RNA polymerase II targets pre-mRNA splicing factors to transcription sites in vivo

Molecular Cell

Volumn 3, Issue 6, 1999, Pages 697-705

  Misteli, Tom ^a   Spector, David L ^b  

^a NATIONAL CANCER INSTITUTE   (United States)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RNA POLYMERASE II;

ARTICLE; CARBOXY TERMINAL SEQUENCE; EXON; GENE MAPPING; GENE TARGETING; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; IN SITU HYBRIDIZATION; INTRON; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; RNA SPLICING; WESTERN BLOTTING;

EID: 0033153543     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(01)80002-2     Document Type: Article

References (67)

1. Bartolomei, M.S., and Corden, J.L. (1987). Localization of an alphaamanitin resistance mutation in the gene encoding the largest subunit of mouse RNA polymerase II. Mol. Cell. Biol. 7, 586-594.
2. Báuren, G., and Wieslander, L. (1994). Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell 76, 183-192.
3. Beyer, A.L., and Osheim, Y.N. (1988). Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes Dev. 2, 754-765.
4. Bisotto, S., Lauriault, P., Duval, M., and Vincent, M. (1995). Colocalization of a high molecular mass phosphoprotein of the nuclear matrix (p255) with spliceosomes. J. Cell Sci. 108, 1873-1882.
5. Bregman, D.B., Du, L., van der Zee, S., and Warren, S.L. (1995). Transcription-dependent redistribution of the large subunit of RNA polymerase II to discrete nuclear domains. J. Cell Biol. 129, 287-298.
6. Cáceres, J.F., and Krainer, A.R. (1993). Functional analysis of pre-mRNA splicing factor SF2/ASF structural domains. EMBO J. 12, 4715-472 6.
7. Cáceres, J.F., Misteli, T., Screaton, G., Spector, D.L., and Krainer, A.R. (1997). Role of the modular domains of SR-proteins in subnuclear localization and alternative splicing specificity. J. Cell Biol. 138, 225-238.
8. Cáceres, J.F., Screaton, G.R., and Krainer, A.R. (1998). A specific subset of SR proteins shuttles continuously between the nucleus and the cytoplasm. Genes Dev. 12, 55-66.
9. Cho, E.-J., Takagi, T., Moore, C.R., and Buratowski, S. (1997). mRna capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev. 11, 3319-3326.
10. Colot, H.V., Stutz, F., and Rosbash, M. (1996). The yeast splicing factor Mud13p is a commitment complex component and corresponds to CBP20, the small subunit of the nuclear cap-binding complex. Genes Dev. 10, 1699-1708.
11. Corden, J.L., and Ingles, C.J.(1992). Carboxy-terminal domain of the largest subunit of eukaryotic RNA polymerase II. In Transcriptional Regulation, S.L. McKnight and K.R. Yamamoto, eds. (Plainview, NY: Cold Spring Harbor Press), pp. 81-108.
12. Corden, J.L., and Patturajan, M. (1997). A CTD function linking transcription to splicing. Trends Biochem. Sci. 22, 413-416.
13. Dahmus, M.E. (1996). Reversible phosphorylation of the C-terminal domain of RNA polymerase II. J. Biol. Chem. 27, 19009-19012.
14. Dirks, R.W., de Pauw, E.S.D., and Raap, A.K. (1997). Splicing factors associate with nuclear HCMV-IE transcripts after transcriptional activation of the gene, but dissociate upon transcription inhibition: Evidence for a dynamic organization of splicing factors. J. Cell Sci. 110, 505-51 3.
15. Du, L., and Warren, S.L. (1997). A functional interaction between the carboxy-terminal domain of RNA polymerase II and pre-mRNA splicing. J. Cell Biol. 136, 5-18.
16. Dubois, M.F., Nguyen, V.T., Bellier, S., and Bensaude, O. (1994). Inhibitors of transcription such as 5,6-dichloro-1-beta-D- ribofuranosylbenzimidazole and isoquinoline sulfonamide derivatives (H-8 and H-7) promote dephosphorylation of the carboxyl-terminal domain of RNA polymerase II largest subunit. J. Biol. Chem. 269, 13331-13336.
17. Fakan, S. (1994). Perichromatin fibrils are in situ forms of nascent transcripts. Trends Cell Biol. 4, 86-90.
18. Fresco, L.D., and Buratowski, S. (1996). Conditional mutants of the yeast mRNA capping enzyme show that the cap enhances, but is not required for, mRNA splicing. RNA 2, 584-596.
19. Fu, X.-D. (1995). The superfamily of arginine/serine-rich splicing factors. RNA 1, 663-680.
20. Fu, X.-D., and Maniatis, T. (1990). Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus. Nature 343, 437-441.
