Activation of RNA polymerase II transcription

Current Opinion in Cell Biology

Volumn 11, Issue 3, 1999, Pages 330-335

  Berk, Arnold J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS RECEPTOR; PROTEIN SUBUNIT; RNA POLYMERASE II; TATA BINDING PROTEIN;

EXCISION REPAIR; GENETIC TRANSCRIPTION; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN PURIFICATION; PROTEIN STRUCTURE; REVIEW; TRANSCRIPTION INITIATION; YEAST;

MAMMALIA;

EID: 0033152516     PISSN: 09550674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0955-0674(99)80045-3     Document Type: Review

References (51)

1. Berger S: Histone acetylases and transcriptional activation. Curr Opin Cell Biol 1999, 11:336-341.
2. Verrijzer CP, Tjian R: TAFs mediate transcriptional activation and promoter selectivity. Trends Biochem Sci 1996, 21:338-342.
3. Meyer VE, Young RA: RNA polymerase II holoenzymes and subcomplexes. J Biol Chem 1998, 273:27757-27760.
4. 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. Sixteen subunits of the Mediator subcomplex of the RNA polymerase II holoenzyme were characterized and their genes identified in the yeast genome. The requirement of the newly identified components for viability was determined and the Pol II carboxy-terminal domain was shown to be required for transcriptional stimulation by Mediator in vitro.
5. Tirode F, Busso D, Coin F, Egly JM: Reconstitution of the transcription factor TFIIH: Assignment of functions for the three enzymatic subunits, XPB, XPD, and Cdk7. Mol Cell 1999, 3:87-95. Nine subunit TFIIH was reconstituted by co-infecting cells with baculovirus recombinants individually expressing each one. Inactivating point mutations in the two helicase subunits and the Cdk7 protein kinase subunit were also reconstituted and their activities in basal transcription with recombinant GTFs analyzed.
6. Greenblatt J: RNA polymerase II holoenzyme and transcriptional regulation. Curr Opin Cell Biol 1997, 9:310-319.
7. Holstege FCP, Jennings EG, Wyrick JJ, Lee TI, Hengatner CJ, Green MR, Golub TR, Lander ES, Young RA: Dissecting the regulatory circuitry of a eukaryotic genome. Cell 1998, 95:717-728. DNA microarrays of virtually all S. cerevisiae genes were used to characterize the mRNAs expressed following a temperature shift in strains with ts mutations of the genes encoding several transcription proteins and in viable strains with deletions of others. Srb4, the Kin28 protein kinase subunit of TFIIH, and TAF17 were found to be required for transcription of most genes. Mutations in the genes encoding Srb5, Med6 and Srb10 affected only a fraction of genes, suggesting that these subunits of the holoenzyme respond to specific classes of activators and repressors.
8. Ptashne M, Gann A: Transcriptional activation by recruitment. Nature 1997, 386:569-577. See annotation [9•].
9. Keveaney 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. In these reviews [8•,9•] the authors present arguments that activators function primarily by stimulating the binding of a pre-initiation complex to a neighboring promoter as opposed to regulating the activity of a pre-bound pre-initiation complex.
10. 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. Binding of GTFs and holoenzyme components to a tethered template plus and minus activator in extracts from wild-type yeast and strains with mutations in the genes encoding several of the GTFs and holoenzyme subunits is assayed. The results indicate that TFIIA and TFIID bind first, followed by holoenzyme, and that the TATA-box sequence has a substantial influence on promoter strength independent of factor binding.
11. Kobayashi N, Horn PJ, Sullivan SM, Triezenberg SJ, Boyer TG, Berk AJ: Da-complex assembly activity required for VP16C transcription activation. Mol Cell Biol 1998, 18:4023-4031.
12. Carlson M: Genetics of transcriptional regulation in yeast: Connections to the RNA polymerase CTD. Annu Rev Cell Dev Biol 1997, 13:1-23.
13. Hengartner CJ, Meyer 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.
14. 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. A multiprotein complex is isolated from HeLa cells that contains homologs of the yeast Mediator. The complex inhibits activated in vitro transcription in a system with highly purified GTFs and the in vitro coactivator PC4. The complex phosphorylates the Pol II CTD at both Ser2 and Ser5 of the canonical heptapeptide repeat.
