Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 31814
In silico Analysis of Human microRNAs Targeting Influenza a Viruses (subtype H1N1, H5N1 and H3N2)

Authors: Kritsada Khongnomnan, Wittaya Poomipak, Yong Poovorawan, Sunchai Payungporn


In this study, three subtypes of influenza A viruses (pH1N1, H5N1 and H3N2) which naturally infected human were analyzed by bioinformatic approaches to find candidate human cellular miRNAs targeting viral genomes. There were 76 miRNAs targeting influenza A viruses. Among these candidates, 70 miRNAs were subtypes specifically targeting each subtype of influenza A virus including 21 miRNAs targeted subtype H1N1, 27 miRNAs targeted subtype H5N1 and 22 miRNAs targeted subtype H3N2. The remaining 6 miRNAs target on multiple subtypes of influenza A viruses. Uniquely, hsa-miR-3145 is the only one candidate miRNA targeting PB1 gene of all three subtypes. Obviously, most of the candidate miRNAs are targeting on polymerase complex genes (PB2, PB1 and PA) of influenza A viruses. This study predicted potential human miRNAs targeting on different subtypes of influenza A viruses which might be useful for inhibition of viral replication and for better understanding of the interaction between virus and host cell.

Keywords: Human miRNAs, Influenza A viruses, H1N1, H5N1, H3N2

Digital Object Identifier (DOI):

