Distinct activated and non-activated RNA polymerase II complexes in yeast

EMBO Journal

Volumn 15, Issue 17, 1996, Pages 4654-4664

  Akhtar, Asifa ^a   Faye, Gerard ^b   Bentley, David L ^c  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^b INSTITUT CURIE   (France)

^c AMGEN INSTITUTE   (Canada)

Author keywords

Activation; C terminal domain; Elongation; RNA polymerase II; Transcription

Indexed keywords

FUNGAL PROTEIN; GALACTOSE; MUTANT PROTEIN; PHOSPHOTRANSFERASE; RNA POLYMERASE II;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DNA PROTEIN COMPLEX; DNA TRANSCRIPTION; ENZYME ACTIVATION; ENZYME LOCALIZATION; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION; YEAST;

EID: 0029791943     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1002/j.1460-2075.1996.tb00842.x     Document Type: Article

References (73)

1. Akoulitchev, S., Makela, T., Weinberg, R. and Reinberg, D. (1995) Requirement for TFIIH kinase activity in transcription by RNA polymerase II. Nature, 377, 657-660.
2. Allison, L.A. and Ingles, C.J. (1989) Mutations in RNA polymerase II enhance or suppress mutations in GAL4. Proc. Natl Acad. Sci. USA, 86, 2794-2798.
3. Arndt, K.M., Ricupero, H.S. and Winston, F. (1995) TBP mutants defective in activated transcription in vivo. EMBO J., 14, 1490-1497.
4. Barberis, A., Pearlberg, J., Simkovich, N., Farrell, S., Reinagel, P., Bamdad, C., Sigal, G. and Ptashne, M. (1995) Contact with a component of the polymerase II holoenzyme suffices for gene activation. Cell, 81, 359-368.
5. Bartel, P., Chien, C., Sternglanz, R. and Fields, S. (1993) Using the two-hybrid system to detect protein-protein interactions. In Hartley, D. (ed.), Cellular Interactions in Development. Oxford University Press, Oxford, UK, pp. 153-179.
6. Bentley, D. (1995) Regulation of transcriptional elongation by RNA polymerase II. Curr. Opin. Genet. Dev., 5, 210-216.
7. Berger, S.L., Pina, B., Silverman, N., Marcus, G.A., Agapite, J., Regier, J.L., Triezenberg, S.J. and Guarente, L. (1992) Genetic isolation of ADA2: a potential transcriptional adaptor required for function of certain acidic activation domains. Cell, 70, 251-265.
8. Blau, J., Xiao, H., McCracken, S., O'Hare, R., Greenblatt, J. and Bentley, D. (1996) Three functional classes of transcriptional activation domains. Mol. Cell. Biol., 16, 2044-2055.
9. Cai, H. and Luse, D.S. (1987) Transcription initiation by RNA polymerase II in vitro. Properties of preinitiation, initiation, and elongation complexes. J. Biol. Chem., 262, 298-304.
10. Chen, J., Ding, M. and Pederson, D. (1994) Binding of TFIID to the CYC1 TATA boxes in yeast occurs independently of upstream activating sequences. Proc. Natl Acad. Sci. USA, 91, 11909-11913.
11. Cismowski, M., Laff, G., Solomon, M. and Reed, S. (1995) K1N28 encodes a C-terminal domain kinase that controls mRNA transcription in Saccharomyces cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity. Mol. Cell. Biol., 15, 2983-2992.
12. Citron, B.A. and Donelson, J.E. (1984) Sequence of the Saccharomyces GAL region and its transcription in vivo. J. Bacteriol., 158, 269-278.
13. Drapkin, R. and Reinberg, D. (1994) The multifunctional TFIIH complex and transcriptional control. Trends Biochem. Sci., 19, 504-508.
14. Elion, E.A. and Warner, J.R. (1986) An RNA polymerase I enhancer in Saccharomyces cerevisiae. Mol. Cell. Biol., 6, 2089-2097.
