Redefining the genetics of murine gammaherpesvirus 68 via transcriptome-based annotation

Cell Host and Microbe

Volumn 7, Issue 6, 2010, Pages 516-526

  Johnson, L Steven ^a   Willert, Erin K ^a   Virgin, Herbert W ^a  

^a WASHINGTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; TRANSCRIPTOME;

ARTICLE; BASE PAIRING; DNA HYBRIDIZATION; DNA MICROARRAY; DNA SYNTHESIS; EPSTEIN BARR VIRUS; GAMMA HERPES VIRUS 68; GAMMAHERPESVIRINAE; GENE EXPRESSION; GENE MAPPING; GENETIC TRANSCRIPTION; HERPES VIRUS SAIMIRI; INFORMATION PROCESSING; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN SYNTHESIS; RNA PROBE; VIRAL GENETICS;

MURINAE;

EID: 77956548303     PISSN: 19313128     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chom.2010.05.005     Document Type: Article

References (34)

1. Allen, R. D., Dickerson, S., and Speck, S. H. (2006). Identification of spliced gammaherpesvirus 68 LANA and v-cyclin transcripts and analysis of their expression in vivo during latent infection. J. Virol. 80, 2055-2062.
2. Assarsson, E., Greenbaum, J. A., Sundstrom, M., Schaffer, L., Hammond, J. A., Pasquetto, V., Oseroff, C., Hendrickson, R. C., Lefkowitz, E. J., Tscharke, D. C., et al. (2008a). Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proc. Natl. Acad. Sci. USA 105, 2140-2145.
3. Assarsson, E., Greenbaum, J. A., Sundstrom, M., Schaffer, L., Hammond, J. A., Pasquetto, V., Oseroff, C., Hendrickson, R. C., Lefkowitz, E. J., Tscharke, D. C., et al. (2008b). Reply to Satheshkumar and Moss: Poxvirus transcriptom analysis. Proc. Natl. Acad. Sci. USA 105, E63-E64.
4. Besemer, J., and Borodovsky, M. (2005). GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 33, W451-W454.
5. Cai, X., Lu, S., Zhang, Z., Gonzalez, C. M., Damania, B., and Cullen, B. R. (2005). Kaposi's sarcoma-associated herpesvirus expresses an array of viral micro-RNAs in latently infected cells. Proc. Natl. Acad. Sci. USA 102, 5570-5575.
6. Cai, X., Schafer, A., Lu, S., Bilello, J. P., Desrosiers, R. C., Edwards, R., Raab-Traub, N., and Cullen, B. R. (2006). Epstein-Barr virus microRNAs are evolutionarily conserved and differentially expressed. PLoS Pathog. 2, e23. 10.1371/journal.ppat.0020023.
7. Carninci, P., Yasuda, J., and Hayashizaki, Y. (2008). Multifaceted mammalian transcriptome. Curr. Opin. Cell. Biol. 20, 274-280.
8. Conrad, N. K., and Steitz, J. A. (2005). A Kaposi's sarcoma virus RNA element that increases the nuclear abundance of intronless transcripts. EMBO J. 24, 1831-1841.
9. David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C. J., Bofkin, L., Jones, T., Davis, R. W., and Steinmetz, L. M. (2006). A high-resolution map of transcription in the yeast genome. Proc. Natl. Acad. Sci. USA 103, 5320-5325.
10. DeZalia, M., and Speck, S. H. (2008). Identification of closely spaced but distinct transcription initiation sites for the murine gammaherpesvirus 68 latency-associated M2 gene. J. Virol. 82, 7411-7421.
11. Diebel, K. W., Smith, A. L., and Van Dyk, L. F. (2010). Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters. RNA 16, 170-185.
12. Ebrahimi, B., Dutia, B. M., Roberts, K. L., Garcia-Ramirez, J. J., Dickinson, P., Stewart, J. P., Ghazal, P., Roy, D. J., and Nash, A. A. (2003). Transcriptome profile of murine gammaherpesvirus-68 lytic infection. J. Gen. Virol. 84, 99-109.
13. ENCODE Project Consortium, Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., et al. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816.
14. Gray, K. S., Allen, R. D., III, Farrell, M. L., Forrest, J. C., and Speck, S. H. (2009). Alternatively initiated gene 50/RTA transcripts expressed during murine and human gammaherpesvirus reactivation from latency. J. Virol. 83, 314-328.
15. He, Y., Vogelstein, B., Velculescu, V. E., Papadopoulos, N., and Kinzler, K. W. (2008). The antisense transcriptomes of human cells. Science 322, 1855-1857.