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1327


[1] V. Ambrod, "microRNAs: tiny regulators with great potential," Cell., vol. 107, no. 7, Dec. 2001, pp. 823-826.
[2] J. C. Carrington, and V. Ambros, "Role of microRNAs in plant and animal development," Science., vol. 301, no. 5631, Jul. 2003, pp. 336-338.
[3] R. F. Ketting, S. E. Fischer, E. Bernstein, T. Sigen, G. J. Hannon, and R. H. Plasterk, "Dicer functions in RNA interference and in synthesis of small RNA involved in development timing in C. elegans," Gene. Dev ., vol. 15, no. 20, Oct. 2001, pp. 2654-2659.
[4] D. P. Bartel, "MicroRNAs: genomics, biogenesis, mechanism, and function," Cell., vol. 116, no. 2, Jan. 2004, pp. 281-297.
[5] M. Chekulaeve, and W. Filipowicz, "Mechanisms of miRNA-mediated post-transcriptional regulation in animal cells," Curr. Opin. Cell. Biol., vol. 21, no. 3, Jun. 2009, pp. 452-460.
[6] E. C. Lai, "MicroRNAs are complementary to 3-UTR sequence motifs that mediate negative post-transcriptional regulation," Nat. Genet., vol. 30, no. 4, Apr. 2002, pp. 363-364.
[7] S. Kuersten, and E. B. Goodwin, "The power of the 3-UTR: translational control and development," Nat. Rev. Genet., vol. 4, no. 8, Aug. 2003, pp. 626-637.
[8] J. Brennecke, A. Stark, R. B. Russell, and S. M. Cohen, "Principles of miRNA-target recognition," PLoS. Biol., vol. 3, no. 3, Mar. 2005, pp. 404-428.
[9] H. W. Hwang, and J. T. Mendell, "MicroRNAs in cell proliferation, cell death, and tumorigenesis," Br. J. Cancer., vol. 94, no. 6, Mar. 2006, pp. 776-780.
[10] S. Pfeffer, A. Sewer, M. Q. Lagos, R. Sheridan, C. Sander, F. A. Grässer, L. F. van Dyk, C. K. Ho, S. Shuman, and other, "Identification of microRNAs of the herpesvirus family," Nat. Methods., vol. 2, no. 4, Apr. 2005, pp. 269-276.
[11] A. K. Lo, K. F. To, K. W. Lo, R. W. Lung, J. W. Hui, G. Liao, and D. Hayward, "Modulation of LMP1 protein expression by EBV-encoded microRNAs," PNAS., vol. 104, no. 41, Oct. 2007, pp. 16164-16169.
[12] C. S. Sullivan, A. T. Grundhoff, S. Tevethia, J. M. Pipas, and D. Ganem, "SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells," Nature., vol. 435, no. 7042, Jun. 2005, pp. 682-686.
[13] S. Omoto, M. Ito, Y. Tsutsumi, Y. Ichikawa, H. Okuyama, E. A. Brisibe, N. K. Saksena, and Y. R. Fujii, “HIV-1 nef suppression by virally encoded microRNA,” Retrovirology., vol. 1, no. 44, Dec. 2004.
[14] C. H. Lecellier, P. Dunoyer, K. Arar, J. Lehmann-Che, S. Eyquem, C. Himber, A. Saib, and O. Voinnet, “A cellular microRNA mediates antiviral defense in human cells,” Science., vol. 308, no. 5721, Apr. 2005, pp. 557–560.
[15] M. Otsuka, Q. Jing, P. Georgel, L. New, J. Chen, J. Mols, Y. J. Kang, Z. Jiang, X. Du, and others, “Hypersusceptibility to vesticular stomatitis virus infection in Dicer1-deficient mice is due to impaired miR24 and miR93 expression,” Immunityl., vol. 27, no. 1, Jul. 2007, pp. 123–134.
[16] C. L. Jopling, M. Yi, A. M. Lancaster, S. M. Lemon, and P. Sarnow, “Modulation of hepatitis C virus RNA abundance by a liver-specific microRNA,” Science., vol. 309, no. 5740, Sep. 2005, pp. 1577–1581.
[17] K. G. Nicholson, J. M. Wood, and M. Zambon, “Influenza,” Lancet., vol. 3623, no. 9397, Jan. 2003, pp. 1733–1745.
[18] D. M. Fleming, P. Chakraverty, C. Sadler, and P. Litton, “Combined clinical and virological surveillance of influenza in winters of 1992 and 1993-1994,” BMJl, vol. 311, no. 7000, Jul. 1995, pp. 1733-1745.
[19] Novel Swine-Origen Influenza A (H1N1) Virus Investigation Team, F. S. Dawood, S. Jain, L. Finelli, M. W. Shaw, S. Lindstrom, R. J. Garten. L. V. Gubareva, and X. Xu, “Emergence of a novel swine-origin Influenza A (H1N1) virus in humans,” N Engl J Med., vol. 360, no. 25, Jun. 2009, pp. 2605-2615.
[20] CDC, “Swine Influenza A (H1N1) infection in two children-Southern California, March-April 2009,” MMWR., vol. 58, no. 15, Apr. 2009, pp. 400–402.
[21] CDC., “Update: Influenza A (H3N2)v transmission and guidelines-five states, 2011,” MMWR., vol. 60, no. 51-52, Jan. 2011, pp. 1741–1744.
[22] T. H. Tran, T. L. Nguyen, T. D. Nguyen, T. S. Luong, P. M. Pham, V. C. Nguyen, T. S. Pham, C. D. Vo, T. Q. Le, T. T. Ngo, B. K. Dao, P. P. Le, T. T. Nguyen, T. L. Hoang, V. T. Cao, T. G. Le, D. T. Nguyen, H. N. Le, K. T. Nguyen, H. S. Le, V. T. Le, D. Christiane, T. T. Tran, J. de Menno, C. schultsz, P. Cheng, W. Lim, P. Horby, J. Farrar, and World Health Organization International Avian Influenza Investigative Team, “Avian influenza (H5N1) in 10 patients in Vietnam,” N Engl J Med., vol. 350, no. 12, Mar. 2004, pp. 1179–1188.
[23] S. Griffiths-Jones, “The microRNA registry,” Nucleic Acids Res., vol. 32, Jan. 2004, pp. D109–111.
[24] S. Griffiths-Jones, R. J. Grocock, S. van Dongen, A. Bateman, and A. J. Enright, “miRBase: microRNA sequences, targets and gene nomenclature,” Nucleic Acids Res., vol. 34, Jan. 2006, pp. D140–104.
[25] S. Griffiths-Jones, H. K. Saini, S. van Dongen, and A. J. Enright, “miRBase: tools for microRNA genomics,” Nucleic Acids Res., vol. 36, Jan. 2006, pp. D154–158.
[26] A. Kozomara, and S. Griffiths-Jones, “miRBase: integrating microRNA annotation and deep-sequencing data,” Nucleic Acids Res., vol. 39, Jan. 2009, pp. D152-157.
[27] J. Kruger, and M. Rehsmeier, “RNAhybrid: microRNA target prediction easy, fast and flexible,” Nucleic Acids Res., vol. 34, Jul. 2006, pp. W451–454.
[28] L. Song, H. Liu, S. Gao, W. Jiang, and W. Huang, “Cellular microRNAs inhibit replication of the H1N1 influenza A virus in infected cells,” J Virol., vol. 84, no. 17, Sep. 2010, pp. 8849–8860.
[29] R. J. Garten, C. T. Davis, C. A. Russell, B. Shu, S. Lindstrom, A. Balish, W. M. Sessions, X. Xu, E. Skepner, V. Deyde, M. Okomo-Adhiambo, L. Gubareva, J. Barnes,C. B. Smith, S. L. Emery, M. J. Hillman, P. Rivailler, J. Smagala, M. de Graaf, D. F. Burke, R. A. Fouchier, C. Pappas, C. M. Alpuche-Aranda, H. López-Gatell, H. Olivera, I. López, C. A. Myers, D. Faix, P. J. Blair, C. Yu, K. M. Keene, P. D. Dotson Jr, D. Boxrud, A. R. Sambol, S. H. Abid, K. StGeorge, T. Bannerman, A. L. Moore, D. J. Stringer, P. Blevins, G. J. Demmler-Harrison, M. Ginsberg, P. Kriner, S. Waterman, S. Smole, H. F. Guevara, E. A. Belongia, P. A. Clark, S. T. Beatrice, R. Donis, J. Katz, F. Finelli, C. B. Bridges, M. Shaw, D. B. Jernigan, T. M. Uyeki, D. J. Smith, A. I. Klimov, and N. J. Cox , “Antigenic and genetic characteristics of swine-origin 2009 A (H1N1) influenza viruses circulating in humans,” Science., vol. 325, no. 5937, Jul. 2009, pp. 197–201.