A global analysis of evolutionary conservation among known and predicted gammaherpesvirus microRNAs

Journal of Virology

Volumn 84, Issue 2, 2010, Pages 716-728

  Walz, Nicole ^a   Christalla, Thomas ^a   Tessmer, Uwe ^a   Grundhoff, Adam ^a  

^a LEIBNIZ INSTITUTE FOR EXPERIMENTAL VIROLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; VIRUS RNA;

ANIMAL CELL; ARTICLE; COMPUTER ANALYSIS; EPSTEIN BARR VIRUS; GENE CLUSTER; GENE LOCUS; GENE SEQUENCE; GENE STRUCTURE; GENETIC CONSERVATION; HERPES VIRUS; NONHUMAN; PRIORITY JOURNAL; RHADINOVIRUS; RNA ANALYSIS; RNA SEQUENCE; VIRUS GENE;

ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GAMMAHERPESVIRINAE; GENOME, VIRAL; HERPESVIRUS 4, HUMAN; HUMANS; LYMPHOCRYPTOVIRUS; MACACA MULATTA; MICRORNAS; MOLECULAR SEQUENCE DATA; RHADINOVIRUS; SEQUENCE ALIGNMENT;

CERCOPITHECINE HERPESVIRUS 15; CERCOPITHECINE HERPESVIRUS 17; HERPESVIRIDAE; HUMAN HERPESVIRUS 4;

EID: 73849115727     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.01302-09     Document Type: Article