15. Myers LC, Gustafsson CM, Hayashibara KC, Brown PO, Kornberg RD: Mediator protein mutations that selectively abolish activated transcription. Proc Natl Acad Sci USA 1999, 96:67-72. Mediator was prepared from yeast strains with deletions in non-essential Mediator subunits. Some deletions abolished in vitro activation by Gal4-VP16 but not by Gcn4. DNA microarray genome-wide analysis of RNA from one of these strains (ΔAmed2) showed a significant decrease in ∼3% of genes in cells grown on galactose or under heat-shock conditions. These results show that some holoenzyme subunits mediate activation by specific classes of activators.
16. 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. A holoenzyme complex is characterized that is different from the most abundant one in yeast. Results are presented indicating that it functions in the expression of a specific class of genes.
17. Hahn S: The role of TAFs in RNA polymerase II transcription. Cell 1998, 95:579-582.
18. Koleske AJ, Young RA: An RNA polymerase holoenzyme responsive to activators. Nature 1994, 368:466-469.
19. 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.
20. Oelgesohiager 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.
21. Apone LM, Virbasius CA, Holstege FCP, Wang J, Young RA, Green MR: Broad, but not universal transcriptional requirement for yTAFII17, a hisonte H3-like TAFII present in TFIID and SAGA. Mol Cell 1998, 2:653-661. See annotation [23•].
22. Michel B, Komarnitsky P, Buratowski S: histone-like TAFs are essential for transcription in vivo. Mol Cell 1998, 2:663-673. See annotation [23•].
23. Moqtaderi Z, Keveaney M, Struhl K: The histone H3-like TAF is broadly required for transcription in yeast. Mol Cell 1998, 2:675-682. In papers [21•,22••,23•], and also [7••], the authors demonstrate that TAF17 is required for transcription of most yeast genes. In [22••] they make a strong argument that TAFIIs are generally required for Pol II transcription in vivo in yeast.
24. Goodrich JA, Hoey T, Thut CJ, ADmon A, Tjian R: Drosophila TAFII40 interacts with both a VP16 activation domain and the basal transcription factor TFIIB. Cell 1993, 75:519-530.
25. Natarajan K, Jackson BM, Rhee E, Hinnebusch AG: ytafii61 has a general role in RNA polymerase II transcription and is required by Gcn4p to recruit SAGA coactivator complex. Mol Cell 1998, 2:683-692. In this paper the authors show that reduced expression of the essential histone H2B-like domain of yeast TAF61 causes a generalized reduction in Pol II transcription.
26. Grant PA, Schietz D, Pray-Grant MG, Steger DJ, Reese JC, Yeates JR, Workman JL: A subset of TAFIIs are integral components of the SAGA complex required for nucleosome acetylation and transcription stimulation. Cell 1998, 94:45-53. The SAGA complex, a yeast multiprotein complex containing Gcn5 and exhibiting nucleosomal histone H3 acetyltransferase activity, was characterized. Several of the subunits were shown to be TAFIIs including the TAFIIs with histone-like domains shown in Table 1 of this review. SAGA isolated from a ts TAF68 strain retained the ability to acetylate free histone H3 but lost the ability to acetylate H3 in nucleosomes and to stimulate transcription in vitro from nucleosomal templates. The results suggest that the presumptive histone octamer-like structure formed by the histone-like TAFIIs is required to target the acetylase activity to nucleosomes and that the acetylation of nucleosomes is required for activation of nucleosomal templates.
27. 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.
28. Gu W, Malik S, Ito M, Yuan CX, Fondell JD, Zhang X, Martinez E, Qin J, Roeder RG: A novel SRB/MED-containing cofactor complex, SMCC, involved in transcription regulation. Mol Cell 1999 3:97-108. A multiprotein complex containing homologs of yeast SRB/Mediator subunits is described. Similar to the complex described in [14•], SMCC represses activated transcription in an in vitro system with purified GTFs and PC4; but in the absence of TFIIH, where no transcription is observed in the absence of the complex, addition of the complex does allow transcription, but only in the presence of activator. This demonstrates a potential for activating transcription similarly to yeast Mediator, although TFIIH is probably required for transcription in vivo, given the general requirement of TFIIH for in vivo transcription in yeast [7••].