15. Estojak, J., Brent, R. and Golemis, E.A. (1995) Correlation of two-hybrid affinity data with in vitro measurements. Mol. Cell. Biol., 15, 5820-5829.
16. Feaver, W.J., Svejstrup, J.Q., Henry, N.L. and Kornberg, R.D. (1994) Relationship of cdk-activating kinase and RNA polymerase II CTD kinase TFIIH/TFIIK. Cell, 79, 1103-1109.
17. Feilotter, H.E., Hannon, G.J., Ruddell, C.J. and Beach, D. (1994) Construction of an improved host strain for two hybrid screening. Nucleic Acids Res., 22, 1502-1503.
18. Fields, S. and Song, O. (1989) A novel genetic system to detect protein-protein interactions. Nature, 340, 245-247.
19. Gallwitz, D. and Sures, J. (1980) Structure of a split yeast gene: complete nucleotide sequence of the actin gene in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 77, 2546-2550.
20. Gerber, H.P., Hagmann, M., Seipel, K., Georgiev, O., West, M.A., Litingtung, Y., Schaffner, W. and Corden, J.L. (1995) RNA polymerase II C-terminal domain required for enhancer-driven transcription. Nature, 374, 660-662.
21. Giardina, C. and Lis, J.T. (1993) DNA melting on yeast RNA polymerase II promoters. Science, 261, 759-762.
22. Guarente, L. (1983) Yeast promoters and lacZ fusions designed to study expression of cloned genes in yeast. Methods Enzymol., 101, 181-191.
23. Hahn, S., Hoar, E.T. and Guarente, L. (1985) Each of three TATA elements' specifies a subset of the transcription initiation sites at the CYC-1 promoter of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 82, 8562-8566.
24. Harbury, P.A. and Struhl, K. (1989) Functional distinctions between yeast TATA elements. Mol. Cell. Biol., 9, 5298-5304.
25. Hengartner, C.J., Thompson, C.M, Zhang, J., Chao, D.M., Liao, S.M. Koleske, A.J., Okamura, S. and Young, R.A. (1995) Association of an activator with an RNA polymerase II holoenzyme. Genes Dev., 9, 897-910.
26. Henikoff, S. and Eghtedarzadeh, M.K. (1987) Conserved arrangement of nested genes at the Drosophila Gart locus. Genetics, 117, 711-725.
27. Hill, D.E., Hope, I.A., Macke, J.P. and Struhl, K. (1986) Saturation mutagenesis of the yeast HIS3 regulatory site: requirements for transcriptional induction and for binding by GCN4 activator protein. Science, 234, 451-457.
28. Izban, M.G. and Luse, D.S. (1991) Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing. Genes Dev., 5, 683-696.
29. Jerome, J.F. and Jaehning, J.A. (1986) mRNA transcription in nuclei isolated from Saccharomyces cerevisiae. Mol. Cell. Biol., 6, 1633-1639.
30. Jiang, Y. and Stillman, D. (1992) Involvement of the SIN4 global transcriptional regulator in chromatin structure of Saccharomyces cerevisiae. Mol. Cell. Biol., 12, 4503-4514.
31. Jiang, Y., Yan, M. and Gralla, J. (1996) A three-step pathway of transcriptional initiation leading to promoter clearance at an activated RNA polymerase II promoter. Mol. Cell. Biol., 16, 1614-1621.
32. Johnston, M. (1987) A model fungal gene regulatory mechanism: the GAL genes of Saccharomyces cerevisiae. Microbiol. Rev., 51, 458-476.
33. Kang, M.E. and Dahmus, M.E. (1993) RNA polymerase IIA and polymerase IIO have distinct roles during transcription from the TATA-less murine dihydrofolate reductase promoter. J. Biol. Chem., 268, 25033-25040.
34. Kao, S.Y., Calman, A.F., Luciw, P.A. and Peterlin, B.M. (1987) Anti-termination of transcription within the long terminal repeat of HIV-1 by tat gene product. Nature, 330, 489-493.
