MicroRNAome of Spodoptera frugiperda cells (Sf9) and its alteration following baculovirus infection

Journal of General Virology

Volumn 94, Issue PART 6, 2013, Pages 1385-1397

  Mehrabadi, Mohammad ^a,b   Hussain, Mazhar ^a   Asgari, Sassan ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b UNIVERSITY OF TEHRAN   (Iran)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; URACIL;

ARTICLE; BACULOVIRUS INFECTION; BIOINFORMATICS; BOMBYX MORI; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; SPODOPTERA FRUGIPERDA; VIRUS CELL INTERACTION; VIRUS INFECTION;

EID: 84877932592     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.051060-0     Document Type: Article

References (66)

1. Aboobaker, A. A., Tomancak, P., Patel, N., Rubin, G. M. & Lai, E. C. (2005). Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proc Natl Acad Sci U S A 102, 18017-18022.
2. Asgari, S. (2011). Role of microRNAs in insect host-microorganism interactions. Front Physiol 2, 48.
3. Asgari, S. (2013). MicroRNA functions in insects. Insect Biochem Mol Biol 43, 388-397.
4. Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
5. Bartel, D. P. (2009). MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233.
6. Becam, I., Rafel, N., Hong, X., Cohen, S. M. & Milán, M. (2011). Notch-mediated repression of bantam miRNA contributes to boundary formation in the Drosophila wing. Development 138, 3781-3789.
7. Breitenbach, J. E., Shelby, K. S. & Popham, H. J. R. (2011). Baculovirus induced transcripts in hemocytes from the larvae of Heliothis virescens. Viruses 3, 2047-2064.
8. Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B. & Cohen, S. M. (2003). bantam Encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113, 25-36.
9. Carinhas, N., Robitaille, A. M., Moes, S., Carrondo, M. J. T., Jenoe, P., Oliveira, R. & Alves, P. M. (2011). Quantitative proteomics of Spodoptera frugiperda cells during growth and baculovirus infection. PLoS ONE 6, e26444.
10. Carmel, I., Shomron, N. & Heifetz, Y. (2012). Does base-pairing strength play a role in microRNA repression? RNA 18, 1947-1956.
11. Cristino, A. S., Tanaka, E. D., Rubio, M., Piulachs, M. D. & Belles, X. (2011). Deep sequencing of organ-and stage-specific microRNAs in the evolutionarily basal insect Blattella germanica (L.) (Dictyoptera, Blattellidae). PLoS ONE 6, e19350.
12. Cullen, B. R. (2006). Viruses and microRNAs. Nat Genet 38 (Suppl), S25-S30.
13. Cullen, B. R. (2009). Viral and cellular messenger RNA targets of viral microRNAs. Nature 457, 421-425.
14. Czech, B. & Hannon, G. J. (2011). Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet 12, 19-31.
15. Czech, B., Malone, C. D., Zhou, R., Stark, A., Schlingeheyde, C., Dus, M., Perrimon, N., Kellis, M., Wohlschlegel, J. A. & other authors (2008). An endogenous small interfering RNA pathway in Drosophila. Nature 453, 798-802.
16. Fernandez-Valverde, S. L., Taft, R. J. & Mattick, J. S. (2010). Dynamic isomiR regulation in Drosophila development. RNA 16, 1881-1888.
17. Fullaondo, A. & Lee, S. Y. (2012). Identification of putative miRNA involved in Drosophila melanogaster immune response. Dev Comp Immunol 36, 267-273.
18. Ghildiyal, M., Xu, J., Seitz, H., Weng, Z. & Zamore, P. D. (2010). Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16, 43-56.
19. Gomez-Orte, E. & Belles, X. (2009). MicroRNA-dependent metamorphosis in hemimetabolan insects. Proc Natl Acad Sci U S A 106, 21678-21682.
20. Griffiths-Jones, S., Hui, J. H. L., Marco, A. & Ronshaugen, M. (2011). MicroRNA evolution by arm switching. EMBO Rep 12, 172-177.
21. Guerra-Assunção, J. A. & Enright, A. J. (2010). MapMi: automated mapping of microRNA loci. BMC Bioinformatics 11, 133.
22. Hofacker, I. L. (2003). Vienna RNA secondary structure server. Nucleic Acids Res 31, 3429-3431.
