Transcription: Basal factors and activation

Current Opinion in Genetics and Development

Volumn 6, Issue 2, 1996, Pages 151-158

  Ranish, Jeffrey A ^a   Hahn, Steven ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN; MESSENGER RNA; RNA POLYMERASE II; TATA BINDING PROTEIN; TRANSCRIPTION FACTOR;

CELL CYCLE; COMPLEX FORMATION; DNA REPAIR; MESSENGER RNA SYNTHESIS; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA INTERACTION; REVIEW; TRANSCRIPTION REGULATION;

EID: 0029892282     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(96)80044-X     Document Type: Article

References (77)

1. Maldonado E, Reinberg D: News on initiation and elongation of transcription by RNA polymerase II. Curr Opin Cell Biol 1995, 7:352-361.
2. Zawel L, Reinberg D: Common themes in assembly of eukaryotic transcription complexes. Annu Rev Biochem 1995, 64:533-561.
3. Drapkin R, Reinberg D: The multifunctional TFIIH complex and transcriptional control. Trends Biochem Sci 1994, 19:504-508.
4. Kim JL, Nikolov DB, Burley SK: Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 1993, 365:520-527.
5. Kim Y, Geiger JH, Hahn S, Sigler PB: Crystal structure of a yeast TBP/TATA-box complex. Nature 1993, 365:512-520.
6. Bagby S, Kim S, Maldonado E, Tong KI, Reinberg D, Ikura M: Solution structure of the carboxy-terminal core domain of human TFIIB: similarity to cyclin A and interaction with TATA binding protein. Cell 1995, 82:857-867. This paper presents the structure of the TFIIB CTD as solved by NMR. This domain has a fold very similar to cyclin A.
7. •] suggests a conformational change of TFIIB upon DNA binding.
8. Hahn S: Transcription: efficiency in activation. Nature 1993, 363:672-673.
9. Lee S, Hahn S: Model for binding of transcription factor TFIIB to the TBP-DNA complex. Nature 1995, 376:609-612. The TFIIB binding site in the TBP-DNA complex is mapped by DNA deletions and hydroxyl radical footprinting. These results predict that TFIIB contacts the carboxy-terminal stirrup of TBP as well as DNA upstream and downstream of the TATA box. This agrees very well with the TFIIB crystal structure.
10. Kim TK, Hashimoto S, Kelleher FRJ, Flanagan PM, Kornberg RD, Horikoshi M, Roeder RG: Effects of activation-defective TBP mutations on transcription initiation in yeast. Nature 1994, 369:252-255. Describes TBP mutants that are specifically defective in supporting activation in vitro. The mutants display a variety of defects. One mutant interacts poorly with a VP16 affinity column; another mutant fails to form TBP/IIA/DNA complexes; another fails to form TBP/IIB/DNA complexes. In immobilized template assays with purified factors, some mutants were defective in recruiting/stabilizing TFIIB in the presence of Gal4-VP16.
11. •] to model the orientation of factors in the PIC.
12. Coulombe BL, Greenblatt J: Topological localization of the human transcription factors IIA, IIB, TATA box-binding protein, and RNA polymerase II-associated protein 30 on a class II promoter. J Biol Chem 1994, 269:19962-19967. Protein-DNA crosslinking is used to map where factors TFIIA, TFIIB, and TFIIF are in close proximity to the DNA.
13. Verrijzer CP, Yokomori K, Chen J, Tjian R: Drosophila TAFII150: similarity to yeast gene TSM1 and specific binding to core promoter DNA. Science 1994, 264:933-941. TAF150 from Drosophila was purified and cloned. The TAF150 sequence is homologous to an essential yeast gene of unknown function, TSM1. The authors show that TSM1 is an apparent yeast TAF and that dTAF150 has sequence-specific binding activity for the lnr region of the adenovirus major late promoter. TAF150 in combination with TBP generates a footprint very similar to TFIID. These results suggest that TAF150 normally interacts with the lnr element.