References (38)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Bartel, D. P. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136:215-233.
3. Barth, S., T. Pfuhl, A. Mamiani, C. Ehses, K. Roemer, E. Kremmer, C. Jaker, J. Hock, G. Meister, and F. A. Grasser. 2008. Epstein-Barr virusencoded microRNA miR-BART2 down-regulates the viral DNA polymerase BALF5. Nucleic Acids Res. 36:666-675.
4. Bonnet, E., J. Wuyts, P. Rouze, and Y. Van de Peer. 2004. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20:2911-2917.
5. Brodersen, P., and O. Voinnet. 2009. Revisiting the principles of microRNA target recognition and mode of action. Nat. Rev. Mol. Cell Biol. 10:141-148.
6. Buck, A. H., J. Santoyo-Lopez, K. A. Robertson, D. S. Kumar, M. Reczko, and P. Ghazal. 2007. Discrete clusters of virus-encoded microRNAs are associated with complementary strands of the genome and the 7.2-kilobase stable intron in murine cytomegalovirus. J. Virol. 81:13761-13770.
7. Cai, X., S. Lu, Z. Zhang, C. M. Gonzalez, B. Damania, and B. R. Cullen. 2005. Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proc. Natl. Acad. Sci. U. S. A. 102: 5570-5575.
8. Cai, X., A. Schafer, S. Lu, J. P. Bilello, R. C. Desrosiers, R. Edwards, N. Raab-Traub, and B. R. Cullen. 2006. Epstein-Barr virus microRNAs are evolutionarily conserved and differentially expressed. PLoS Pathog. 2:e23.
9. Carthew, R. W., and E. J. Sontheimer. 2009. Origins and mechanisms of miRNAs and siRNAs. Cell 136:642-655.
10. Cheung, S. T., D. P. Huang, A. B. Hui, K. W. Lo, C. W. Ko, Y. S. Tsang, N. Wong, B. M. Whitney, and J. C. Lee. 1999. Nasopharyngeal carcinoma cell line (C666-1) consistently harbouring Epstein-Barr virus. Int. J. Cancer 83: 121-126.
11. Dolken, L., J. Perot, V. Cognat, A. Alioua, M. John, J. Soutschek, Z. Ruzsics, U. Koszinowski, O. Voinnet, and S. Pfeffer. 2007. Mouse cytomegalovirus microRNAs dominate the cellular small RNA profile during lytic infection and show features of posttranscriptional regulation. J. Virol. 81:13771-13782.
12. Gottwein, E., N. Mukherjee, C. Sachse, C. Frenzel, W. H. Majoros, J. T. Chi, R. Braich, M. Manoharan, J. Soutschek, U. Ohler, and B. R. Cullen. 2007. A viral microRNA functions as an orthologue of cellular miR-155. Nature 450:1096-1099.
13. Griffiths-Jones, S. 2004. The microRNA registry. Nucleic Acids Res. 32: D109-D111.
14. Griffiths-Jones, S., R. J. Grocock, S. van Dongen, A. Bateman, and A. J. Enright. 2006. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34:D140-D144.
15. Grundhoff, A., C. S. Sullivan, and D. Ganem. 2006. A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses. RNA 12:733-750.
16. Hofacker, I. L., W. Fontana, P. F. Stadler, S. Bonhoeffer, P. Tacker, and P. Schuster. 1994. Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125:167-188.
17. Kim, V. N., J. Han, and M. C. Siomi. 2009. Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol. 10:126-139.
18. Landgraf, P., M. Rusu, R. Sheridan, A. Sewer, N. Iovino, A. Aravin, S. Pfeffer, A. Rice, A. O. Kamphorst, M. Landthaler, C. Lin, N. D. Socci, L. Hermida, V. Fulci, S. Chiaretti, R. Foa, J. Schliwka, U. Fuchs, A. Novosel, R. U. Muller, B. Schermer, U. Bissels, J. Inman, Q. Phan, M. Chien, D. B. Weir, R. Choksi, G. De Vita, D. Frezzetti, H. I. Trompeter, V. Hornung, G. Teng, G. Hartmann, M. Palkovits, R. Di Lauro, P. Wernet, G. Macino, C. E. Rogler, J. W. Nagle, J. Ju, F. N. Papavasiliou, T. Benzing, P. Lichter, W. Tam, M. J. Brownstein, A. Bosio, A. Borkhardt, J. J. Russo, C. Sander, M. Zavolan, and T. Tuschl. 2007. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129:1401-1414.
19. Marshall, V., T. Parks, R. Bagni, C. D. Wang, M. A. Samols, J. Hu, K. M. Wyvil, K. Aleman, R. F. Little, R. Yarchoan, R. Renne, and D. Whitby. 2007. Conservation of virally encoded microRNAs in Kaposi sarcoma-associated herpesvirus in primary effusion lymphoma cell lines and in patients with Kaposi sarcoma or multicentric Castleman disease. J. Infect. Dis. 195:645-659.
20. Nachmani, D., N. Stern-Ginossar, R. Sarid, and O. Mandelboim. 2009. Diverse herpesvirus microRNAs target the stress-induced immune ligand MICB to escape recognition by natural killer cells. Cell Host Microbe 5:376-385.
21. Pfeffer, S., A. Sewer, M. Lagos-Quintana, R. Sheridan, C. Sander, F. A. Grasser, L. F. van Dyk, C. K. Ho, S. Shuman, M. Chien, J. J. Russo, J. Ju, G. Randall, B. D. Lindenbach, C. M. Rice, V. Simon, D. D. Ho, M. Zavolan, and T. Tuschl. 2005. Identification of microRNAs of the herpesvirus family. Nat. Methods 2:269-276.
22. Pfeffer, S., M. Zavolan, F. A. Grasser, M. Chien, J. J. Russo, J. Ju, B. John, A. J. Enright, D. Marks, C. Sander, and T. Tuschl. 2004. Identification of virus-encoded microRNAs. Science 304:734-736.
23. Rivailler, P., A. Carville, A. Kaur, P. Rao, C. Quink, J. L. Kutok, S. Westmoreland, S. Klumpp, M. Simon, J. C. Aster, and F. Wang. 2004. Experimental rhesus lymphocryptovirus infection in immunosuppressed macaques: an animal model for Epstein-Barr virus pathogenesis in the immunosuppressed host. Blood 104:1482-1489.
24. Samols, M. A., J. Hu, R. L. Skalsky, and R. Renne. 2005. Cloning and identification of a microRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus. J. Virol. 79:9301-9305.
25. Schafer, A., X. Cai, J. P. Bilello, R. C. Desrosiers, and B. R. Cullen. 2007. Cloning and analysis of microRNAs encoded by the primate gamma-herpesvirus rhesus monkey rhadinovirus. Virology 364:21-27.
26. Seo, G. J., C. J. Chen, and C. S. Sullivan. 2009. Merkel cell polyomavirus encodes a microRNA with the ability to autoregulate viral gene expression. Virology 383:183-187.
27. Seo, G. J., L. H. Fink, B. O'Hara, W. J. Atwood, and C. S. Sullivan. 2008. Evolutionarily conserved function of a viral microRNA. J. Virol. 82:9823-9828.
28. Skalsky, R. L., M. A. Samols, K. B. Plaisance, I. W. Boss, A. Riva, M. C. Lopez, H. V. Baker, and R. Renne. 2007. Kaposi's sarcoma-associated herpesvirus encodes an ortholog of miR-155. J. Virol. 81:12836-12845.
29. Sullivan, C. S., and A. Grundhoff. 2007. Identification of viral microRNAs. Methods Enzymol. 427:3-23.
30. Sullivan, C. S., A. T. Grundhoff, S. Tevethia, J. M. Pipas, and D. Ganem. 2005. SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature 435:682-686.
31. Sullivan, C. S., C. K. Sung, C. D. Pack, A. Grundhoff, A. E. Lukacher, T. L. Benjamin, and D. Ganem. 2009. Murine polyomavirus encodes a microRNA that cleaves early RNA transcripts but is not essential for experimental infection. Virology 387:157-167.
32. Umbach, J. L., and B. R. Cullen. 2009. The role of RNAi and microRNAs in animal virus replication and antiviral immunity. Genes Dev. 23:1151-1164.
33. Umbach, J. L., M. F. Kramer, I. Jurak, H. W. Karnowski, D. M. Coen, and B. R. Cullen. 2008. MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs. Nature 454:780-783.
34. Visone, R., and C. M. Croce. 2009. MiRNAs and cancer. Am. J. Pathol. 174:1131-1138.
35. Xia, T., A. O'Hara, I. Araujo, J. Barreto, E. Carvalho, J. B. Sapucaia, J. C. Ramos, E. Luz, C. Pedroso, M. Manrique, N. L. Toomey, C. Brites, D. P. Dittmer, and W. J. Harrington, Jr. 2008. EBV microRNAs in primary lymphomas and targeting of CXCL-11 by ebv-mir-BHRF1-3. Cancer Res. 68:1436-1442.
36. Zeng, Y., and B. R. Cullen. 2006. Recognition and cleavage of primary microRNA transcripts. Methods Mol. Biol. 342:49-56.
37. Zhao, Y., Y. Yao, H. Xu, L. Lambeth, L. P. Smith, L. Kgosana, X. Wang, and V. Nair. 2009. A functional microRNA-155 ortholog encoded by the oncogenic Marek's disease virus. J. Virol. 83:489-492.
38. Zhu, J. Y., T. Pfuhl, N. Motsch, S. Barth, J. Nicholls, F. Grasser, and G. Meister. 2009. Identification of novel Epstein-Barr virus microRNA genes from nasopharyngeal carcinomas. J. Virol. 83:3333-3341.