23. Hussain, M. & Asgari, S. (2010). Functional analysis of a cellular microRNA in insect host-ascovirus interaction. J Virol 84, 612-620.
24. Hussain, M., Frentiu, F. D., Moreira, L. A., O'Neill, S. L. & Asgari, S. (2011). Wolbachia uses host microRNAs to manipulate host gene expression and facilitate colonization of the dengue vector Aedes aegypti. Proc Natl Acad Sci U S A 108, 9250-9255.
25. Hussain, M., Walker, T., O'Neill, S. L. & Asgari, S. (2013). Blood meal induced microRNA regulates development and immune associated genes in the Dengue mosquito vector, Aedes aegypti. Insect Biochem Mol Biol 43, 146-152.
26. Iovino, N., Pane, A. & Gaul, U. (2009). miR-184 has multiple roles in Drosophila female germline development. Dev Cell 17, 123-133.
27. Jehle, J. A., Lange, M., Wang, H., Hu, Z., Wang, Y. & Hauschild, R. (2006). Molecular identification and phylogenetic analysis of baculoviruses from Lepidoptera. Virology 346, 180-193.
28. Kadener, S., Menet, J. S., Sugino, K., Horwich, M. D., Weissbein, U., Nawathean, P., Vagin, V. V., Zamore, P. D., Nelson, S. B. & Rosbash, M. (2009). A role for microRNAs in the Drosophila circadian clock. Genes Dev 23, 2179-2191.
29. King, L. A. & Possee, R. D. (1992). The Baculovirus Expression System: A Laboratory Guide. London: Chapman & Hall.
30. Kozomara, A. & Griffiths-Jones, S. (2011). miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39 (Database issue), D152-D157.
31. Krüger, J. & Rehmsmeier, M. (2006). RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34 (Web Server issue), W451-W454.
32. Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. (2001). An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858-862.
33. Lecellier, C.-H., Dunoyer, P., Arar, K., Lehmann-Che, J., Eyquem, S., Himber, C., Saïb, A. & Voinnet, O. (2005). A cellular microRNA mediates antiviral defense in human cells. Science 308, 557-560.
34. Lee, R. C., Feinbaum, R. L. & Ambros, V. (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854.
35. Lee, L. W., Zhang, S., Etheridge, A., Ma, L., Martin, D., Galas, D. & Wang, K. (2010). Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA 16, 2170-2180.
36. Lewis, B. P., Burge, C. B. & Bartel, D. P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20.
37. Li, Y. & Padgett, R. W. (2012). bantam Is required for optic lobe development and glial cell proliferation. PLoS ONE 7, e32910.
38. Ma, F., Liu, X., Li, D., Wang, P., Li, N., Lu, L. & Cao, X. (2010). MicroRNA-466l upregulates IL-10 expression in TLR-triggered macrophages by antagonizing RNA-binding protein tristetraprolinmediated IL-10 mRNA degradation. J Immunol 184, 6053-6059.
39. Marco, A., Hui, J. H. L., Ronshaugen, M. & Griffiths-Jones, S. (2010). Functional shifts in insect microRNA evolution. Genome Biol Evol 2, 686-696.
40. Morin, R. D., O'Connor, M. D., Griffith, M., Kuchenbauer, F., Delaney, A., Prabhu, A.-L., Zhao, Y., McDonald, H., Zeng, T. & other authors (2008). Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 18, 610-621.
41. Nielsen, C. B., Shomron, N., Sandberg, R., Hornstein, E., Kitzman, J. & Burge, C. B. (2007). Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA 13, 1894-1910.
42. Nobiron, I., O'Reilly, D. R. & Olszewski, J. A. (2003). Autographa californica nucleopolyhedrovirus infection of Spodoptera frugiperda cells: a global analysis of host gene regulation during infection, using a differential display approach. J Gen Virol 84, 3029-3039.
43. Parrish, J. Z., Xu, P., Kim, C. C., Jan, L. Y. & Jan, Y. N. (2009). The microRNA bantam functions in epithelial cells to regulate scaling growth of dendrite arbors in Drosophila sensory neurons. Neuron 63, 788-802.
44. Pasquinelli, A. E. (2012). MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet 13, 271-282.