14. Javahery R, Khachi A, Lo K, Zenzie-Gregory B, Smale ST: DNA sequence requirements for transcriptional initiator activity in mammalian cells. Mol Cell Biol 1994, 14:116-127.
15. Kokubo T, Gong D, Yamashita S, Horikoshi M, Roeder RG, Nakatani Y: Drosophila 230 kD TFIID subunit, a functional homolog of the human cell cycle gene product, negative regulates DNA binding of the TATA box-binding subunit of TFIID. Genes Dev 1993, 7:1033-1046.
16. Verrijzer CP, Chen J-L, Yokomori K, Tjian R: Binding of TAFs to core elements directs promoter selectivity by RNA polymerase II. Cell 1995, 81:1115-1125. The authors find that TAF250 in combination with TAF150 can destabilize the binding of TBP to promoters lacking an lnr element, showing that TAFs can alter the DNA-binding specificity of TBP.
17. •].
18. Goodrich JA, Tjian R: Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II. Cell 1994, 77:145-156. An abortive initiation assay is used to probe the function of basal factors in initiation. These authors find that a minimal system of TBP, TFIIB, Pol II, and TFIIF can form an open complex and synthesize the first RNA phosphodiester bond. This minimal system is not sufficient for synthesis of long transcripts. Furthermore, they find that TFIIE and TFIIH are needed for promoter clearance.
19. •] also show that premelting of the promoter can eliminate the requirement for certain basal factors and ATP.
20. •].
21. •] demonstrate that premelting of the promoter can eliminate the requirement for ATP, TFIIE and TFIIH.
22. Young RA: RNA polymerase II. Annu Rev Biochem 1991, 60:689-715.
23. Akoulitchev S, Makela T, Weinberg RA, Reinberg D: Requirement for TFIIH kinase activity in transcription by RNA polymerase II. Nature 1995, 377:557-560. By using an abortive initiation assay, these authors show that Pol II lacking the CTD can form PICs but cannot form the first phosphodiester bond in the replicated RNA. The kinase activity of TFIIH is not necessary for initiation of transcription but functions at a later step. These results also suggest a separate role for TFIIH in promoter clearance and/or elongation of Pol II.
24. Koleske AJ, Buratowski S, Nonet M, Young RA: A Novel transcription factor reveals a functional link between the RNA polymerase CTD and TFIID. Cell 1992, 69:883-894.
25. Gerber H-P, Hagmann M, Seipel K, Gerogiev O, West MAL, Litingtung Y, Schaffner W, Corden JL: RNA polymerase II carboxy-terminal domain required for enhancer-driven transcription. Nature 1995, 374:660-662.
26. Zawel L, Kuman KP, Reinberg D: Recycling of the general transcription factors during RNA polymerase II transcription. Genes Dev 1995, 9:1479-1490. By using immobilized promoter templates and a highly purified transcription system, these authors follow the fate of the basal factors after initiation. They find that TFIID is the only factor that stably associates with the promoter after initiation. TFIIB and TFIIE are released soon after initiation, and TFIIH is released last.
27. Choy B, Green MR: Eukaryotic activators function during multiple steps of preinitiation complex assembly. Nature 1993, 366:531-536.
28. Koleske AJ, Young RA: The RNA polymerase II holoenzyme and its implications for gene regulation. Trends Biochem 1995, 20:113-114.
29. Koleske AJ, Young RA: An RNA polymerase II holoenzyme responsive to activators. Nature 1994, 368:466-469. This paper describes the purification and composition of holoenzyme from yeast. Transcription is reconstituted by the addition of TBP and TFIIE to holoenzyme.
30. Kim YJ, Bjorklund S, Li Y, Sayre MH, Kornberg RD: A multiprotein mediator of transcriptional activation and its interaction with the carboxy-terminal repeat domain of RNA Polymerase II. Cell 1994, 77:599-608. This paper desribes the purification of a form of holoenzyme. Unlike the holoenzyme detailed in [28] this form lacks TFIIB and TFIIH. This holoenzyme has a higher specific activity than core Pol II in reconstituted transcription assays. Also, an anti-CTD affinity column separates holoenzyme into a mediator complex and core Pol II. The mediator contains the SRBs and Gal11, and it stimulates basal and activated transcription.
