Polypyrimidine tract binding protein modulates efficiency of polyadenylation

Molecular and Cellular Biology

Volumn 24, Issue 10, 2004, Pages 4174-4183

  Castelo Branco, Pedro ^a,c   Furger, Andre ^a,b   Wollerton, Matthew ^d   Smith, Christopher ^d   Moreira, Alexandra ^c   Proudfoot, Nick ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d UNIVERSITY OF PORTO   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; POLYPYRIMIDINE TRACT BINDING PROTEIN; DNA; GLOBIN; RECOMBINANT PROTEIN;

ARTICLE; CONTROLLED STUDY; DNA FLANKING REGION; GENE OVEREXPRESSION; GENE SEQUENCE; GENETIC COMPLEMENTATION; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; IN VITRO STUDY; INTRON; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN METABOLISM; RNA CLEAVAGE; RNA INTERFERENCE; RNA METABOLISM; RNA PROCESSING; SIGNAL TRANSDUCTION; GENETICS; HELA CELL; METABOLISM; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; DNA; GLOBINS; HELA CELLS; HUMANS; POLYADENYLATION; POLYPYRIMIDINE TRACT-BINDING PROTEIN; RECOMBINANT PROTEINS; RNA INTERFERENCE; RNA, MESSENGER;

EID: 2942629589     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.24.10.4174-4183.2004     Document Type: Article

References (64)

