Splicing speckles are not reservoirs of RNA polymerase II, but contain an inactive form, phosphorylated on serine2 residues of the C-terminal domain

Molecular Biology of the Cell

Volumn 17, Issue 4, 2006, Pages 1723-1733

  Xie, Sheila Q ^a   Martin, Sonya ^a,c   Guillot, Pascale V ^a   Bentley, David L ^b   Pombo, Ana ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; POLYADENYLIC ACID; RNA POLYMERASE II; SERINE; ANTIBODY; PHOSPHOSPECIFIC ANTIBODY; RNA;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CELL NUCLEUS; CHROMATIN STRUCTURE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME INHIBITION; FROZEN SECTION; GENE EXPRESSION; HELA CELL; HUMAN; HUMAN CELL; NUCLEOLUS; PRIORITY JOURNAL; PROTEIN DOMAIN; RNA SPLICING; SEQUENCE ANALYSIS; SPLICEOSOME; SPLICING SPECKLE; TRANSCRIPTION REGULATION; DRUG EFFECT; ENZYMOLOGY; GENETIC TRANSCRIPTION; GENETICS; IMMUNOLOGY; METABOLISM; PHOSPHORYLATION; PROTEIN TERTIARY STRUCTURE; ULTRASTRUCTURE;

ANTIBODIES; ANTIBODIES, PHOSPHO-SPECIFIC; CELL NUCLEUS STRUCTURES; HELA CELLS; HUMANS; PHOSPHORYLATION; PROTEIN STRUCTURE, TERTIARY; RNA; RNA POLYMERASE II; RNA SPLICING; SERINE; TRANSCRIPTION, GENETIC;

EID: 33646725833     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.E05-08-0726     Document Type: Article

References (64)