16. Hwang, S., Wu, T. T., Tong, L. M., Kim, K. S., Martinez-Guzman, D., Colantonio, A. D., Uittenbogaart, C. H., and Sun, R. (2008). Persistent gammaherpesvirus replication and dynamic interaction with the host in vivo. J. Virol. 82, 12498-12509.
17. Kieff, E., and Rickinson, A. (2007). Epstein-Barr Virus and its replication. In Fields Virology, D. Knipe and P. Howley, eds. (Philadelphia: Lippincott, Williams Wilkins), pp. 2605-2654.
18. Mackett, M., Stewart, J. P., de V Pepper, S., Chee, M., Efstathiou, S., Nash, A., and Arrand, J. R. (1997). Genetic content and preliminary transcriptional analysis of a representative region of murine gammaherpesvirus 68. J. Gen. Virol. 78, 1425-1433.
19. Majerciak, V., Yamanegi, K., and Zheng, Z. M. (2006). Gene structure and expression of Kaposi's sarcoma-associated herpesvirus ORF56, ORF57, ORF58, and ORF59. J. Virol. 80, 11968-11981.
20. May, J. S., Coleman, H. M., Boname, J. M., and Stevenson, P. G. (2005). Murine gammaherpesvirus-68 ORF28 encodes a non-essential virion glycoprotein. J. Gen. Virol. 86, 919-928.
21. Mills, R., Rozanov, M., Lomsadze, A., Tatusova, T., and Borodovsky, M. (2003). Improving gene annotation of complete viral genomes. Nucleic Acids Res. 31, 7041-7055.
22. Nash, A. A., Dutia, B. M., Stewart, J. P., and Davison, A. J. (2001). Natural history of murine gamma-herpesvirus infection. Philos. Trans. R. Soc. Lond. B Biol. Sci. 356, 569-579.
23. Neyts, J., and De, C. E. (1998). In vitro and in vivo inhibition of murine gamma herpesvirus 68 replication by selected antiviral agents. Antimicrob. Agents Chemother. 42, 170-172.
24. Parry, C. M., Simas, J. P., Smith, V. P., Stewart, C. A., Minson, A. C., Efstathiou, S., and Alcami, A. (2000). A broad spectrum secreted chemokine binding protein encoded by a herpesvirus. J. Exp. Med. 191, 573-578.
25. Pfeffer, S., Sewer, A., Lagos-Quintana, M., Sheridan, R., Sander, C., Grasser, F. A., Van Dyk, L. F., Ho, C. K., Shuman, S., Chien, M., et al. (2005). Identification of microRNAs of the herpesvirus family. Nat. Methods 2, 269-276.
26. Puglielli, M. T., Desai, N., and Speck, S. H. (1997). Regulation of EBNA gene transcription in lymphoblastoid cell lines: characterization of sequences downstream of BCR2 (Cp). J. Virol. 71, 120-128.
27. Rimessi, P., Bonaccorsi, A., Sturzl, M., Fabris, M., Brocca-Cofano, E., Caputo, A., Melucci-Vigo, G., Falchi, M., Cafaro, A., Cassai, E., et al. (2001). Transcription pattern of human herpesvirus 8 open reading frame K3 in primary effusion lymphoma and Kaposi's sarcoma. J. Virol. 75, 7161-7174.
28. Rochford, R., Lutzke, M. L., Alfinito, R. S., Clavo, A., and Cardin, R. D. (2001). Kinetics of murine gammaherpesvirus 68 gene expression following infection of murine cells in culture and in mice. J. Virol. 75, 4955-4963.
29. Satheshkumar, P. S., and Moss, B. (2008). Poxvirus transcriptome analysis. Proc. Natl. Acad. Sci. USA 105, E62.
30. Song, M. J., Hwang, S. M., Wong, W. H., Wu, T. T., Lee, S. M., Liao, H. I., and Sun, R. (2005). Identification of viral genes essential for replication of murine gamma-herpesvirus 68 using signature-tagged mutagenesis. Proc. Natl. Acad. Sci. USA 102, 3805-3810.
31. Stein, L. D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A., and Lewis, S. (2002). The generic genome browser: a building block for a model organism system database. Genome Res. 12, 1599-1610.
32. Taylor, J. L., Bennett, H. N., Snyder, B. A., Moore, P. S., and Chang, Y. (2005). Transcriptional analysis of latent and inducible Kaposi's sarcoma-associated herpesvirus transcripts in the K4 to K7 region. J. Virol. 79, 15099-15106.
33. Virgin, H. W., Latreille, P., Wamsley, P., Hallsworth, K., Weck, K. E., Dal Canto, A. J., and Speck, S. H. (1997). Complete sequence and genomic analysis of murine gammaherpesvirus 68. J. Virol. 71, 5894-5904.
34. Weck, K. E., Barkon, M. L., Yoo, L. I., Speck, S. H., and Virgin, H. W. (1996). Mature B cells are required for acute splenic infection, but not for establishment of latency, by murine gammaherpesvirus 68. J. Virol. 70, 6775-6780.