Selection of a nonconsensus branch point is influenced by an RNA stem- loop structure and is important to confer stability to the herpes simplex virus 2-kilobase latency-associated transcript

Journal of Virology

Volumn 71, Issue 8, 1997, Pages 5849-5860

  Krummenacher, Claude ^a,b   Zabolotny, Janice M ^b   Fraser, Nigel W ^b  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b WISTAR INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PYRIMIDINE; VIRUS RNA;

ALTERNATIVE RNA SPLICING; ANIMAL CELL; ARTICLE; CELL STRAIN COS1; CONTROLLED STUDY; GENE MAPPING; HERPES SIMPLEX VIRUS 2; INTRON; LATENT VIRUS INFECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYADENYLATION; PRIORITY JOURNAL; RNA STRUCTURE; RNA TRANSCRIPTION; SITE DIRECTED MUTAGENESIS; VIRUS MUTANT;

EID: 0030741818     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.71.8.5849-5860.1997     Document Type: Article

References (59)

1. Arenas, J., and J. Hurwitz. 1987. Purification of a RNA debranching activity from Hela cells. J. Biol. Chem. 262:4274-4279.
2. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. A. Smith, J. G. Seidmen, and K. Struhl. 1987. Current protocols in molecular biology. Greene Publishing Associates and Wiley-Interscience, New York, N.Y.
3. Block, T. M., S. L. Deshmane, J. Masonis, J. Maggioncalda, T. Valyi-Nagy, and N. W. Fraser. 1992. An HSV LAT null mutant reactivates slowly from latent infection and makes small plaques on CV-1 monolayers. Virology 192:618-630.
4. Block, T. M., J. G. Spivack, I. Steiner, S. Deshmane, M. T. McIntosh, R. P. Lirette, and N. W. Fraser. 1990. A herpes simplex virus type 1 latency-associated transcript mutant reactivates with normal kinetics from latent infection. J. Virol. 64:3417-3426.
5. Bloom, D. C., J. M. Hill, G. Devi-Rao, E. K. Wagner, L. T. Feldman, and J. G. Stevens. 1996. A 348-base-pair region in the latency-associated transcript facilitates herpes simplex virus type 1 reactivation. J. Virol. 70:2449-2459.
6. Carter, K. L., and B. Roizman. 1996. Alternatively spliced mRNAs predicted to yield frame-shift proteins and stable intron 1 RNAs of the herpes simplex virus 1 regulatory gene alpha 0 accumulate in the cytoplasm of infected cells. Proc. Natl. Acad. Sci. USA 93:12535-12540.
7. Castanotto, D., and J. J. Rossi. 1992. Small sequence insertions within the branch point region dictate alternative sites of lariat formation in a yeast intron. Nucleic Acids Res. 20:6649-6655.
8. Chapman, K. B., and J. D. Boeke. 1991. Isolation and characterization of the gene encoding yeast debranching enzyme. Cell 65:483-492.
9. Deatly, A. M., J. G. Spivack, E. Lavi, and N. W. Fraser. 1987. RNA from an immediate early region of the HSV-1 genome is present in the trigeminal ganglia of latently infected mice. Proc. Natl. Acad. Sci. USA 84:3204-3208.
10. Deatly, A. M., J. G. Spivack, E. Lavi, D. R. O'Boyle II, and N. W. Fraser. 1988. Latent herpes simplex virus type 1 transcripts in peripheral and central nervous system tissues of mice map to similar regions of the viral genome. J. Virol. 62:749-756.
11. Devi-Rao, G. B., S. A. Goodart, L. M. Hecht, R. Rochford, M. A. Rice, and E. K. Wagner. 1991. Relationship between polyadenylated and nonpolyadenylated herpes simplex virus type 1 latency-associated transcripts. J. Virol. 65:2179-2190.
