, B. (2007) microRNA: An Emerging Therapeutic. Chem Med Chem 2: 789-792.
81. Schwab, R., Ossowski, S., Riester, M., Warthmann, N., and Weigel, D. (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18: 1121-1133.
82. Sontheimer, E.J., and Carthew, R.W. (2004) Molecular biology. Argonaute journeys into the heart of RISC. Science 305: 1409-1410.
83. Sullivan, C.S., Grundhoff, A.T., Tevethia, S., Pipas, J.M., and Ganem, D. (2005) SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature 435: 682-686.
84. Tijsterman, M., and Plasterk, R.H. (2004) Dicers at RISC; the mechanism of RNAi. Cell 117: 1-3.
85. Triboulet, R., Mari, B., Lin, Y.L., Chable-Bessia, C., Bennasser, Y., Lebrigand, K., et al. (2007) Suppression of microRNA-silencing pathway by HIV-1 during virus replication. Science 315: 1579-1582.
86. Weinberg, M.S., and Morris, K.V. (2006) Are viral-encoded microRNAs mediating latent HIV-1 infection? DNA Cell Biol 25: 223-231.
87. Wu, L., Fan, J., and Belasco, J.G. (2006) MicroRNAs direct rapid deadenylation of mRNA. Proc Natl Acad Sci USA 103: 4034-4039.
88. Yeung, M.L., Bennasser, Y., Myers, T.G., Jiang, G., Benkirane, M., and Jeang, K.T. (2005) Changes in microRNA expression profiles in HIV-1-transfected human cells. Retrovirology 2: 81.
89. Yi, R., Qin, Y., Macara, I.G., and Cullen, B.R. (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 17: 3011-3016.
90. Yi, R., Doehle, B.P., Qin, Y., Macara, I.G., and Cullen, B.R. (2005) Overexpression of exportin 5 enhances RNA interference mediated by short hairpin RNAs and microRNAs. RNA 11: 220-226.
91. Ying, S.Y., and Lin, S.L. (2006) Current perspectives in intronic micro RNAs (miRNAs). J Biomed Sci 13: 5-15.
92. Yoon, S., and De, M.G. (2006) Computational identification of microRNAs and their targets. Birth Defects Res C Embryo Today 78: 118-128.
93. Zelphati, O., and Szoka, F.C., Jr (1996) Intracellular distribution and mechanism of delivery of oligonucleotides mediated by cationic lipids. Pharm Res 13: 1367-1372.
94. Zeng, Y., and Cullen, B.R. (2004) Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res 32: 4776-4785.
95. Zhang, B., Pan, X., and Anderson, T.A. (2006) MicroRNA: A new player in stem cells. J Cell Physiol 209: 266-269.