RNA polymerase II as a control panel for multiple coactivator complexes

Current Opinion in Genetics and Development

Volumn 9, Issue 2, 1999, Pages 132-139

  Hampsey, Michael ^a   Reinberg, Danny ^a,b  

^a RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; DNA; RNA; RNA POLYMERASE II; TRANSCRIPTION FACTOR;

BACTERIUM; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA INTERACTION; REVIEW; RNA SYNTHESIS; TRANSCRIPTION REGULATION; YEAST;

BACTERIA (MICROORGANISMS); EUKARYOTA; MAMMALIA;

EID: 0033118984     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(99)80020-3     Document Type: Article

References (79)

1. Krakow JS, Daley K, Karstadt M: Azotobacter vinelandii RNA polymerase. VII. Enzyme transitions during unprimed r[I-C] synthesis. Proc Natl Acad Sci USA 1969, 62:432-437.
2. Burgess RR, Travers AA, Dunn JJ, Bautz EK: Factor stimulating transcription by RNA polymerase. Nature 1969, 221:43-46.
3. Helmann JD, Chamberlin MJ: Structure and function of bacterial sigma factors. Annu Rev Biochem 1988, 57:839-872.
4. Miller A, WooD D, Ebright RH, Rothman-Denes LB: RNA polymerase beta' subunit: A target of DNA binding-independent activation [see comments]. Science 1997, 275:1655-1657.
5. BuSby S, Ebright RH: Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 1994, 79:743-746.
6. ZaweL L, Reinberg D: Common themes in assembly and function of eukaryotic transcription complexes. Annu Rev Biochem 1995, 64:533-561.
7. ZaweL L, Reinberg D: Initiation of transcription by RNA polymerase II: A multi-step process. Prog Nucleic Acid Res Mol Biol 1993, 44:67-108.
8. Hampsey M: Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev 1998, 62:465-503.
9. Orphanides G, Lagrange T, Reinberg D: The general transcription factors of RNA polymerase II. Genes Dev 1996, 10:2657-2683.
10. Greenblatt J: RNA polymerase II holoenzyme and transcriptional regulation. Curr Opin Cell Biol 1997, 9:310-319.
11. Myer VE, Young RA: RNA polymerase II holoenzymes and subcomplexes. J Biol Chem 1998, 273:27757-27760.
12. Nonet ML, Young RA: Intragenic and extragenic suppressors of mutations in the heptapeptide repeat domain of Saccharomyces cerevisiae RNA polymerase II. Genetics 1989, 123:715-724.
13. Hengartner CJ, Thompson CM, Zhang J, Chao DM, Liao Sm, Koleske AJ, Okamura S, Young RA: Association of an activator with an RNA polymerase II holoenzyme. Genes Dev 1995, 9:897-910.
14. Koleske AJ, Young RA: An RNA polymerase II holoenzyme responsive to activators [see comments]. Nature 1994, 368:466-469.
15. Koleske AJ, Young RA: The RNA polymerase II holoenzyme and its implications for gene regulation. Trends Biochem Sci 1995, 20:113-116.
16. Thompson CM, Young RA: General requirement for RNA polymerase II holoenzymes in vivo. Proc Natl Acad Sci USA 1995, 92:4587-4590.
17. Flanagan PM, Kelleher RJ, Sayre MH, Tschochner H, Kornberg RD: A mediator required for activation of RNA polymerase II transcription in vitro. Nature 1991, 350:436-438.
18. Li Y, Bjorklund S, Jiang YW, Kim YJ, Lane WS, Stillman DJ, Kornberg RD: Yeast global transcriptional regulators Sin4 and Rgr1 are components of mediator complex/RNA polymerase II holoenzyme. Proc Natl Acad Sci USA 1995, 92:10864-10868.
19. Gustafsson CM, Myers LC, Beve J, Spahr H, Lui M, Erdjument-Bromage H, Tempst P, Kornberg RD: Identification of new mediator subunits in the RNA polymerase II holoenzyme from Saccharomyces cerevisiae. J Biol Chem 1998, 273:30851-30854.
20. Myers LC, Gustafsson CM, Bushnell DA, Lui M, Erdjument-Bromage H, Tempst P, Kornberg RD: The med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain. Genes Dev 1998, 12:45-54.
21. Liao SM, Zhang J, Jeffery DA, Koleske AJ, Thompson CM, Chao DM, Viljoen M, Van Vuuren HJ, Young RA: A kinase-cyclin pair in the RNA polymerase II holoenzyme [see comments]. Nature 1995, 374:193-196.
22. Carlson M: Genetics of transcriptional regulation in yeast: Connections to the RNA polymerase II CTD. Annu Rev Cell Dev Biol 1997, 13:1-23.
23. Wilson CJ, Chao DM, Imbalzano AN, Schnitzler G R, Kingston RE, Young RA: RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell 1996, 84:235-244.