1. Ashe, H. L., J. Monks, M. Wijgerde, P. Fraser, and N. J. Proudfoot. 1997. Intergenic transcription and trans-induction of the human β-globin locus. Genes Dev. 11:2494-2509.
2. Ashe, M. P., P. Griffin, W. James, and N. J. Proudfoot. 1995. Poly(A) site selection in the HIV-1 provirus: inhibition of promoter-proximal polyadenylation by the downstream major splice donor site. Genes Dev. 9:3008-3025.
3. Ashe, M. P., A. Furger, and N. J. Proudfoot. 2000. Poly(A) site occlusion in the 5′LTR of the HIV-1 provirus principally depends on the close proximity of U1 snRNP, stem loop 1. RNA 6:170-177.
4. Black, D. L. 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72:291-336.
5. Brackenridge, S., and N. J. Proudfoot. 2000. Recruitment of a basal polyadenylation factor by the upstream sequence element of the human lamin B2 polyadenylation signal. Mol. Cell. Biol. 20:2660-2669.
6. Brown, P. H., L. S. Tiley, and B. R. Cullen. 1991. Efficient polyadenylation within the human immunodeficiency virus type 1 long terminal repeat requires flanking U3-specific sequences. J. Virol. 65:3340-3343.
7. Burge, C. B., T. Tuschl, and P. A. Sharp. 1999. Splicing of precursors to mRNAs by the spliceosomes. In R. F. Gesteland, T. R. Cech, and J. F. Atkins (ed.), The RNA world, p. 525-560. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
8. Carswell, S., and J. C. Alwine. 1989. Efficiency of utilization of the simian virus 40 late polyadenylation site: effects of upstream sequences. Mol. Cell. Biol. 9:4248-4258.
9. Cherrington, J., and D. Ganem. 1992. Regulation of polyadenylation in HIV: contributions of promoter proximity and upstream sequences. EMBO J. 11:1513-1542.
10. Colgan, D., and J. L. Manley. 1997. Mechanism and regulation of mRNA polyadenylation. Genes Dev. 11:2755-2766.
11. Chou, M.-Y., J. G. Underwood, J. Nikolic, M. H. T. Luu, and D. L. Black. 2000. Multisite RNA binding and release of polypyrimidine tract binding protein during the regulation of c-src neural-specific splicing. Mol. Cell 5:949-950.
12. Davis, L., M. Kuehl, and J. Battey. 1994. Basic methods in molecular biology. Appleton & Lange, Norwalk, Conn.
13. DeZazzo, J. D., J. E. Kilpatrick, and M. J. Imperiale. 1991. Involvement of long terminal repeat U3 sequences overlapping the transcription control region in human immunodeficiency virus type 1 mRNA 3′ end formation. Mol. Cell. Biol. 11:1624-1630.
14. Dye, M. J., and N. J. Proudfoot. 1999. Terminal exon definition occurs cotranscriptionally and promotes termination of RNA polymerase II. Mol. Cell 3:371-378.
15. Eggermont, J., and N. J. Proudfoot. 1993. Poly(A) signals and transcriptional pause sites combine to prevent interference between RNA polymerase II promoters. EMBO J. 12:2539-2548.
16. Elbashir, S. M., J. Harborth, W. Lendeckel, A. Yalcin, K. Weber, and T. Tuschl. 2001. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411:494-498.
17. Enriquez-Harris, P., N. Levitt, D. Briggs, and N. J. Proudfoot. 1991. A pause site for RNA polymerase II is associated with termination of transcription. EMBO J. 10:1833-1842.
18. Furger, A., J. Monks, and N. J. Proudfoot. 2001. The retroviruses human immunodeficiency virus type 1 and Moloney murine leukemia virus adopt radically different strategies to regulate promoter-proximal polyadenylation. J. Virol. 75:11735-11746.
19. Furger, A., J. M. O'Sullivan, A. Binnie, B. A. Lee, and N. J. Proudfoot. 2002. Promoter proximal splice sites enhance transcription. Genes Dev. 16:2792-2799.
20. Garcia-Blanco, M. A., S. F. Jamison, and P. A. Sharp. 1989. Identification and purification of a 62,000-dalton protein that binds specifically to the polypyrimidine tract of introns. Genes Dev. 3:1874-1886.
21. Gehring, N. H., U. Frede, G. Neu-Yilik, P. Hundsdoerfer, B. Vetter, M. W. Hentze, and A. E. Kulozik. 2001. Increased efficiency of mRNA 3′ end formation: a new genetic mechanism contributing to hereditary thrombophilia. Nat. Genet. 28:389-392.
22. Ghetti, A., S. Pinol-Roma, W. M. Michael, C. Morandi, and G. Dreyfuss. 1992. HnRNP I, the polypyrimidine tract binding protein: distinct nuclear localization and association with hnRNAs. Nucleic Acids Res. 20:3671-3678.
23. Gil, A., P. A. Sharp, S. F. Jamison, and M. A. Garcia-Blanco. 1991. Characterization of cDNAs encoding the polypyrimidine tract-binding protein. Genes Dev. 5:1224-1236.
24. Gilmartin, G. M., E. S. Fleming, and J. Oetjen. 1992. Activation of HIV-1 pre-mRNA 3′ processing in vitro requires both an upstream element and TAR. EMBO J. 11:4419-4428.
25. Gilmartin, G. M., and J. R. Nevins. 1991. Molecular analyses of two poly(A) site-processing factors that determine the recognition and efficiency of cleavage of the pre-mRNA. Mol. Cell. Biol. 11:2432-2438.
26. Gosert, R., K. H. Chang, R. Rijnbrand, M. Yi, D. V. Sangar, and S. M. Lemon. 2000. Transient expression of cellular polypyrimidine-tract binding protein stimulates cap-independent translation directed by both picornaviral and flaviviral internal ribosome entry sites in vivo. Mol. Cell. Biol. 20:1583-1595.
27. Hannon, G. J. 2002. RNA interference. Nature 418:244-251.
28. Lin, C. H., and J. G. Patton. 1995. Regulation of alternative 3′ splice site selection by constitutive splicing factors. RNA 1:234-245.
29. Lou, H., D. M. Helfman, R. F. Gagel, and S. M. Berget. 1999. Polypyrimidine tract binding protein positively regulates inclusion of an alternative 3′ terminal exon. Mol. Cell. Biol. 19:78-85.
