Distribution of pre-mRNA splicing factors at sites of RNA polymerase II transcription

Genes and Development

Volumn 11, Issue 9, 1997, Pages 1148-1159

  Neugebauer, Karla M ^a,b   Roth, Mark B ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

nuclear organization; Pre mRNA splicing; RNA polymerase II; SR proteins

Indexed keywords

MESSENGER RNA PRECURSOR; RNA POLYMERASE II;

ARTICLE; CONTROLLED STUDY; HELA CELL; HUMAN; HUMAN CELL; MESSENGER RNA SYNTHESIS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; RNA SPLICING; TRANSCRIPTION REGULATION;

EID: 0030959371     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.11.9.1148     Document Type: Article

References (57)

1. Alzhanova-Ericsson, A.T., X. Sun, N. Visa, E. Kiseleva, T. Wurtz, and B. Daneholt. 1996. A protein of the SR family of splicing factors binds extensively to exonic Balbiani ring pre-mRNA and accompanies the RNA from the gene to the nuclear pore. Genes & Dev. 10: 2881-2893.
2. Amero, S.A., G. Raychaudhuri, C.L. Cass, W.J. van Venrooij, W.J. Habets, A.R. Krainer, and A.L. Beyer. 1992. Independent deposition of heterogeneous nuclear ribonucleoproteins and small nuclear ribonucleoprotein particles at sites of transcription. Proc. Natl. Acad. Sci. 89: 8409-8413.
3. Ayane, M., U. Preuss, G. Kohler, and P.J. Nielson. 1991. A differentially expressed murine RNA encoding a protein with similarities to two types of nucleic acid binding motifs. Nucleic Acids Res. 19: 1273-1278.
4. Bauren, G., W.-Q. Jiang, K. Bernholm, F. Gu, and L. Wieslander. 1996. Demonstration of a dynamic, transcription-dependent organization of pre-mRNA splicing factors in polytene nuclei. J. Cell Biol. 133: 929-941.
5. Black, D.L. 1995. Finding splice sites within a wilderness of RNA. RNA 1: 763-771.
6. Bridge, E., D.-X. Xia, M. Carmo-Fonseca, B. Cardinali, A.I. Lamond, and U. Pettersson. 1995. Dynamic organization of splicing factors in adenovirus-infected cells. J. Virol. 69: 281-290.
7. Caceres, J.F., S. Stamm, D.M. Helfman, and A.R. Krainer. 1994. Regulation of alternative splicing in vivo by over expression of antagonistic splicing factors. Science 265: 1706-1709.
8. Carmo-Fonseca, M., D. Tollervey, R. Pepperkok, S.M.L. Barabino, A. Merdes, C. Brunner, P.D. Zamore, M.R. Green, E. Hurt, and A.I. Lamond. 1991. Mammalian nuclei contain foci which are highly enriched in components of the pre-mRNA splicing machinery. EMBO J. 10: 195-206.
9. Carmo-Fonseca, M., R. Pepperkok, M.T. Carvalho, and A.I. Lamond. 1992 Transcription-dependent colocalization of the U1, U2, U4/U6, and US snRNPs in coiled bodies. J. Cell Biol. 117: 1-14.
10. Carrington, W.A., R.M. Lynch, E.D.W. Moore, G. Isenberg, K.E. Fogarty, and F.S. Fay. 1995. Superresolution three-dimensional images of fluorescence in cells with minimal light exposure. Science 268: 1483-1487.
11. Champlin, D.T., M. Frasch, H. Saumweber, and J.T. Lis. 1991. Characterization of a Drosophila protein associated with boundaries of transcriptionally active chromatin. Genes & Dev. 5: 1611-1621.
12. Darnell, J.E. 1982. Variety in the level of gene control in eucaryotic cells. Nature 297: 365-371.
13. Fakan, S. 1994. Perichromatin fibrils are in situ forms of nascent transcripts. Trends Cell Biol. 4: 86-90.
14. Fakan, S., G. Leser, and T.E. Martin. 1984. Ultrastructural distribution of nuclear ribonucleoproteins as visualized by immunocytochemistry on thin sections. J. Cell Biol. 98: 358-363.
15. Fu, X.-D. 1993. Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature 365: 82-85.