24. Shi X, Finkelstein A, Wolf AJ, Wade PA, Burton ZF, Jaehning JA: Paf1p, an RNA polymerase II-associated factor in Saccharomyces cerevisiae, may have both positive and negative roles in transcription. Mol Cell Biol 1996, 16:669-676.
25. Shi X, Chang M, Wolf AJ, Chang CH, Frazer-Abel AA, Wade PA, Burton ZF, Jaehning JA: Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-Containing holoenzyme. Mol Cell Biol 1997, 17:1160-1169.
26. ++-inducible CUP1 gene is transcribed by RNAPII lacking the CTD. CUP1 and HSP82 transcription also persists after inactivation of the Kin28 CTD kinase or the Srb4 mediator subunit. These results are consistent with those presented in [27•] and demonstrate that the SRB/mediator is not universally required for activated transcription.
27. Lee D, Lis JT: Transcriptional activation independent of TFIIH kinase and the RNA polymerase II mediator in vivo. Nature 1998, 393:389-392. Similar to the results presented in [26••], activation of the CUP1 and SSA4 genes persists upon inactivation of the Kin28 CTD kinase, or the Srb4 or Srb6 mediator subunits. These results indicate that activation can occur by at least two distinct pathways, one of which is independent of the SRB/mediator.
28. Svejstrup JQ, Li Y, Fellows J, Gnatt A, Bjorklund S, Kornberg RD: Evidence for a mediator cycle at the initiation of transcription. Proc Natl Acad Sci USA 1997, 94:6075-6078.
29. Chao DM, Gadbois EL, Murray PJ, Anderson SF, Sonu MS, Parvin JD, Young RA: A mammalian SRB protein associated with an RNA polymerase II holoenzyme. Nature 1996, 380:82-85.
30. Maldonado E, Shiekhattar R, Sheldon M, Cho H, Drapkin R, Rickert P, Lees E, Anderson CW, Linn S, Reinberg D: A human RNA polymerase II complex associated with SRB and DNA-repair proteins [published erratum appears in Nature 1996:384]. Nature 1996, 381:86-89.
31. Pan G, Aso T, Greenblatt J: Interaction of elongation factors TFIIS and elongin A with a human RNA polymerase II holoenzyme capable of promoter-specific initiation and responsive to transcriptional activators. J Biol Chem 1997, 272:24563-24571.
32. Cho H, Orphanides G, Sun X, Yang XJ, Ogryzko V, Lees E, Nakatani Y, Reinberg D: A human RNA polymerase II complex containing factors that modify chromatin structure. Mol Cell Biol 1998, 18:5355-5363.
33. Neish AS, Anderson SF, Schlegel BP, Wei W, Parvin JD: Factors associated with the mammalian RNA polymerase II holoenzyme. Nucleic Acids Res 1998, 26:847-853.
34. Sun X, Zhang Y, Cho H, Rickert P, Lees E, Lane W, Reinberg D: NAT, a human complex containing Srb polypeptides that functions as a negative regulator of activated transcription. Mol Cell 1998, 2:213-222. The NAT complex - containing human homologs of the Srb7, Srb10, Srb11, Rgr1 and Med6 proteins - is isolated by conventional chromatography and Srb10/CDK8-affinity purification. NAT is a negative regulator of activated transcription that interacts with RNAPII in a manner distinct from the SRB/mediator complex.
35. Hengartner CJ, Myer VE, Liao SM, Wilson CJ, Koh SS, Young RA: Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases. Mol Cell 1998, 2:43-53.
36. Lu H, ZaweL L, Fisher L, Egly JM, Reinberg D: Human general transcription factor IIH phosphorylates the C-terminal domain of RNA polymerase 11 [see comments]. Nature 1992, 358:641-645.
37. Yuryev A, Corden JL: Suppression analysis reveals a functional difference between the serines in positions two and five in the consensus sequence of the C-terminal domain of yeast RNA polymerase II. Genetics 1996, 143:661-671.
38. Gu W, Malik S, Ito M, Yuan C-X, Fondell JD, Zhang X, MartinEz E, Qin J, Roeder RG: A novel human SRB/MED-containing cofactor complex (SMCC) involved in transcription regulation. Mol Cell 1999, 3:97-108.
39. Jiang YW, Veschambre P, Erdjument-Bromage H, Tempst P, Conaway JW, Conaway RC, Kornberg RD: Mammalian mediator of transcriptional regulation and its possible role as an end-point of signal transduction pathways. Proc Natl Acad Sci USA 1998, 95:8538-8543.