1. Bird, G., Zorio, D.A.R., and Bentley, D. L. (2004). RNA polymerase II carboxy-terminal domain phosphorylation is required for cotranscriptional pre-mRNA splicing and 3′-end formation. Mol. Cell. Biol. 24, 8963-8969.
2. 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.
3. Branco, M. R., Xie, S. Q., Martin, S., and Pombo, A. (2005). Correlative microscopy using Tokuyasu cryosections: applications for immunolabeling and in situ hybridization. In: Cell Imaging, ed. D. Stephens: Scion Publishing, 201-217.
4. Bregman, D. B., Du, L., Li, Y., Ribisi, S., and Warren, S. L. (1994). Cytostellin distributes to nuclear regions enriched with splicing factors. J. Cell Sci. 107, 387-396.
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. Carmo-Fonseca, M., Pepperkok, R., Carvalho, M. T., and Lamond, A. I. (1992). Transcription-dependent colocalization of the U1, U2, U4/U6, and U5 snRNPs in coiled bodies. J. Cell Biol. 117, 1-14.
7. Cho, E. J., Kobor, M. S., Kim, M., Greenblatt, J., and Buratowski, S. (2001). Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain. Genes Dev. 35, 3319-3329.
8. Clemson, C. M., and Lawrence, J. B. (1996). Multifunctional compartments in the nucleus: insights from DNA and RNA localization. J. Cell. Biochem. 62, 181-190.
9. Cmarko, D., Verschure, P. J., Martin, T. E., Dahmus, M. E., Krause, S., Fu, X. D., van Driel, R., and Fakan, S. (1999). Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection. Mol. Biol. Cell 10, 211-223.
10. Colwill, K., Pawson, T., Andrews, B., Prasad, J., Manley, J. L., Bell, J. C., and Duncan, P. I. (1996). The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution. EMBO J. 15, 265-275.
11. Doyle, O., Corden, J. L., Murphy, C., and Gall, J. G. (2002). The distribution of RNA polymerase II largest subunit (RPB1) in the Xenopus germinal vesicle. J. Struct. Biol. 140, 154-166.
12. Emili, A., Shales, M., McCracken, S., Xie, W., Tucker, P. W., Kobayashi, R., Blencowe, B. J., and Ingles, C. J. (2002). Splicing and transcription- associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD. RNA 8, 1102-1111.
13. Fay, F. S., Taneja, K. L., Shenoy, S., Lifshitz, L., and Singer, R. H. (1997). Quantitative digital analysis of diffuse and concentrated nuclear distributions of nascent transcripts, SC35 and poly(A). Exp. Cell Res. 231, 27-37.
14. Fox, A. H., Bond, C. S., and Lamond, A. I. (2005). P54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in a RNA-dependent manner. Mol. Biol. Cell 16, 4304-5315.
15. Fox, A. H., Lam, Y. W., Leung, A. K., Lyon, C. E., Andersen, J., Mann, M., and Lamond, A. I. (2002). Paraspeckles. A novel nuclear domain. Curr. Biol. 12, 13-25.
16. 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.
17. 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.
18. Gui, J. F., Lane, W. S., and Fu, X. D. (1994). A serine kinase regulates intracellular localization of splicing factors in the cell cycle. Nature 369, 678-682.
19. Guillot, P. V., Xie, S. Q., Hollinshead, M., and Pombo, A. (2004). Fixation-induced redistribution of hyperphosphorylated RNA polymerase II in the nucleus of human cells. Exp. Cell Res. 295, 460-468.
20. Handwerger, K. E., Cordero, J. A., and Gall, J. G. (2005). Cajal bodies, nucleoli, and speckles in the Xenopus oocyte nucleus have a low-density, sponge-like structure. Mol. Biol. Cell 16, 202-211.
21. Herrmann, C. H., and Mancini, M. A. (2001). The Cdk9 and cyclin T subunits of TAK/P-TEFb localize to splicing factor-rich nuclear speckle regions. J. Cell Sci. 114, 1491-1503.
22. Hirose, Y., Tacke, R., and Manley, J. L. (1999). Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev. 13, 1234-1239.
23. Iborra, F. J., Jackson, D. A., and Cook, P. R. (1998). The path of transcripts from extra-nucleolar synthetic sites to nuclear pores: transcripts in transit are concentrated in discrete structures containing SR proteins. J. Cell Sci. 111, 2269-2282.
24. 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.
25. Jackson, D. A., Iborra, F. J., Manders, E. M., and Cook, P. R. (1998). Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol. Biol. Cell 9, 1523-1536.
26. Johnson, C., Primorac, D., McKinstry, M., McNeil, J., Rowe, D., and Lawrence, J. B. (2000). Tracking COL1A1 RNA in osteogenesis imperfecta: splice-defective transcripts initiate transport from the gene but are retained within the SC35 domain. J. Cell Biol. 150, 417-432.
27. Jones, E., Kimura, H., Vigneron, M., Wang, Z., Roeder, R. G., and Cook, P. R. (2000). Isolation and characterization of monoclonal antibodies directed against subunits of human RNA polymerases I, II, and III. Exp. Cell Res. 254, 163-172.
28. Jones, J. C., Phatnani, H. P., Haystead, T. A., MacDonald, J. A., Alam, S. M., and Greenleaf, A. L. (2004). C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats. J. Biol. Chem. 279, 24957-24964.
29. Kameoka, S., Duque, P., and Konarska, M. M. (2004). p54(nrb) associates with the 5′ splice site within large transcription/splicing complexes. EMBO J. 23, 1782-1791.
30. Kimura, H., Sugaya, K., and Cook, P. R. (2002). The transcription cycle of RNA polymerase II in living cells. J. Cell Biol. 159, 777-782.
31. Kobor, M. S., and Greenblatt, J. (2002). Regulation of transcription elongation by phosphorylation. Biochim. Biophys. Acta 1577, 261-275.
32. Komarnitsky, P., Cho, E. J., and Buratowski, S. (2000). Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14, 2452-2460.
33. Kruhlak, M. J., Lever, M. A., Fischle, W., Verdin, E., Bazett-Jones, D. P., and Hendzel, M. J. (2000). Reduced mobility of the alternate splicing factor (ASF) through the nucleoplasm and steady state speckle compartments. J. Cell Biol. 150, 41-51.