16. Fu, X.-D. and T. Maniatis. 1990. Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus. Nature 343: 437-441.
17. Harlow, E. and D. Lane. 1988. Antibodies: A laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
18. Heinrichs, V. and B.S. Baker. 1995. The Drosophila SR protein RBP1 contributes to the regulation of doublesex alternative splicing by recognizing RBP1 RNA target sequences. EMBO J. 14: 3987-4000.
19. Hiraoka, Y., J.R. Swedlow, M.R. Paddy, D.A. Agard, and J.W. Sedat. 1991. Three dimensional multiple-wavelength fluorescence microscopy for the structural analysis of biological phenomena. Semin. Cell Biol. 2: 153-165.
20. Huang, S. and D.L. Spector. 1992. U1 and U2 small nuclear RNAs are present in nuclear speckles. Proc. Natl. Acad. Sci. 89: 305-308.
21. _. 1996. Intron-dependent recruitment of pre-mRNA splicing factors to sites of transcription. J. Cell Biol. 133: 719-732.
22. Iborra, F.J., A. Pombo, D.A. Jackson, and P.R. Cook. 1996. Active RNA polymerases are localized within discrete transcription "factories" in human nuclei. J. Cell Sci. 109: 1427-1436.
23. Jackson, D.A., A.B. Hassan, R.J. Errington, and P.R. Cook. 1993. Visualization of focal sites of transcription within human nuclei. EMBO J. 12: 1059-1065.
24. Jimenez-Garcia, L.F. and D.L. Spector. 1993. In vivo evidence that transcription and splicing are coordinated by a recruiting mechanism. Cell 73: 47-59.
25. Jimenez-Garcia, L.F., M.de L. Segura-Valdez, R.L. Ochs, L.I. Rothblum, R. Hannan, and D.L. Spector. 1994. Nucleologenesis: U3 snRNA-containing prenucleolar bodies move to sites of active pre-rRNA transcription after mitosis. Mol. Biol. Cell 5: 955-966.
26. Johnson, G.D., R.S. Davidson, K.C. McNamee, G. Russell, D. Goodwin, and E.J. Holborow. 1982. Fading of immunofluorescence during microscopy: A study of the phenomenon and its remedy. J. Immunol. Methods 55: 231-242.
27. Kim, Y.-J., P. Zuo, J.L. Manley, and B.S. Baker. 1992. The Drosophila RNA-binding protein RBP1 is localized to transcriptionally active sites of chromosomes and shows a functional similarity to human splicing factor ASF/SF2. Genes & Dev. 6: 2569-2579.
28. Kiseleva, E., T. Wurtz, N. Visa, and B. Daneholt. 1994. Assembly and disassembly of spliceosomes along a specific premessenger RNP fiber. EMBO J. 13: 6052-6061.
29. Lerner, E.R., M.R. Lerner, C.A. Janeway, and J.A. Steitz. 1981. Monoclonal antibodies to nucleic acid-containing cellular constituents: Probes for molecular biology and autoimmune disease. Proc. Natl. Acad. Sci. 78: 2737-2741.
30. Manley, J.L. and R. Tacke. 1996. SR proteins and splicing control. Genes & Dev. 10: 1569-1579.
31. Matera, A.G., K.T. Tycowski, J.A. Steitz, and D.C. Ward. 1994. Organization of small nucleolar ribonucleoproteins (snoRNPs) by fluorescence in situ hybridization and immunocytochemistry. Mol. Biol. Cell 5: 1289-1299.
32. Matunis, E.L., M.J. Matunis, and G. Dreyfuss. 1993. Association of individual hnRNP proteins and snRNPs with nascent transcripts. J. Cell Biol. 121: 219-228.
33. Mattaj, I. 1994. Splicing in space. Nature 372: 727-728.
34. Moore, M.J., C.C. Query, and P.A. Sharp. 1993. Splicing of precursors to mRNA by the spliceosome. In The RNA world (ed. R.F. Gesteland and A.F. Atkins), pp. 303-357. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
35. Osheim, Y.N., O.L. Miller, Jr., and A.L. Beyer. 1985. RNP particles at splice junction sequences on Drosophila chorion transcripts. Cell 43: 143-151.
36. Penman, S., I. Smith, and E. Holtzman. 1966. Ribosomal RNA synthesis and processing in a particulate site in the HeLa cell nucleus. Science 154: 786-789.