40. Kim YJ, Bjorklund S, Li Y, Sayre MH, Kornberg RD: A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 1994, 77:599-608.
41. Fondell JD, Ge H, Roeder RG: Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex. Proc Natl Acad Sci USA 1996, 93:8329-8333.
42. Rachez C, Suldan Z, Ward J, Chang CP, Burakov D, Erdjument-Bromage H, Tempst P, Freedman LP: A novel protein complex that interacts with the vitamin D3 receptor in a ligand-dependent manner and enhances VDR transactivation in a cell-free system. Genes Dev 1998, 12:1787-1800.
43. 3 receptor in a ligand-dependent manner on chromatin-assembled templates. DRIP appears to be identical to ARC [48•] and highly similar or identical to TRAP [44].
44. Yuan CX, Ito M, Fondell JD, Fu ZY, Roeder RG: The TRAP220 component of a thyroid hormone receptor-associated protein (TRAP) coactivator complex interacts directly with nuclear receptors in a ligand-dependent fashion. Proc Nat! Acad Sci USA 1998, 95:7939-7944.
45. Ryu S, Zhou S, Ladurner AG, Tjian R: The transcriptional co-factor complex CRSP is required for activity of the enhancer binding protein Sp1. Nature 1999, 397:446-450. The first mammalian complex with structural and functional similarities to yeast SRB/mediator is identified. This complex, designated CRSP, mediates activation by the glutamine-rich activator Sp1.
46. Janknecht R, Hunter T: Transcription. A growing coactivator network. Nature 1996, 383:22-23.
47. Näär AM, Beaurang PA, Robinson KM, Oliner JD, Avizonis D, Scheek S, Zwicker J, Kadonaga JT, Tjian R: Chromatin, TAFs, and a novel multiprotein coactivator are required for synergistic activation by Sp1 and Srebp-1a In vitro. Genes Dev 1998, 12:3020-3031.
48. Näär AM, Beaurang PA, Zhou S, Abraham S, Solomon W, Tjian R: Composite coactivator ARC mediates chromatin-directed transcriptional activation. Nature 1999, in press. A complex, designated ARC, containing mediator subunits in association with CBP, is demonstrated to be required for synergistic activation. ARC function requires chromatin templates and includes CRSP, DRIP, TRAP and NAT subunits. ARC underscores the modular nature of coactivator complexes.
49. Hampsey M, Reinberg D: Transcription: Why are TAFs essential? Curr Biol 1997, 7:R44-R46.
50. Roberts SM, Winston F: Essential functional interactions of SAGA, a Saccharomyces cerevisiae complex of Spt, Ada, and Gcn5 proteins, with the Snf/Swi and Srb/mediator complexes. Genetics 1997, 147:451-465.
51. Walker SS, Reese JC, Apone LM, Green MR: Transcription activation in cells lacking TAFIIS [see comments]. Nature 1996, 383:185-188.
52. Moqtaderi Z, Bai Y, Poon D, Weil PA, Struhl K: TBP-associated factors are not generally required for transcriptional activation in yeast [see comments]. Nature 1996, 383:188-191.
53. Wu SY, Chiang CM: Properties of PC4 and an RNA polymerase II complex in directing activated and basal transcription in vitro. J Biol Chem 1998, 273:12492-12498.
54. Wu SY, Kershnar E, Chiang CM: Tafii-independent activation mediated by human TBP in the presence of the positive cofactor PC4. EMBO J 1998, 17:4478-4490.
55. Oelgeschlager T, Tao Y, Kang YK, Roeder RG: Transcription activation via enhanced preinitiation complex assembly in a human cell-free system lacking TAFIIs. Mol Cell 1998, 1:925-931. These studies are the first to suggest that activation can occur in a mammalian-derived extract in the absence of TAFs, thereby suggesting functional redundancy among TAFs and other complexes required for activation.
56. Drysdale CM, Jackson BM, McVeigh R, Klebanow ER, Bai Y, Kokubo T, Swanson M, Nakatani Y, Weil PA, Hinnebusch AG: The Gcn4p activation domain interacts specifically in vitro with RNA polymerase II holoenzyme, TFIID, and the Adap-Gcn5p coactivator complex. Mol Cell Biol 1998, 18:1711 -1724.
57. Ogryzko VV, Kotani T, Zhang X, Schlitz RL, Howard T, Yang XJ, Howard BH, Qin J, Nakatani Y: Histone-like TAFs within the PCAF histone acetylase complex. Cell 1998, 94:35-44.