12. Dobson, A. T., F. Sederati, G. Devi-Rao, J. Flanagan, M. J. Farrell, J. G. Stevens, E. K. Wagner, and L. T. Feldman. 1989. Identification of the latency-associated transcript promoter by expression of rabbit beta-globin mRNA in mouse sensory nerve ganglia latently infected with a recombinant herpes simplex virus. J. Virol. 63:3844-3851.
13. Doerig, C., L. I. Pizer, and C. L. Wilcox. 1991. An antigen encoded by the latency-associated transcript in neuronal cell cultures latently infected with herpes simplex virus type 1. J. Virol. 65:2724-2727.
14. Dominski, Z., and R. Kole. 1994. Identification and characterization by antisense oligonucleotides of exon and intron sequences required tor splicing. Mol. Cell. Biol. 14:7445-7454.
15. Estes, P. A., N. E. Cooke, and S. A. Liebhaber. 1992. A native RNA secondary structure controls alternative splice-site selection and generates two human growth hormone isoforms. J. Biol. Chem. 267:14902-14908.
16. Farrell, M. J., A. T. Dobson, and L. T. Feldman. 1991. Herpes simplex virus latency-associated transcript is a stable intron. Proc. Natl. Acad. Sci. USA 88:790-794.
17. Fraser, N. W., T. M. Block, and J. G. Spivack. 1992. The latency-associated transcripts of herpes simplex virus: RNA in search of function. Virology 191:1-8.
18. Fraser, N. W., J. G. Spivack, Z. Wroblewska, T. Block, S. L. Deshmane, T. Valyi-Nagy, R. Natarajan, and R. Gesser. 1991. A review of the molecular mechanism of HSV-1 latency. Curr. Eye Res. 10(Suppl.):1-14.
19. Gaur, R. K., J. Valcarcel, and M. R. Green. 1995. Sequential recognition of the pre-mRNA branch point by U2AF65 and a novel spliceosome-associated 28-kDa protein. RNA 1:407-417.
20. Goguel, V., Y. Wang, and M. Rosbash. 1993. Short artificial hairpins sequester splicing signals and inhibit yeast pre-mRNA splicing. Mol. Cell. Biol. 13:6841-6848.
21. Hara, T., M. Ichihara, M. Takagi, and A. Miyajima. 1995. Interleukin-3 (IL-3) poor-responsive inbred mouse strains carry the identical deletion of a branch point in the IL-3 receptor alpha subunit gene. Blood 85:2331-2336.
22. Hill, J. M., F. Sederati, R. T. Javier, E. K. Wagner, and J. G. Stevens. 1990. Herpes simplex virus latent phase transcription facilitates in vivo reactivation. Virology 174:117-125.
23. Horton, R. M. 1993. In vitro recombination and mutagenesis of DNA, p. 251-261. In B. A. White (ed.), PCR protocols: current methods and applications. Humana Press Inc., Totowa, N.J.
24. Jacquier, A., and M. Rosbash. 1986. RNA splicing and intron turnover are greatly diminished by a mutant yeast branch point. Proc. Natl. Acad. Sci. USA 83:5835-5839.
25. Kuivenhoven, J. A., H. Weibusch, P. H. Pritchard, H. Funke, R. Benne, G. Assmann and J. J. P. Kastelein. 1996. An intronic mutation in a lariat branchpoint sequence is a direct cause of an inherited human disorder (fish-eye disease). J. Clin. Invest. 98:358-364.
26. Leib, D. A., C. L. Bogard, M. Kosz-Vnenchak, K. A. Hicks, D. M. Coen, D. M. Knipe and P. A. Schaffer. 1989. A deletion mutant of the latency-associated transcript of herpes simplex virus type 1 reactivates from the latent infection. J. Virol. 63:2893-2900.
27. McGeoch, D. J., C. Cunningham, G. McIntyre, and A. Dolan. 1991. Comparative sequence analysis of the long repeat regions and adjoining parts of the long unique regions in the genomes of herpes simplex viruses types 1 and 2. J Gen. Virol. 69:1531-1574.