31. Thompson CM, Young RA: General requirement for RNA polymerase II holoenzymes in vivo. Proc Natl Acad Sci USA 1995, 92:4587-4590. This paper presents convincing evidence for the role of SRBs in transcription in vivo. Using yeast strains carrying temperature-sensitive alleles of either SRB4 or SRB6, transcription from nine Pol II promoters rapidly decreases after shifting to the nonpermissive temperature.
32. Thompson CM, Koleske AJ, Chao DM, Young RA: A multisubunit complex associated with TATA binding protein and the RNA polymerase II CTD in yeast. Cell 1993, 73:1367-1375.
33. Ossipow V, Tassan J-P, Nigg EA, Schibler U: A mammalian RNA polymerase II holoenzyme containing all components required for promoter specific transcription initiation. Cell 1995, 83:137-146.
34. Wolffe AP: Transcription: in tune with the histones. Cell 1994, 77:13-16.
35. Auble DT, Hansen KE, Mueller CGF, Lane WS, Thorner J, Hahn S: Mott, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism. Genes Dev 1994, 8:1920-1934. After purification and protein sequencing, an activity which inhibits TBP binding to DNA by an ATP-dependent mechanism is shown to be Mot1. In vivo and in vitro evidence is presented that supports the claim that Mot1 is a global represser of Pol II transcription.
36. Côté J, Quinn J, Workman JL, Peterson CL: Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 1994, 265:53-60. In this paper, a yeast SWI/SNF complex is purified and shown to contain 10 subunits including SWI1, SWI2/SNF2, SWI3, SNF5, and SNF6. Under certain conditions, the complex stimulates the binding of Gal4 derivatives to nucleosomal DNA by 10-30 fold. This stimulation seems to require ATP hydrolysis, as a complex containing an ATPase mutant is less active than the wild-type complex. Evidence for an ATP-dependent interaction between nucleosomal DNA and the complex is presented.
37. Kwon H, Imbalzano AN, Khavari PA, Kingston RE, Green MR: Nucleosome disruption and enhancement of activator binding by a human SWI/SNF complex. Nature 1994, 370:477-481. Two human SWI/SNF complexes are purified here, and a DNA-dependent ATPase activity is detected. The complex can alter nucleosomal structure in an ATP-dependent manner and stimulate the binding of Gal4 derivatives to nucleosomal DNA.
38. Auble DT, Hahn S: An ATP-dependent inhibitor of TBP binding to DNA. Genes Dev 1993, 7:844-856.
39. Bentley DL: Regulation of transcriptional elongation by RNA polymerase II. Curr Opin Genet Dev 1995, 5:210-216.
40. Joliot V, Demma M, Prywes R: Interaction with RAP74 subunit of TFIIF is required for transcriptional activation by serum response factor. Nature 1995, 373:632-635.
41. Tansey WP, Herr W: The ability to associate with activation domains in vitro is not required for TBP to support activated transcription in vivo. Proc Natl Acad Sci USA 1996, 93:10550-10554. Mutations in TBP that disrupt its ability to interact with the activation domains of VP16 or p53 on glutathione S-transferase, GST, affinity columns do not disrupt the ability of TBP to respond to activators in vivo. Also, TBP interacts with a region of VP16 that is distinct from the activation domain in vitro, but this region does not activate transcription in vivo. The results suggest that TBP interaction with activation domains in vitro does not necessarily reflect the ability to respond to activators in vivo.
42. Tjian R, Maniatis T: Transcriptional activation: a complex puzzle with few easy pieces. Cell 1994, 77:5-8.
43. Kaiser K, Stelzer G, Meisterernst M: The coactivator p15 (PC4) initiates transcriptional activation during TFIIA-TFIID-promoter complex formation. EMBO J 1995, 14:3520-3527.