21. Gerber, H.-P., Hagman, M., Seipel, K., Georgiev, O., West, M.A.L., Litingtung, Y., Schaffner, W., and Corden, J.L. (1995). RNA polymerase II C-terminal domain required for enhancer-driven transcription. Nature 374, 660-662.
22. Grande, M.A., van der Kraan, I., de Jong, L., and van Driel, R. (1997). Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. J. Cell Sci. 110, 1781-1791.
23. Green, M.R., Maniatis, T., and Melton, D.A. (1983). Human betaglobin pre-mRNA synthesized in vitro is accurately spliced in Xenopus oocyte nuclei. Cell 32, 681-694.
24. Greenleaf, A.L. (1993). Positive patches and negative noodles: Linking RNA processing to transcription? Trends Biochem. Sci. 18, 117-119.
25. Habets, W.J., Hoet, M.H., DeJong, B.A.W., VanDer Kemp, A., and Van Venrooij, W.J. (1986). Mapping of B cell epitopes on small nuclear ribonucleoproteins that react with human autoantibodies as well as with experimentally induced mouse monoclonal antibodies. J. Immunol. 143, 2560-2566.
26. Hendzel, M.J., Kruhlak, M.J., and Bazett-Jones, D.P. (1998). Organization of highly acetylated chromatin around sites of heterogeneous nuclear RNA accumulation. Mol. Biol. Cell 9, 2491-2507.
27. Hirose, Y., and Manley, J.L. (1998). RNA polymerase II is an essential mRNA polyadenylation factor. Nature 395, 93-96.
28. Huang, S., and Spector, D.L. (1991). Nascent pre-mRNA transcripts are associated with nuclear regions enriched in splicing factors. Genes Dev. 5, 2288-230 2.
29. Huang, S., and Spector, D.L. (1996). Intron-dependent recruitment of pre-mRNA splicing factors to sites of transcription. J. Cell Biol. 131, 719-732.
30. Iborra, F.J., Pombo, A., Jackson, D.A., and Cook, P.R. (1996). Active RNA polymerases are localized within discrete transcription 'factories' in human nuclei. J. Cell Sci. 109, 1427-1436.
31. Inoue, K., Ohno, M., Sakamoto, H., and Shimura, Y. (1989). Effect of the cap structure on pre-mRNA splicing in Xenopus oocyte nuclei. Genes Dev. 3, 1472-1479.
32. Izaurralde, E., Lewis, J., McGuigan, C., Jankowska, M., Darzynkiewicz, E., and Mattaj, I.W. (1994). A nuclear cap binding protein complex involved in pre-mRNA splicing. Cell 78, 657-668.
33. Jackson, D.A., Hassan, A.B., Errington, R.J., and Cook, P.R. (1993). Visualization of focal sites of transcription within human nuclei. EMBO J. 12, 1059-1065.
34. Kadonaga, J.T. (1998). Eukaryotic transcription: An interlaced network of transcription factors and chromatin-modifying machines. Cell 92, 307-313.
35. Kim, E., Du, L., Bregman, D.B., and Warren, S.L. (1997). Splicing factors associate with hyperphosphorylated RNA polymerase II in the absence of pre-mRNA. J. Cell Biol. 136, 19-28.
36. Krainer, A.R. (1988). Pre-mRNA splicing by complementation with purified human U1, U2, U4/U6 and U5 snRNPs. Nucleic Acids Res. 16, 9415-9429.
37. Lamond, A.I., and Earnshaw, W.C. (1998). Structure and function in the nucleus. Science 280, 547-553.
38. Langer, P.R., Waldrop, A.A., and Ward, D.C. (1981). Enzymatic synthesis of biotin labeled polynucleotides: Novel nucleic acid affinity probes. Proc. Natl. Acad. Sci. USA 78, 6633-6637.
39. Lewis, J.D., Gorlich, D., and Mattaj, I.W. (1996). A yeast cap binding protein complex (yCBC) acts at an early step in pre-mRNA splicing. Nucleic Acids Res. 24, 3332-3336.
40. Maiti, S., Doskow, J., Li, S., Nhim, R.P., Lindsey, J.S., and Wilkinson, M.F. (1996). The Pem homeobox gene. Androgen-dependent and -independent promoters and tissue-specific alternative RNA splicing. J. Biol. Chem. 271, 17536-17546.
41. Manley, J.L., and Tacke, R. (1996). SR proteins and splicing control. Genes Dev. 10, 1569-1579.
42. McCracken, S., Fong, N., Rosonina, E., Yankulov, K., Brothers, G., Siderovski, D., Hessel, A., Foster, S., Shuman, S., and Bentley, D.L. (1997a). 5′-Capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II. Genes Dev. 11, 3306-3318.
43. McCracken, S., Fong, N., Yankulov, K., Ballantyne, S., Pan, G., Greenblatt, J., Patterson, S.D., Wickens, M., and Bentley, D.L. (1997b). The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385, 357-361.
44. Misteli, T., and Spector, D.L. (1996). Serine/threonine phosphatase 1 modulates the subnuclear distribution of pre-mRNA splicing factors. Mol. Biol. Cell 7, 1559-1572.
45. Misteli, T., Cáceres, J.F., and Spector, D.L. (1997). The dynamics of a pre-mRNA splicing factor in living cells. Nature 387, 523-527.