37. Petterson, I., M. Hinterberger, T. Mimori, E. Gottlieb, and J.A. Steitz. 1984. The structure of mammalian small nuclear ribonuclearproteins. J. Biol. Chem. 259: 5907-5914.
38. Ramchatesingh, J., A.M. Zahler, K.M. Neugebauer, M.B. Roth, and T.A. Cooper. 1995. A subset of SR proteins activates splicing of the cardiac troponin T alternative exon by direct interactions with an exonic enhancer. Mol Cell. Biol. 15: 4898-4907.
39. Ring, H.Z. and J.T. Lis. 1994. The SR protein B52/SRp55 is essential for Drosophila development. Mol. Cell. Biol. 14: 7499-7506.
40. Rosbash, M. and R.H. Singer. 1993. RNA travel: Tracks from DNA to cytoplasm. Cell 75: 399-401.
41. Roth, M.B., C. Murphy, and J. Gall. 1989. A monoclonal antibody that recognizes a phosphorylated epitope stains lampbrush chromosome loops and small granules in the amphibian germinal vesicle. J. Cell Biol. 111: 2217-2223.
42. Roth, M.B., A.M. Zahler, and J.A. Stolk. 1991. A conserved family of nuclear phosphoproteins localized to sites of polymerase II transcription. J. Cell Biol. 115: 587-596.
43. Spector, D.L. 1990. Higher order nuclear organization: Three-dimensional distribution of small nuclear ribonucleoprotein particles. Proc. Natl. Acad. Sci. 87: 147-151.
44. Spector, D.L., X.-D. Fu, and T. Maniatis. 1991. Associations between distinct pre-mRNA splicing components and the cell nucleus. EMBO J. 10: 3467-3481.
45. Tacke, R. and J.L. Manley. 1995. The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J. 14: 3540-3551.
46. Taggart, R.T. and M. Samloff. 1983. Stable antibody-producing murine hybridomas. Science 219: 1228-1230.
47. Tuma, R., J.A. Stolk, and M.B. Roth. 1993. Identification and characterization of a sphere organelle protein. J. Cell Biol. 122: 767-773.
48. Valcarcel, J. and M.R. Green. 1996. The SR protein family: Pleiotropic functions in pre-mRNA splicing. Trends Biochem. Sci. 21: 296-301.
49. Wansink, D.G., W. Schul, I. van der Kraan, B. van Steensel, R. van Driel, and L. de Jong. 1993. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus. J. Cell Biol. 122: 283-293.
50. Wansink, D.G., R.L.H. Neilssen, and L. de Jong. 1994. In vitro splicing of pre-mRNA containing bromouridine. Mol. Biol. Rep. 19: 109-113.
51. Wu, Z., C. Murphy, H.G. Callan, and J.G. Gall. 1993. Small nuclear ribonucleoproteins and heterogeneous nuclear ribonucleoproteins in the amphibian germinal vesicle: Loops, spheres, and snurposomes. J. Cell Biol. 113: 465-483.
52. Xing, Y., C.V. Johnson, P.T. Moen, J.A. McNeil, and J.B. Lawrence. 1995. Nonrandom gene organization: Structural arrangements of specific pre-mRNA transcription and splicing within SC-35 domains. J. Cell Biol. 131: 1635-1647.
53. Zachar, Z., J. Kramer, I.P. Mims, and P.M. Bingham. 1993. Evidence for channeled diffusion of pre-mRNAs during nuclear RNA transport in metazoans. J. Cell Biol. 121: 729-742.
54. Zahler, A.M., W.S. Lane, J.A. Stolk, and M.B. Roth. 1992. SR proteins: A conserved family of pre-mRNA splicing factors. Genes & Dev. 6: 837-847.
55. Zahler, A.M., K.M. Neugebauer, W.S. Lane, and M.B. Roth. 1993a. Distinct functions of SR proteins in alternative pre-mRNA splicing. Science 260: 219-222.
56. Zahler, A.M., K.M. Neugebauer, J.A. Stolk, and M.B. Roth. 1993b. Human SR proteins and isolation of a cDNA encoding SRp75. Mol. Cell. Biol. 13: 4023-4028.
57. Zhang, G., K.L. Taneja, R.H. Singer, and M.R. Green. 1994. Localization of pre-mRNA splicing in mammalian nuclei Nature 372: 809-812.