30. Maniatis, T., E. F. Fritsch, and J. Sambrook. 1982. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
31. Markovtsov, V., J. M. Nikolic, J. A. Goldman, C. W. Turck, M. Y. Chou, and D. L. Black. 2000. Cooperative assembly of an hnRNP complex induced by a tissue-specific homolog of polypyrimidine tract binding protein. Mol. Cell. Biol. 20:7463-7479.
32. Millevoi, S., F. Geraghty, B. Idowu, J. L. Y. Tam, M. Antoniou, and S. Vagner. 2002. A novel function for the U2AF65 splicing factor in promoting pre-mRNA 3′-end processing. EMBO Rep. 3:869-874.
33. Mitchell, S. A., K. A. Spriggs, M. J. Coldwell, R. J. Jackson, and A. E. Willis. 2003. The Apaf-1 internal ribosome entry segment attains the correct structural conformation for function via interactions with PTB and unr. Mol. Cell 11:757-771.
34. Moore, M. J. 2000. Intron recognition comes of age. Nat. Struct. Biol. 7:14-16.
35. Moore, M. J. 2002. Nuclear RNA turnover. Cell 108:431-434.
36. Moreira, A., Y. Takagaki, S. Brackenridge, M. Wollerton, J. L. Manley, and N. J. Proudfoot. 1998. The upstream sequence element of the C2 complement poly(A) signal activates mRNA 3′ end formation by two distinct mechanisms. Genes Dev. 12:2522-2534.
37. Moreira, A., M. Wollerton, J. Monks, and N. J. Proudfoot. 1995. Upstream sequence elements enhance poly(A) site efficiency of the C2 complement gene and are phylogenetically conserved. EMBO J. 14:3809-3819.
38. Niwa, M., C. C. MacDonald, and S. M. Berget. 1992. Are vertebrate exons scanned during splice site selection? Nature 360:277-280.
39. Niwa, M., S. D. Rose, and S. M. Berget. 1990. In vitro polyadenylation is stimulated by the presence of an upstream intron. Genes Dev. 4:1552-1559.
40. Patton, J. G., S. A. Mayer, P. Tempst, and B. Nadal Ginard. 1991. Characterization and molecular cloning of polypyrimidine tract-binding protein: a component of a complex necessary for pre-mRNA splicing. Genes Dev. 5:1237-1251.
41. Perez, I., C. H. Lin, J. G. McAfee, and J. G. Patton. 1997. Mutation of PTB binding sites causes misregulation of alternative 3′ splice site selection in vivo. RNA 3:764-778.
42. Perez, I., J. G. McAfee, and J. G. Patton. 1997. Multiple RRMs contribute to RNA binding specificity and affinity for polypyrimidine tract binding protein. Biochemistry 36:11881-11890.
43. Plant, K. E., S. J. Routledge, and N. J. Proudfoot, N. J. 2001. Intergenic transcription in the human beta-globin gene cluster. Mol. Cell. Biol. 21: 6507-6514.
44. Proudfoot, N. J. 1991. Poly(A) signals. Cell 64:671-674.
45. Proudfoot, N. J. 1996. Ending the message is not so simple. Cell 87:779-781.
46. Proudfoot, N. J. 2001. Genetic dangers in poly(A) signals. EMBO Rep. 2:891-892.
47. Reed, R., and E. Hurt. 2002. A conserved mRNA export machinery coupled to pre-mRNA splicing. Cell 22:523-531.
48. Robida, M. D., and R. Singh. 2003. Drosophila polypyrimidine-tract binding protein (PTB) functions specifically in the male germ line. EMBO J. 22:2924-2933.
49. Ruskin, B., and M. R. Green. 1985. Role of the 3′ splice site consensus sequence in mammalian pre-mRNA splicing. Nature 317:732-734.
50. Singh, R., J. Valcarcel, and M. R. Green. 1995. Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins. Science 268:1173-1176.
51. Smith, C. W., and J. Valcarcel. 2000. Alternative pre-mRNA splicing: the logic of combinatorial control. Trends Biochem. Sci. 25:381-388.
52. Takagaki, Y., and J. Manley. 1997. RNA recognition by the human polyadenylation factor CstF. Mol. Cell. Biol. 17:3907-3914.
53. Takagaki, Y., J. L. Manley, C. C. MacDonald, J. Wilusz, and T. A. Shenk. 1990. A multisubunit factor, CstF, is required for polyadenylation of mammalian pre-mRNAs. Genes Dev. 4:2112-2120.
54. Vagner, S., C. Vagner, and I. W. Mattaj. 2000. The carboxyl terminus of vertebrate poly(A) polymerase interacts with U2AF 65 to couple 3′-end processing and splicing. Genes Dev. 14:403-413.
55. Valcarcel, J., and F. Gebauer. 1997. Post-transcription regulation: the dawn of PTB. Curr. Biol. 7:705-708.
56. Valsamakis, A., S. Zeichner, S. Carswell, and J. C. Alwine. 1991. The human immunodeficiency virus type 1 polyadenylation signal: a 3′ long terminal repeat element upstream of the AAUAAA necessary for efficient polyadenylation. Proc. Natl. Acad. Sci. USA 88:2108-2112.
57. Wagner, E. J., and M. A. Garcia-Blanco. 2001. Polypyrimidine tract binding protein antagonizes exon definition. Mol. Cell. Biol. 10:3281-3288.
58. Wagner, E. J., and M. A. Garcia-Blanco. 2002. RNAi-mediated PTB depletion leads to enhanced exon definition. Mol. Cell 10:943-949.
59. Wilusz, C. J., W. Wang, and S. W. Peltz. 2001. Curbing the nonsense: the activation and regulation of mRNA surveillance. Genes Dev. 15:2781-2785.
60. Wilusz, J., and T. Shenk. 1988. A 64 kd nuclear protein binds to RNA segments that include the AAUAAA polyadenylation motif. Cell 52:221-228.
61. Wollerton, M. C., C. Gooding, F. Robinson, E. C. Brown, R. J. Jackson, and C. W. J. Smith. 2001. Differential alternative splicing activity of isoforms of polypyrimidine tract binding protein (PTB). RNA 7:819-832.
62. Wollerton, M. C., C. Gooding, E. J. Wagner, M. A. Garcia-Blanco, and C. W. J. Smith. 2004. Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. Mol. Cell 13:91-100.
63. Zamore, P. D., J. G. Patton, and M. R. Green. 1992. Cloning and domain structure of the mammalian splicing factor U2AF. Nature 355:609-614.
64. Zhao, J., L. Hyman, and C. Moore. 1999. Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev. 63:405-445.