46. Misteli, T., Caceres, J.F., Clement, J.Q., Krainer, A.R., Wilkinson, M.F., and Spector, D.L. (1998). Serine phosphorylation of SR proteins is required for their recruitment to sites of transcription in vivo. J. Cell Biol. 143, 297-307.
47. Misteli, T., and Spector, D.L. (1998). The cellular organization of gene expression. Curr. Opin. Cell Biol. 10, 322-331.
48. Mortillaro, M.J., Blencowe, B.J., Wei, X., Nakayasu, H., Du, L., Warren, S.L., Sharp, P.A., and Berezney, R. (1996). A hyperphosphorylated form of the large subunit of RNA polymerase II is associated with splicing complexes and the nuclear matrix. Proc. Natl. Acad. Sci. USA 93, 8253-8257.
49. Neugebauer, K.M., and Roth, M.B. (1997). Transcription units as RNA processing units. Genes Dev. 11, 3279-3285.
50. Ohno, M., and Shimura, Y. (1996). A human RNA helicase-like protein, HRH1, facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. Genes Dev. 10, 997-1007.
51. Patturajan, M., Wei, X., Berezney, R., and Corden, J.L. (1998). A nuclear matrix protein interacts with the phosphorylated C-terminal domain of RNA polymerase II. Mol. Cell. Biol. 18, 2406-2415.
52. Schwer, B., and Shuman, S. (1996). Conditional inactivation of mRNA capping enzyme affects yeast pre-mRNA splicing in vivo. RNA 2, 574-583.
53. Schwer, B., Mao, X., and Shuman, S. (1998). Accelerated mRNA decay in conditional mutants of yeast mRNA capping enzyme. NuCleic Acids Res. 26, 2050-2057.
54. Shuman, S. (1997). Origins of mRNA identity: Capping enzymes bind to the phosphorylated C-terminal domain of RNA polymerase II. Proc. Natl. Acad. Sci. USA 94, 12758-12760.
55. Snaar, S.P., Vincent, M., and Dirks, R.W. (1999). RNA polymerase II localizes at sites of human cytomegalovirus immediate-early RNA synthesis and processing. J. Hist. Cytochem. 47, 245-254.
56. Spector, D.L., Goldman, R.D., and Leinwand, L.A. (1998). Cells: A Laboratory Manual (Plainview, NY: Cold Spring Harbor Press), pp. 105.1-105. 4.
57. Steinmetz, E.J. (1997). Pre-mRNA processing and the CTD of RNA polymerase II: The tail that wags the dog? Cell 89, 491-494.
58. Vincent, M., Lauriault, P., Dubois, M.F., Lavoie, S., Bensaude, O., and Chabot, B. (1996). The nuclear matrix protein p255 is a highly phosphorylated form of RNA polymerase II largest subunit which associates with spliceosomes. Nucleic Acids Res. 24, 4649-4652.
59. Wansink, D.G., Schul, W., van der Kraan, I., van Steensel, B., van Driel, R., and de Jong, L. (1993). Fluorescent labelling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J. Cell Biol. 122, 282-293.
60. Wu, J., and Maniatis, T. (1993). Specific interactions between proteins implicated in splice site selection and regulated alternative splicing. Cell 75, 1061-107 0.
61. Xing, Y., Johnson, C.V., Moen, P.T., McNeil, J.A., and Lawrence, J.B. (1995). Nonrandom gene organization: Structural arrangements of specific pre-mRNA transcription and splicing with SC-35 domains. J. Cell Biol. 131, 1635-1647.
62. Yankulov, K., Yamashita, K., Roy, R., Egly, J.M., and Bentley, D.L. (1995). The transcriptional elongation inhibitor 5,6-dichloro-1-beta-D- ribofuranosylbenzimidazole inhibits transcription factor IIH-associated protein kinase. J. Biol. Chem. 270, 23922-23925.
63. Yankulov, K.Y., Pandes, M., McCracken, S., Bouchard, D., and Bentley, D.L. (1996). TFIIH functions in regulating transcriptional elongation by RNA polymerase II in Xenopus oocytes. Mol. Cell. Biol. 16, 3291-3299.
64. Yue, Z., Maldonado, E., Pillutla, R., Cho, H., Reinberg, D., and Shatkin, A.J. (1997). Mammalian capping enzyme complements mutant saccharomyces cerevisiae lacking mRNA guanylyltransferase and selectively binds the elongating form of RNA polymerase II. Proc. Natl. Acad. Sci. USA 94, 12898-12903.
65. Yuryev, A., Patturajan, M., Litingtung, Y., Joshi, R.V., Gentile, C., Gebara, M., and Corden, J.L. (1996). The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc. Natl. Acad. Sci. USA 93, 6975-6980.
66. Zeng, C., Kim, E., Warren, S.L., and Berget, S.M. (1997). Dynamic relocation of transcription and splicing factors dependent upon transcriptional activity. EMBO J. 16, 1401-1412.
67. Zhang, G., Taneja, K.L., Singer, R.H., and Green, M.R. (1994). Localization of pre-mRNA splicing in mammalian nuclei. Nature 372, 809-812.