45. Peng, H. W., Slattery, M. & Mann, R. S. (2009). Transcription factor choice in the Hippo signaling pathway: homothorax and yorkie regulation of the microRNA bantam in the progenitor domain of the Drosophila eye imaginal disc. Genes Dev 23, 2307-2319.
46. Popham, H. J. R., Grasela, J. J., Goodman, C. L. & McIntosh, A. H. (2010). Baculovirus infection influences host protein expression in two established insect cell lines. J Insect Physiol 56, 1237-1245.
47. Possee, R. D., Griffiths, C. M., Hitchman, R. B., Chambers, A., Murguia-Meca, F., Danquah, J., Jeshtadi, A. & King, L. A. (2010). Baculoviruses: biology, replication and exploitation. In Insect Virology. Edited by S. Asgari & K. N. Johnson, Chapter 2. Norwich, UK: Caister Academic Press.
48. Rao, Z., He, W., Liu, L., Zheng, S., Huang, L. & Feng, Q. (2012). Identification, expression and target gene analyses of Micrornas in Spodoptera litura. PLoS ONE 7, e37730.
49. Rehmsmeier, M., Steffen, P., Hochsmann, M. & Giegerich, R. (2004). Fast and effective prediction of microRNA/target duplexes. RNA 10, 1507-1517.
50. Reinhart, B. J., Slack, F. J., Basson, M., Pasquinelli, A. E., Bettinger, J. C., Rougvie, A. E., Horvitz, H. R. & Ruvkun, G. (2000). The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901-906.
51. Rubio, M., de Horna, A. & Belles, X. (2012). MicroRNAs in metamorphic and non-metamorphic transitions in hemimetabolan insect metamorphosis. BMC Genomics 13, 386.
52. Ruby, J. G., Stark, A., Johnston, W. K., Kellis, M., Bartel, D. P. & Lai, E. C. (2007). Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 17, 1850-1864.
53. Salem, T. Z., Zhang, F., Xie, Y. & Thiem, S. M. (2011). Comprehensive analysis of host gene expression in Autographa californica nucleopolyhedrovirus-infected Spodoptera frugiperda cells. Virology 412, 167-178.
54. Seto, A. G., Kingston, R. E. & Lau, N. C. (2007). The coming of age for Piwi proteins. Mol Cell 26, 603-609.
55. Singh, C. P., Singh, J. & Nagaraju, J. (2012). A baculovirus-encoded MicroRNA (miRNA) suppresses its host miRNA biogenesis by regulating the exportin-5 cofactor Ran. J Virol 86, 7867-7879.
56. Siomi, M. C., Sato, K., Pezic, D. & Aravin, A. A. (2011). PIWIinteracting small RNAs: the vanguard of genome defence. Nat Rev Mol Cell Biol 12, 246-258.
57. Skalsky, R. L. & Cullen, B. R. (2010). Viruses, microRNAs, and host interactions. Annu Rev Microbiol 64, 123-141.
58. Skalsky, R. L., Vanlandingham, D. L., Scholle, F., Higgs, S. & Cullen, B. R. (2010). Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus. BMC Genomics 11, 119.
59. Tomari, Y., Du, T. & Zamore, P. D. (2007). Sorting of Drosophila small silencing RNAs. Cell 130, 299-308.
60. Vasudevan, S. (2012). Posttranscriptional upregulation by microRNAs. Wiley Interdiscip Rev RNA 3, 311-330.
61. Wightman, B., Ha, I. & Ruvkun, G. (1993). Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855-862.
62. Winter, J., Jung, S., Keller, S., Gregory, R. I. & Diederichs, S. (2009). Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 11, 228-234.
63. Yang, Y., Xu, S., Xia, L., Wang, J., Wen, S., Jin, P. & Chen, D. (2009). The bantam microRNA is associated with Drosophila fragile X mental retardation protein and regulates the fate of germline stem cells. PLoS Genet 5, e1000444.
64. Yu, X., Zhou, Q., Li, S.-C., Luo, Q., Cai, Y., Lin, W. C., Chen, H., Yang, Y., Hu, S. & Yu, J. (2008). The silkworm (Bombyx mori) microRNAs and their expressions in multiple developmental stages. PLoS ONE 3, e2997.
65. Zhang, Y., Zhou, X., Ge, X., Jiang, J., Li, M., Jia, S., Yang, X., Kan, Y., Miao, X. & other authors (2009). Insect-specific microRNA involved in the development of the silkworm Bombyx mori. PLoS ONE 4, e4677.
66. Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406-3415.