28. McGeoch, D. J., M. A. Dalrymple, A. J. Davison, A. Dolan, M. C. Frame, D. McNab, L. J. Perry, J. E. Scott, and P. Taylor. 1988. The complete DNA sequence of the long unique region in the genome ot herpes simplex virus type 1. J. Gen. Virol. 69:1531-1574.
29. Mitchell, W. J., R. P. Lirette, and N. W. Fraser. 1990. Mapping of low abundance latency associated RNA in the trigeminal ganglia of mice latently infected with herpes simplex virus type 1. J. Gen. Virol. 71:125-132.
30. Moore, M. J., C. C. Query, and P. A. Sharp. 1993. Splicing of precursors to messenger RNAs by the spliceosome, p. 1-30. In R. F. Gesteland and J. F. Atkins (ed.), The RNA world. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
31. Nam, K., R. H. Hudson, K. B. Chapman, K. Ganeshan, M. J. Damha, and J. D. Boeke. 1994. Yeast lariat debranching enzyme. Substrate and sequence specificity. J. Biol. Chem. 269:20613-20621.
32. Norton, P. A. 1994. Polypyrimidine tract sequences direct selection of alternative branch sites and influence protein binding. Nucleic Acids Res. 22: 3854-3860.
33. Perng, G. C., H. Ghiasi, S. M. Slanina, A. B. Nesburn, and S. L. Wechsler. 1996. The spontaneous reactivation function of the herpes simplex virus type 1 LAT gene resides completely within the first 1.5 kilobases of the 8.3-kilobase primary transcript. J. Virol. 70:976-984.
34. Qian, L., M. N. Vu, M. Carter, and M. F. Wilkinson. 1992. A spliced intron accumulates as a lariat in the nucleus of T cells. Nucleic Acids Res. 20:5345-5350.
35. Query, C. C., S. A. Strobel, and P. A. Sharp. 1996. Three recognition events at the branch-site adenine. EMBO J. 15:1392-1402.
36. Ris-Stalpers, C., M. C. Verleun-Mooijman, T. J. P. d. Blaeij, H. J. Degenhart, J. Trapman, and A. O. Brinkmann. 1994. Differential splicing of human androgen receptor pre-mRNA in X-linked Reifenstein syndrome, because of a deletion involving a putative branch site. Am. J. Hum. Genet. 54:609-617.
37. Rodahl, E., and L. Haarr. 1997. Analysis of the 2-kilobase latency-associated transcript expressed in PC12 cells productively infected with herpes simplex virus type 1: evidence for a stable, nonlinear structure. J. Virol. 71:1703-1707.
38. Roizman, B., and A. E. Sears. 1987. An inquiry into the mechanisms of herpes simplex virus latency. Annu. Rev. Microbiol. 41:543-571.
39. Roscigno, R. F., M. Weiner, and M. A. Garcia-Blanco. 1993. A mutational analysis of the polypyrimidine tract of introns: effects of sequence differences in pyrimidine tracts on splicing. J. Biol. Chem. 268:11222-11229.
40. Saini, K. S., I. C. Summerhayes, and P. Thomas. 1990. Molecular events regulating messenger RNA stability in eukaryotes. Mol. Cell. Biochem. 96: 15-23.
41. Sawtell, N. M., and R. L. Thompson. 1992. Herpes simplex virus type 1 latency-associated transcription unit promotes anatomical site-dependent establishment and reactivation from latency. J. Virol. 66:2157-2169.
42. Schang, L. M., A. Hossain, and C. Jones. 1996. The latency-related gene of bovine herpesvirus 1 encodes a product which inhibits cell cycle progression. J. Virol. 70:3807-3814.
43. Solnick, D. 1985. Alternative splicing caused by RNA secondary structure. Cell 43:667-676.
44. Spivack, J. G., and N. W. Fraser. 1987. Detection of herpes simplex virus type 1 transcripts during latent infection in mice. J. Virol. 61:3841-3847.
