Insights into Polyomaviridae MicroRNA function derived from study of the bandicoot papillomatosis carcinomatosis viruses

Journal of Virology

Volumn 85, Issue 9, 2011, Pages 4487-4500

  Chen, Chun Jung ^a   Kincaid, Rodney P ^a   Seo, Gil Ju ^a   Bennett, Mark D ^b   Sullivan, Christopher S ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b MURDOCH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; VIRUS LARGE T ANTIGEN; VIRUS RNA;

3' UNTRANSLATED REGION; ANTIGEN EXPRESSION; ANTISENSE VECTOR; ARTICLE; BANDICOOT PAPILLOMATOSIS CARCINOMATOSIS VIRUS TYPE 1; CONTROLLED STUDY; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENE MAPPING; GENE TARGETING; GENETIC CONSERVATION; GENETIC ENGINEERING; HUMAN; HUMAN CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYOMA LIKE VIRUS; POLYOMA VIRUS; PRIORITY JOURNAL; REPORTER GENE; RNA ANALYSIS; SEQUENCE HOMOLOGY; STRAIN DIFFERENCE; TRANSCRIPTION REGULATION; VIRUS GENOME;

ANIMALS; ANTIGENS, POLYOMAVIRUS TRANSFORMING; BINDING SITES; GENE EXPRESSION REGULATION, VIRAL; MARSUPIALIA; MICRORNAS; POLYOMAVIRIDAE; POLYOMAVIRUS INFECTIONS; RNA, COMPLEMENTARY; RNA, VIRAL; VIRUS REPLICATION;

METATHERIA; PAPILLOMAVIRIDAE; PERAMELES BOUGAINVILLE; POLYOMAVIRIDAE; POLYOMAVIRUS;

EID: 79955369794     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.02557-10     Document Type: Article

References (51)