58. Grant PA, Schieltz D, Pray-Grant MG, Steger DJ, Reese JC, Yates JR, Workman JL: A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell 1998, 94:45-53.
59. Hahn S: The role of TAFs in RNA polymerase II transcription. Cell 1998, 95:579-582.
60. Wieczorek E, Brand M, Jacq X, Tora L: Function of TAF(II)-containing complex without TBP in transcription by RNA polymerase II [see comments]. Nature 1998, 393:187-191.
61. Hansen SK, Takada S, Jacobson RH, Lis JT, Tjian R: Transcription properties of a cell type-specific TATA-binding protein, TRF. Cell 1997, 91:71-83.
62. Miyao T, Woychik NA: RNA polymerase subunit RPB5 plays a role in transcriptional activation. Proc Natl Acad Sci USA 1998, 95:15281-15286.
63. Xiao H, Friesen JD, Lis JT: Recruiting TATA-binding protein to a promoter: Transcriptional activation without an upstream activator. Mol Cell Biol 1995, 15:5757-5761.
64. Klages N, Strubin M: Stimulation of RNA polymerase II transcription initiation by recruitment of TBP in vivo. Nature 1995, 374:822-823.
65. Chatterjee S, Struhl K: Connecting a promoter-bound protein to TBP bypasses the need for a transcriptional activation domain. Nature 1995, 374:820-822.
66. Stargell LA, Struhl K: A new class of activation-defective TATA-binding protein mutants: Evidence for two steps of transcriptional activation in vivo. Mol Cell Biol 1996, 16:4456-4464.
67. Stargell LA, Struhl K: Mechanisms of transcriptional activation in vivo: Two steps forward. Trends Genet 1996, 12:311 -315.
68. Farrell S, Simkovich N, Wu Y, Barberis A, Ptashne M: Gene activation by recruitment of the RNA polymerase II holoenzyme. Genes Dev 1996, 10:2359-2367.
69. Barberis A, Pearlberg J, Simkovich N, Farrell S, Reinagel P, Bamdad C, Sigal G, Ptashne M: Contact with a component of the polymerase II holoenzyme suffices for gene activation. Cell 1995, 81:359-368.
70. Gonzalez-Couto E, Klages N, Strubin M: Synergistic and promoter-selective activation of transcription by recruitment of transcription factors TFIID and TFIIB. Proc Natl Acad Sci USA 1997, 94:8036-8041.
71. Koh SS, Ansari AZ, Ptashne M, Young RA: An activator target in the RNA polymerase II holoenzyme. Mol Cell 1998, 1:895-904.
72. Lee YC, Min S, Gim BS, Kim YJ: A transcriptional mediator protein that is required for activation of many RNA polymerase II promoters and is conserved from yeast to humans. Mol Cell Biol 1997, 17:4622-4632.
73. Lee YC, Park JM, Min S, Man SJ, Kim Y-J: An activator binding module of yeast RNA polymerase II holoenzyme. Mol Cell Biol 1999, in press.
74. Keaveney M, Struhl K: Activator-mediated recruitment of the RNA polymerase II machinery is the predominant mechanism for transcriptional activation in yeast. Mol Cell 1998, 1:917-924.
75. Ranish JA, Yudkovsky N, Hahn S: Intermediates in formation and activity of the RNA polymerase II preinitiation complex: Holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB. Genes Dev 1999, 13:49-63. This study uses immobilized DNA templates and yeast extracts from wild-type and conditional mutants defective in components of the RNAPII machinery to investigate the assembly and activation of transcription complexes. This is an unbiased study illustrating that PIC assembly can occur by at least two steps: recruitment of TBP and a TFIIB-containing RNAPII complex that requires functional SRBs and the CTD. These studies also demonstrated that PIC formation is not sufficient for activation.
76. Kim TK, Kim TH, Maniatis T: Efficient recruitment of TFIIB and CBP-RNA polymerase II holoenzyme by an interferon-beta enhanceosome in vitro. Proc Natl Acad Sci USA 1998, 95:12191-12196.
77. ZaweL L, Kumar KP, Reinberg D: Recycling of the general transcription factors during RNA polymerase II transcription. Genes Dev 1995, 9:1479-1490.
78. Chamberlin MJ: RNA polymerase - An overview. In RNA Polymerase. Edited by Losick R, Chamberlin M. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 1976:17-67.
79. Lee YC, Kim YJ: Requirement for a functional interaction between mediator components Med6 and Srb4 in RNA polymerase II transcription. Mol Cell Biol 1998, 18:5364-5370.