44. Shykind BM, Kim J, Sharp PA: Activation of the TFIID-TFIIA complex with HMG-2. Genes Dev 1995, 9:1354-1365.
45. Chen J-L, Attardi LD, Verrijzer CP, Yokomori K, Tjian R: Assembly of recombinant TFIID reveals differential coactivator requirements for distinct transcriptional activators. Cell 1994, 79:93-105. The stepwise assembly of a Drosophila TFIID complex composed of TBP and eight recombinant TAFs is described in this paper. The complex can support basal and activated transcription with a specific activity that is similar to that of purified TFIID. The ability of activators to interact with specific TAFs in vitro correlates with the ability of partial TFIID complexes to respond to activators. The results are consistent with a model in which stimulated transcription is mediated, at least partly, by activator-TAF interactions.
46. •].
47. Poon D, Bai Y, Campbell AM, Bjorkllund S, Kim Y-J, Zhou S, Kornberg RD, Weil PA: Identification and characterization of a TFIID-like multiprotein complex for S. cerevisiae. Proc Natl Acad Sci USA 1995, 92:8224-8228. A yeast TFIID complex is purified on an anti-TBP affinity column. In transcription assays with purified factors, addition of TAFs supports a threefold stimulation by Gal4-VP16 without affecting transcription from a basal construct. Four of the TAFs are cloned and sequenced. These TAFs have homology to known Drosophila and human TAFs. Deletion of each of three TAFs is lethal.
48. 11250. Science 1994, 263:811-814.
49. Lee M, Struhl K: Mutations on the DNA-binding surface of TATA-binding protein can specifically impair the response to acidic activators in vivo. Mol Cell Biol 1995, 15:5461-5469.
50. Arndt KM, Ricupero-Hovasse S, Winston F: TBP mutants defective in activated transcription in vivo. EMBO J 1995, 14:1490-1497.
51. Stargell LA, Struhl K: The TBP-TFIIA interaction in the response to acidic activators in vivo. Science 1995, 269:75-78.
52. •].
53. •].
54. •] present evidence that TBP recruitment to the promoter can be rate-limiting in vivo. By using a variety of constructs in which TBP can be brought to a promoter by another DNA binding domain, transcription is stimulated to levels comparable to those obtained by an activator. The results are consistent with models in which activators function in part by recruiting TBP to the promoter.
55. Chen J, Ding M, Pederson DS: Binding of TFIID to the CYC1 TATA boxes in yeast occurs independently of upstream activating sequences. Proc Natl Acad Sci USA 1994, 91:11909-11913.
56. Kang JJ, Auble DT, Ranish JA, Hahn S: Analysis of the yeast transcription factor TFIIA: distinct functional regions and a polymerase 11-specific role in basal and activated transcription. Mol Cell Biol 1995, 15:1234-1243.
57. Ozer J, Moore PA, Bolden AH, Lee A, Rosen CA, Lieberman PM: Molecular cloning of the small (γ) subunit of human TFIIA reveals functions critical for activated transcription. Genes Dev 1994, 8:2324-2335.
58. Sun X, Ma D, Sheldon M, Yeung K, Reinberg D: Reconstitution of human TFIIA activity from recombinant polypeptides: a role in TFIID-mediated transcription. Genes Dev 1994, 8:2336-2348.
59. Yokomori K, Zeidler MP, Chen J-L, Verrijzer CP, Mlodzik M, Tjian R: Drosophila TFIIA directs cooperative DNA binding with TBP and mediates transcriptional activation. Genes Dev 1994, 8:2313-2323.
60. Lieberman PM, Berk AJ: A mechanism for TAFs in transcriptional activation: activation domain enhancement of TFIID-TFIIA-promoter DNA complex formation. Genes Dev 1994, 9:995-1006.
61. Chi T, Lieberman P, Ellwood K, Carey M: A general mechanism for transcriptional synergy by eukaryotic activators. Nature 1995, 377:254-257. In gel shift assays and DNase I footprinting, multiple ZEBRA binding sites stimulate TFIID/TFIIA/DNA complex formation. The stimulation of TFIID/TFIIA/DNA complex correlates with a synergistic transcriptional response. The activator-dependent TFIID/TFIIA/DNA complex differs from the basal TFIID/TFIIA/DNA complex in the ability to stably interact with TFIIB. This interaction seems to be regulated by TAFs. Similar results with Gal4-VP16 suggest a model in which different types of activators can stimulate transcription at an early step in PIC assembly in a synergistic manner.