35. Kim, T.K., Hashimoto, S., Kelleher, R.J., Flanagan, P.M., Kornberg, R.D., Horikoshi, M. and Roeder, R.G. (1994) Effects of activation-defective TBP mutations on transcription initiation in yeast. Nature, 369, 252-255.
36. Kim, Y.J., Bjorklund, S., Li, Y., Sayre, M.H. and Kornberg, R.D. (1994) A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell, 77, 599-608.
37. Klein, C. and Struhl, K. (1994) Increased recruitment of TATA-binding protein to the promoter by transcriptional activation domains in vivo. Science, 266, 280-282.
38. Koleske, A.J. and Young, R.A. (1994) An RNA polymerase-II holoenzyme responsive to activators. Nature, 368, 466-469.
39. Koleske, A.J., Buratowski, S., Nonet, M. and Young, R.A. (1992) A novel transcription factor reveals a functional link between the RNA polymerase II CTD and TFIID. Cell, 69, 883-894.
40. Kruger, W., Peterson, C., Sil, A., Coburn, C., Arents, G., Moudrianakis, E. and Herskowitz, I. (1995) Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription. Genes Dev., 9, 2770-2779.
41. Krumm, A., Meulia, T., Brunvand, M. and Groudine, M. (1992) The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region. Genes Dev., 6, 2201-2213.
42. Krumm, A., Hickey, L. and Groudine, M. (1995) Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation. Genes Dev., 9, 559-572.
43. Laspia, M.F., Rice, A.P. and Mathews, M.B. (1990) Synergy between HIV-1 Tat and adenovirus E1A is principally due to stabilization of transcriptional elongation. Genes Dev., 4, 2397-2408.
44. Liao, S.M., Zhang, J., Jeffery, D.A., Koleske, A.J., Thompson, C.M., Chao, D.M., Viljoen, M., van, V.H.J. and Young, R.A. (1995) A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature, 374, 193-196.
45. Lillie, J.W. and Green, M.R. (1989) Transcription activation by the adenovirus E1a protein. Nature, 338, 39-44.
46. Lis, J. and Wu, C. (1993) Protein traffic on the heat shock promoter: parking, stalling and trucking along. Cell, 74, 1-4.
47. Lu, H., Flores, O., Weinmann, R. and Reinberg, D. (1991) The nonphosphorylated form of RNA polymerase II preferentially associates with the preinitiation complex. Proc. Natl Acad Sci. USA, 88, 10004-10008.
48. Lu, X., Welsh, T. and Peterlin, B. (1993) The human immunodeficiency virus type 1 long terminal repeat specifies two different transcription complexes, only one of which is regulated by Tat. J. Virol., 67, 1752-1760.
49. Makela, T.P., Parvin, J.D., Kim, J., Huber, L.J., Sharp, P.A. and Weinberg, R.A. (1995) A kinase-deficient transcription factor TFIIH is functional in basal and activated transcription. Proc. Natl Acad. Sci. USA, 91, 5174-5178.
50. Nonet, M.L. and Young, R.A. (1989) Intragenic and extragenic suppressors of mutations in the heptapeptide repeat domain of Saccharomyces cerevisiae RNA polymerase II. Genetics, 123, 715-724.
51. Nonet, M., Scafe, C., Sexton, J. and Young, R. (1987a) Eukaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol. Cell. Biol., 7, 1602-1611.
52. Nonet, M., Sweetser, D. and Young, R.A. (1987b) Functional redundancy and structural polymorphism in the large subunit of RNA polymerase II. Cell, 50, 909-915.
53. O'Brien, T., Hardin, S., Greenleaf, A. and Lis, J.T. (1994) Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. Nature, 370, 75-77.