34. Lamond, A. I., and Spector, D. L. (2003). Nuclear speckles: a model for nuclear organelles. Nat. Rev. Mol. Cell. Biol. 4, 605-612.
35. Lavoie, S. B., Albert, A. L., Thibodeau, A., and Vincent, M. (1999). Heat shock-induced alterations in phosphorylation of the largest subunit of RNA polymerase II as revealed by monoclonal antibodies CC-3 and MPM-2. Biochem. Cell Biol. 77, 367-374.
36. Licatalosi, D. D., Geiger, G., Minet, M., Schroeder, S., Cilli, K., McNeil, J. B., and Bentley, D. L. (2002). Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II. Mol. Cell 9, 1101-1111.
37. Maniatis, T., and Reed, R. (2002). An extensive network of coupling among gene expression machines. Nature 416, 499-506.
38. Mintz, P. J., Patterson, S. D., Neuwald, A. F., Spahr, C. S., and Spector, D. L. (1999). Purification and biochemical characterization of interchromatin granule clusters. EMBO J. 18, 4308-4320.
39. Mintz, P. J., and Spector, D. L. (2000). Compartmentalization of RNA processing factors within nuclear speckles. J. Struct. Biol. 129, 241-251.
40. Misteli, T., and Spector, D. L. (1999). RNA polymerase II targets pre-mRNA splicing factors to transcription sites in vivo. Mol. Cell 3, 697-705.
41. Moen, P. T., Jr., Johnson, C. V., Byron, M., Shopland, L. S., de la Serna, I. L., Imbalzano, A. N., and Lawrence, J. B. (2004). Repositioning of muscle-specific genes relative to the periphery of SC-35 domains during skeletal myogenesis. Mol. Biol. Cell 15, 197-206.
42. Molenaar, C., Abdulle, A., Gena, A., Tanke, H. J., and Dirks, R. W. (2004). Poly(A)+ RNAs roam the cell nucleus and pass through speckle domains in transcriptionally active and inactive cells. J. Cell Biol. 165, 191-202.
43. 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.
44. Myojin, R., Kuwahara, S., Yasaki, T., Matsunaga, T., Sakurai, T., Kimura, M., Uesugi, S., and Kurihara, Y. (2004). Expression and functional significance of mouse paraspeckle protein 1 on spermatogenesis. Biol. Reprod. 71, 926-932.
45. Neugebauer, K. M., and Roth, M. B. (1997). Distribution of pre-mRNA splicing factors at sites of RNA polymerase II transcription. Genes Dev. 11, 1148-1159.
46. Nguyen, V. T., Giannoni, F., Dubois, M. F., Seo, S. J., Vigneron, M., Kedinger, C., and Bensaude, O. (1996). In vivo degradation of RNA polymerase II largest subunit triggered by alpha-amanitin. Nucleic Acids Res. 24, 2924-2929.
47. Ospina, J. K., and Matera, A. G. (2002). Proteomics: the nucleolus weighs in. Curr. Biol. 12, R29-R31.
48. Patturajan, M., Schulte, R. J., Sefton, B. M., Berezney, R., Vincent, M., Bensaude, O., Warren, S. L., and Corden, J. L. (1998). Growth-related changes in phosphorylation of yeast RNA polymerase II. J. Biol. Chem. 273, 4689-4694.
49. Phair, R. D., and Misteli, T. (2000). High mobility of proteins in the mammalian cell nucleus. Nature 404, 604-609.
50. Pombo, A., Hollinshead, M., and Cook, P. R. (1999a). Bridging the resolution gap: imaging the same transcription factories in cryosections by light and electron microscopy. J. Histochem. Cytochem. 47, 471-480.
51. Pombo, A., Jackson, D. A., Hollinshead, M., Wang, Z., Roeder, R. G., and Cook, P. R. (1999b). Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J. 18, 2241-2253.
52. Puvion, E., and Puvion-Dutilleul, F. (1996). Ultrastructure of the nucleus in relation to transcription and splicing: roles of perichromatin fibrils and interchromatin granules. Exp. Cell Res. 229, 217-225.
53. Schroeder, S. C., Schwer, B., Shuman, S., and Bentley, D. (2000). Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 14, 2435-2440.
54. Schul, W., van Driel, R., and de Jong, L. (1998). Coiled bodies and U2 snRNA genes adjacent to coiled bodies are enriched in factors required for snRNA transcription. Mol. Biol. Cell 9, 1025-1036.
55. Shopland, L. S., Johnson, C. V., Byron, M., McNeil, J., and Lawrence, J. B. (2003). Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods. J. Cell Biol. 162, 981-990.
56. Shopland, L. S., Johnson, C. V., and Lawrence, J. B. (2002). Evidence that all SC-35 domains contain mRNAs and that transcripts can be structurally constrained within these domains. J. Struct. Biol. 140, 131-139.
57. Spector, D. L., O'Keefe, R. T., and Jimenez-Garcia, L. F. (1993). Dynamics of transcription and pre-mRNA splicing within the mammalian cell nucleus. Cold Spring Harb. Symp. Quant. Biol. 58, 799-805.
58. Sugaya, K., Vigneron, M., and Cook, P. R. (2000). Mammalian cell lines expressing functional RNA polymerase II tagged with the green fluorescent protein. J. Cell Sci. 113, 2679-2683.
59. Warren, S. L., Landolfi, A. S., Curtis, C., and Morrow, J. S. (1992). Cytostellin: a novel, highly conserved protein that undergoes continuous redistribution during the cell cycle. J. Cell Sci. 103, 381-388.
60. Wei, X., Somanathan, S., Samarabandu, J., and Berezney, R. (1999). Three-dimensional visualization of transcription sites and their association with splicing factor-rich nuclear speckles. J. Cell Biol. 146, 543-558.
61. Xie, S. Q., and Pombo, A. (2005). Distribution of different phosphorylated forms of RNA polymerase II in relation to Cajal and PML bodies in human cells: an ultrastructural study. Histochem. Cell. Biol. 125, 21-31.
62. Zeng, C., and Berget, S. M. (2000). Participation of the C-terminal domain of RNA polymerase II in exon definition during pre-mRNA splicing. Mol. Cell. Biol. 20, 8290-8301.
63. 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.
64. Zorio, D. A., and Bentley, D. L. (2004). The link between mRNA processing and transcription: communication works both ways. Exp. Cell Res. 296, 91-97.