62. Roberts SGE, Ha I, Maldonado E, Reinberg D, Green MR: Interaction between an acidic activator and the general transcription factor TFIIB is required for transcriptional activation. Nature 1993, 363:741-744.
63. Kim TK, Roeder RG: Proline-rich activator CTF1 targets the TFIIB assembly step during transcriptional activation. Proc Natl Acad Sci USA 1994, 91:4170-4174.
64. Hori R, Pyo S, Carey M: Protease footprinting reveals a surface on transcription factor TFIIB that serves as an interface for activators and coactivators. Proc Natl Acad Sci USA 1995, 92:6047-6051.
65. Roberts SGE, Green MR: Activator-induced conformational change in general transcription factor TFIIB. Nature 1994, 371:717-720.
66. Colgan J, Wampler S, Manley JL: Interaction between a transcriptional activator and transcription factor IIB in vivo. Nature 1993, 362:549-553.
67. Hahn S: Clamping the TBP stirrup. Nature 1995, 377:481.
68. •], Gal11 appears to be part of holoenzyme. When Gal11 is tethered to a promoter by fusion to the LexA DNA-binding domain, it can activate transcription. Taken together, the results suggest that activators can function in part by recruiting holoenzyme to the promoter through contacts with a component of the complex.
69. Hengartner CJ, Thompson CM, Zhang J, Chao DM, Liao S-M, Koleske AJ, Okamura S, Young RA: Association of an activator with an RNA polymerase II holoenzyme. Genes Dev 1995, 9:897-910.
70. •].
71. •] identify MO15 (CDK7) and cyclin H as components of TFIIH, perhaps linking transcription, DNA repair and cell cycle control.
72. Feaver WJ, Svejstrup JQ, Henry NL, Kornberg RD: Relationship of CDK-activating kinase and RNA polymerase II CTD kinase TFIIH/TFIIK. Cell 1994, 79:1103-1109. This paper shows that KIN28 - the yeast homolog of CDK7 - is a component of yeast TFIIH/TFIIK.
73. Bohr VA, Smith CA, Okumoto DS, Hanawalt PC: DNA repair in an active gene: removal of pyrimidine dimers from the DHFR gene of CHO cells is much more efficient than in the genome overall. Cell 1985, 40:359-369.
74. Svejstrup JQ, Wang Z, Feaver WJ, Wu X, Bushnell DA, Donahue TF, Friedberg EC, Kornberg RD: Different forms of TFIIH for transcriptional and DNA repair: holo-TFIIH and a nucleotide excision repairosome. Cell 1995, 80:21-28. The purification of two forms of yeast TFIIH complexes is presented in this paper. One form is active in transcription and contains the TFIIK (CTD kinase) activity. The other form is not active in transcription, lacks TFIIK, but contains other polypeptides known to function in DNA repair.
75. Drapkin R, Reardon JT, Ansari A, Huang J, Zawel L, Ahn K, Sancar A, Reinberg D: Dual role of TFIIH in DNA excision repair and in transcription by RNA polymerase II. Nature 1994, 368:769-772. Purified TFIIH from human cells was found to complement three cell extracts deficient in excision repair, showing the dual role of TFIIH subunits.
76. Valay J-G, Simon M, Dubois M-F, Bensaude O, Facca C, Faye G: The KIN28 gene is required both for RNA polymerase II mediated transcription and phosphorylation of the Rpb1p CTD. J Mol Biol 1995, 249:535-544.
77. Cismowski MJ, Laff GM, Solomon MJ, Reed SI: KIN28 encodes a carboxy-terminal domain kinase that controls mRNA transcription in S. cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity. Mol Cell Biol 1995, 15:2983-2992.