1. Altschul, S. F., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Applied Biosystems. 2009. Whole-genome discovery and profiling of small RNAs using the SOLiD System. Biotechniques 46:232-234.
3. Bartel, D. P. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136:215-233.
4. Bellare, P., and D. Ganem. 2009. Regulation of KSHV lytic switch protein expression by a virus-encoded microRNA: an evolutionary adaptation that fine-tunes lytic reactivation. Cell Host Microbe 6:570-575.
5. Bennett, M. D., et al. 2010. The first complete papillomavirus genome characterized from a marsupial host: a novel isolate from Bettongia penicillata. J. Virol. 84:5448-5453.
6. Bennett, M. D., et al. 2008. In situ hybridization to detect bandicoot papillomatosis carcinomatosis virus type 1 in biopsies from endangered western barred bandicoots (Perameles bougainville). J. Gen. Virol. 89:419-423.
7. Bennett, M. D., et al. 2008. Genomic characterization of a novel virus found in papillomatous lesions from a southern brown bandicoot (Isoodon obesulus) in Western Australia. Virology 376:173-182.
8. Bernstein, E., A. A. Caudy, S. M. Hammond, and G. J. Hannon. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363-366.
9. Boss, I. W., and R. Renne. 2010. Viral miRNAs: tools for immune evasion. Curr. Opin. Microbiol. 13:540-545.
10. Cai, X., G. Li, L. A. Laimins, and B. R. Cullen. 2006. Human papillomavirus genotype 31 does not express detectable microRNA levels during latent or productive virus replication. J. Virol. 80:10890-10893.
11. Cantalupo, P., et al. 2005. Complete nucleotide sequence of polyomavirus SA12. J. Virol. 79:13094-13104.
12. Carthew, R. W., and E. J. Sontheimer. 2009. Origins and mechanisms of miRNAs and siRNAs. Cell 136:642-655.
13. Cheng, Y., R. M. Miura, and B. Tian. 2006. Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 22:2320-2325.
14. Cole, C. N. 1996. Polyomaviridae: the viruses and their replication, p. 1997-2043. In B. N. Fields, D. M. Knipe, and P. M. Howley (ed.), Fields virology, 3rd ed. Lippincott-Raven Publishers, Philadelphia, PA.
15. Grey, F., H. Meyers, E. A. White, D. H. Spector, and J. Nelson. 2007. A human cytomegalovirus-encoded microRNA regulates expression of multiple viral genes involved in replication. PLoS Pathog. 3:e163.
16. Griffiths-Jones, S. 2006. miRBase: the microRNA sequence database. Methods Mol. Biol. 342:129-138.
17. Grimson, A., et al. 2007. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27:91-105.
18. 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.
19. Hammond, S. M., E. Bernstein, D. Beach, and G. J. Hannon. 2000. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404:293-296.
20. Hussain, M., R. J. Taft, and S. Asgari. 2008. An insect virus-encoded microRNA regulates viral replication. J. Virol. 82:9164-9170.
21. Hutvagner, G., et al. 2001. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293:834-838.
22. Imperiale, M. J., and E. O. Major. 2007. Polyomaviruses, p. 2263-2298. In D. M. Knipe and P. M. Howley (ed.), Fields virology, 5th ed. Lippincott Williams & Wilkins, Philadelphia, PA.
23. Kim, V. N. 2005. MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 6:376-385.
24. Lee, Y., et al. 2003. The nuclear RNase III Drosha initiates microRNA processing. Nature 425:415-419.
25. Lei, X., et al. 2010. Regulation of NF-kappaB inhibitor IkappaBalpha and viral replication by a KSHV microRNA. Nat. Cell Biol. 12:193-199.
26. Lim, L. P., et al. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769-773.
27. Lin, Y. T., et al. 2010. Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs. RNA 16:1540-1558.
28. Lu, F., W. Stedman, M. Yousef, R. Renne, and P. M. Lieberman. 2010. Epigenetic regulation of Kaposi's sarcoma-associated herpesvirus latency by virus-encoded microRNAs that target Rta and the cellular Rbl2-DNMT pathway. J. Virol. 84:2697-2706.
29. Messeguer, X., et al. 2002. PROMO: detection of known transcription regulatory elements using species-tailored searches. Bioinformatics 18:333-334.
30. Murphy, E., J. Vanicek, H. Robins, T. Shenk, and A. J. Levine. 2008. Suppression of immediate-early viral gene expression by herpesvirus-coded microRNAs: implications for latency. Proc. Natl. Acad. Sci. U. S. A. 105:5453-5458.
31. Pomerantz, B. J., and J. A. Hassell. 1984. Polyomavirus and simian virus 40 large T antigens bind to common DNA sequences. J. Virol. 49:925-937.
32. Rector, A., et al. 2007. Ancient papillomavirus-host cospeciation in Felidae. Genome Biol. 8:R57.
33. Reese, M. G. 2001. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput. Chem. 26:51-56.
34. Rumble, S. M., et al. 2009. SHRiMP: accurate mapping of short color-space reads. PLoS Comput. Biol. 5:e1000386.
35. 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.
36. 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.
37. Skalsky, R. L., and B. R. Cullen. 2010. Viruses, microRNAs, and host interactions. Annu. Rev. Microbiol. 64:123-141.
38. Stern-Ginossar, N., et al. 2007. Host immune system gene targeting by a viral miRNA. Science 317:376-381.
39. Sullivan, C. S. 2008. New roles for large and small viral RNAs in evading host defences. Nat. Rev. Genet. 9:503-507.
40. Sullivan, C. S., and B. R. Cullen. 2009. Non-coding regulatory RNAs of the DNA tumor viruses, p. 645-682. In B. Damania and J. M. Pipas (ed.), DNA tumor Viruses. Springer Science, New York, NY.
41. Sullivan, C. S., and A. Grundhoff. 2007. Identification of viral microRNAs. Methods Enzymol. 427:1-23.
42. 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.
43. Sullivan, C. S., et al. 2009. Murine polyomavirus encodes a microRNA that cleaves early RNA transcripts but is not essential for experimental infection. Virology 387:157-167.
44. Tabaska, J. E., and M. Q. Zhang. 1999. Detection of polyadenylation signals in human DNA sequences. Gene 231:77-86.
45. Taganov, K. D., M. P. Boldin, and D. Baltimore. 2007. MicroRNAs and immunity: tiny players in a big field. Immunity 26:133-137.
46. Umbach, J. L., et al. 2008. MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs. Nature 454:780-783.
47. Weber, K., M. E. Bolander, and G. Sarkar. 1998. PIG-B: a homemade monophasic cocktail for the extraction of RNA. Mol. Biotechnol. 9:73-77.
48. Woolford, L., et al. 2009. Prevalence, emergence, and factors associated with a viral papillomatosis and carcinomatosis syndrome in wild, reintroduced, and captive western barred bandicoots (Perameles bougainville). Ecohealth 6:414-425.
49. Woolford, L., et al. 2007. A novel virus detected in papillomas and carcinomas of the endangered western barred bandicoot (Perameles bougainville) exhibits genomic features of both the Papillomaviridae and Polyomaviridae. J. Virol. 81:13280-13290.
50. Zeng, Y., R. Yi, and B. R. Cullen. 2005. Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. EMBO J. 24:138-148.
51. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31:3406-3415.