54. Payne, J.M., Laybourn, P.J. and Dahmus, M.E. (1989) The transition of RNA polymerase II from initiation to elongation is associated with phosphorylation of the carboxyl-terminal domain of subunit IIA. J. Biol. Chem., 264, 19621-19629.
55. Peterson, C.L., Kruger, W. and Herskowitz, I. (1991) A functional interaction between the C-terminal domain of RNA polymerase II and the negative regulator SIN1. Cell, 64, 1135-1143.
56. Roberts, S. and Bentley, D.L. (1992) Distinct modes of transcription read through or terminate at the c-myc attenuator. EMBO J., 11, 1085-1093.
57. Rougvie, A.E. and Lis, J.T. (1988) The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell, 54, 795-804.
58. Rougvie, A.E. and Lis, J.T. (1990) Post-initiation transcriptional control in Drosophila melanogaster. Mol. Cell. Biol., 10, 6041-6045.
59. Scafe, C., Chao, D., Lopes, J., Hirsch, J.P., Henry, S. and Young, R.A. (1990) RNA polymerase II C-terminal repeat influences response to transcriptional enhancer signals. Nature, 347, 491-494.
60. Simon, M., Seraphin, B. and Faye, G. (1986) KIN28, a yeast split gene coding for a putative protein kinase homologous to CDC28. EMBO J., 5, 2697-2701.
61. Stargell, L.A. and Struhl, K. (1995) The TBP-TFIIA interaction in the response to acidic activators in vivo. Science, 269, 75-78.
62. Strobl, L.J. and Eick, D. (1992) Hold back of RNA polymerase II at the transcription start site mediates down-regulation of c-myc in vivo. EMBO J., 11, 3307-3314.
63. Thompson, C.M., Koleske, A.J., Chao, D.M. and Young, R.A. (1993) A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast. Cell, 1361-1375.
64. Tjian, R. and Maniatis, T. (1994) Transcriptional activation - a complex puzzle with few easy pieces. Cell, 77, 5-8.
65. Usheva, A., Maldonado, E., Goldring, A., Lu, H., Houbavi, C., Reinberg, D. and Aloni, Y. (1992) Specific interaction between the nonphosphorylated form of RNA polymerase II and the TATA-binding protein. Cell, 69, 871-881.
66. Valay, J.G., Simon, M. and Faye, G. (1993) The kin28 protein kinase is associated with a cyclin in Saccharomyces cerevisiae. J. Mol. Biol., 234, 307-310.
67. Valay, J.-G., Simon, M., Dubois, M.-F., Bensaude, O., Facca, C. and Faya, G. (1995) The KIN28 gene is required for RNA polymerase II-mediated transcription and phosphorylation of the Rpb1p CTD. J. Mol. Biol., 249, 535-544.
68. Weeks, J.R., Hardin, S.E., Shen, J.J., Lee, J.M. and Greenleaf, A.L. (1993) Locus-specific variation in phosphorylation state of RNA polymerase H in vivo - correlations with gene activity and transcript processing. Genes Dev., 7, 2329-2344.
69. West, M. and Corden, J. (1995) Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations. Genetics, 140, 1223-1233.
70. Xiao, H., Friesen, J. and Lis, J. (1995) Recruiting TATA-binding protein to a promoter:transcriptional activation without an upstream activator. Mol. Cell. Biol., 15, 5757-5761.
71. Yankulov, K.,. Blau, J., Purton, T. Roberts, S. and Bentley, D. (1994) Transcriptional elongation by RNA polymerase II is stimulated by transactivators. Cell, 77, 749-759.
72. Yankulov, K., Yamashita, K., Roy, R., Egly, J.-M. and Bentley, D. (1995) The transcriptional elongation inhibitor 5,6-dichlor-1-β-D-ribofuranosylbenzimidazole inhibits transcription factor IIH-associated protein kinase. J Biol. Chem., 270, 23922-23925.
73. Zawel, L. and Reinberg, D. (1995) Common themes in assembly and function of eukaryotic transcription complexes. Annu. Rev. Biochem., 64, 533-561.