In silico Analysis of Human microRNAs Targeting Influenza a Viruses (subtype H1N1, H5N1 and H3N2)
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.
[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.
[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.
@article{"International Journal of Medical, Medicine and Health Sciences:55874", author = "Kritsada Khongnomnan and Wittaya Poomipak and Yong Poovorawan and Sunchai Payungporn", title = "In silico Analysis of Human microRNAs Targeting Influenza a Viruses (subtype H1N1, H5N1 and H3N2)", abstract = "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", volume = "6", number = "11", pages = "569-7", }