45. Spivack, J. G., and N. W. Fraser. 1988. Expression of herpes simplex virus type 1 (HSV-1) latency-associated transcripts in the trigemina] ganglia of mice during acute infection and reactivation of latent infection. J. Virol. 62:1479-1485.
46. Spivack, J. G., and N. W. Fraser. 1988. Expression of herpes simplex virus type 1 (HSV-1) latency-associated transcripts and transcripts affected by the detection in the avirulent mutant HFEM: evidence for a new class of HSV-1 genes. J. Virol. 62:3281-3287.
47. Spivack, J. G., G. M. Woods, and N. W. Fraser. 1991. Identification of a novel latency-specific splice donor signal within the herpes simplex virus type 1 2.0 kb latency-associated transcript (LAT): translation inhibition of LAT open reading frames by the intron within the 2.0 kb LAT. J. Virol. 65:6800-6810.
48. Staffa, A., and A. Cochrane. 1994. The tat/rev intron of human immunodeficiency virus type 1 is inefficiently spliced because of suboptimal signals in the 3′ splice site. J. Virol. 68:3071-3079.
49. Steiner, I., J. G. Spivack, R. P. Lirette., S. M. Brown, A. R. MacLean, J. Subak-Sharpe, and N. W. Fraser. 1989. Herpes simplex virus type 1 latency-associated transcripts are evidently not essential for latent infection. EMBO J. 8:505-511.
50. Steiner, I., J. G. Spivack, D. R. O'Boyle, E. Lavi, and N. W. Fraser. 1988. Latent herpes simplex virus type 1 transcription in human trigeminal ganglia. J. Virol. 62:3493-3496.
51. Stevens, J. G. 1989. Human herpesviruses: a consideration of the latent state. Microbiol. Rev. 53:318-332.
52. Stevens, J. G., E. K. Wagner, G. B. Devi-Rao, M. L. Cook, and L. T. Feldman. 1987. RNA complementary to a herpes virus gene mRNA is prominent in latently infected neurons. Science 235:1056-1059.
53. Trousdale, M., I. Steiner, J. G. Spivack, S. L. Deshmane, S. M. Brown, A. S. MacLean, J. H. Subak-Sharpe, and N. W. Fraser. 1991. Evidence that the herpes simplex virus type 1 latency-associated transcripts play a role in reactivation of latent infection in vivo. J. Virol. 65:6989-6993.
54. Wagner, E. K., G. Devi-Rao, L. T. Feldman, A. T. Dobson, Y. F. Zhang, J. M. Hill, W. M. Flanagan, and J. G. Stevens. 1988. Physical characterization of the herpes simplex virus latency-associated transcript in neurons. J. Virol. 62:1194-1202.
55. Wagner, E. K., W. M. Flanagan, G. Devi-Rao, Y. F. Zhang, J. M. Hill, K. P. Anderson, and J. G. Stevens. 1988. The herpes simplex virus latency-associated transcript is spliced during the latent phase of infection. J. Virol. 62: 4577-4585.
56. Whitley, R. J. 1990. Herpes simplex viruses, p. 1843-1887. In B. N. Fields (ed.), Virology. Raven Press, New York, N.Y.
57. Wu, T. T., Y. H. Su, T. M. Block, and J. M. Taylor. 1996. Evidence that two latency-associated transcripts of herpes simplex virus type 1 are nonlinear. J. Virol. 70:5962-5967.
58. Zabolotny, J. M., C. Krummenacher, and N. W. Fraser. 1997. The herpes simplex virus type 1 2.0-kilobase latency-associated transcript is a stable intron which branches at a guanosine. J. Virol. 71:4199-4208.
59. Zwaagstra, J., H. Ghiasi, S. M. Slanina, A. B. Nesburn, S. C. Wheatley, K. Lillycrop, J. Wood, D. S. Latchman, K. Patel, and S. L. Wechsler. 1990. Activity of herpes simplex virus type 1 latency-associated transcript (LAT) promoter in neuron-derived cells: evidence for neuron specificity and for a large LAT transcript. J. Virol. 64:5019-5028.