29. 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 manner. Proc Natl Acad Sci USA 1998,95:7939-7944. This paper reports the cDNA cloning of two of the ten subunits of a complex that binds to the thyroid hormone receptor in response to ligand and which stimulates transcription in vitro. TRAP220 (which has also been cloned by others and given alternative names) is shown to bind to multiple nuclear receptors only in the presence of their specific ligands.
30. Ryu S, Zhou S, Ladurner AG, Tjian R: The transcriptional cofactor CRSP is required for activity of the enhancer-binding protein Sp1. Nature 1999 397:446-450. A nine subunit complex containing some homologs to yeast SRB/Mediator subunits of the holoenzyme is purified from HeLa cell nuclear extract on the basis of its ability to support Sp1 activated transcription in an in vitro system with partially purified GTFs and highly purified TFIID. The CRSP complex also supports activation in a highly purified system, but activation strictly requires TAFIIs since it is observed with TFIID but not with TBP.
31. Singh N, Han M: Sur-2, a novel gene, functions late in the let-60 ras-mediated signaling pathway during Caenorhabditis elegans vulval induction. Genes Dev 1995, 9:2251-2265.
32. Jackson BM, Drysdale CM, Natarajan K, Hinnebusch AG: Identification of seven hydrophobic clusters in GCN4 making redundant contributions to transcriptional activation. Mol Cell Biol 1996, 16:5557-5571.
33. Uesugi M, Nyanguile O, Lu H, Levine AJ, Verdine GL. Induced alpha helix in the VP16 activation domain upon binding to a human TAF. Science 1997, 277:1310-1313.
34. Sullivan SM, Horn PJ, Olson VA, Koop AH, Niu W, Ebright RH, Triezenberg SJ: Mutational analysis of transcriptional activation region of the VP16 protein of herpes simplex virus. Nucleic Acids Res 1998, 26:4487-4496.
35. Radhakrishnan I, Perez-Alvarado G, Parker G, Dyson HJ, MOntminy M, Wright PA: Solution structure of the KIX domain of CBP bound to the transactivation domain of CREB: A model for activator-coactivator interactions. Cell 1997, 91:741-752.
36. Nolte RT, Wisely GB, Westin S, Cobb JE, Lambert MH, Kurokawa R, Rosenfeld MG, Willson TM, Glass CK, Milburn MV: Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-γ. Nature 1998, 395:137-143. See annotation [38•].
37. Darimont BD, Wagner RL, Apriletti JW, Stallcup MR, Kushner PJ, Baxter JD, Fletterick RJ, Yamamoto KR: Structure and specificity of nuclear receptor-coactivator interactions. Genes Dev 1998, 12:3343-3356. See annotation [38•].
38. Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, Agard DA, Greene GL: The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 1998, 95:927-937. In papers [36•-38•] the structures of the ligand-binding domains (LBDs) of nuclear receptors bound to LXXLL (NR box) peptides from nuclear receptor co-activators are presented. The requirement for large conformational changes in the LBDs in response to binding their specific ligands is explained. The co-activator peptides form short amphipathic α-helices that interact with shallow hydrophobic grooves in the ligand-bound LBDs.
39. Merika M, Williams AJ, Chen G, Collins T, Thanos D: Recruitment of CBP/p300 by the IFNβ enhancesome is required for synergistic activation of transcription. Mol Cell 1998, 1:277-287.
40. Wathelet MG, Lin CH, Parekh BS, Ronco LV, Howley PM, Maniatis T: Virus infection induces assembly of coordinately activated transcription factors on the IFN-β enhancer in vivo. Mol Cell 1998, 1:507-518.
41. Parker D, Jhala US, Radhakrishnan I, Yaffe MB, Reyes C, Shulman AI, Cantley LC, Wright PE, MOntminy M: Analysis of an activator:coactivator complex reveals an essential role for secondary structure in transcriptional activation. Mol Cell 1998, 2:353-359.
42. Utley RT, Ikeda K, Grant PA, Cotes J, Steger DJ, Eberharter A, John S, Workman JL: Transcriptional activators direct histone acetyltransferase complexes to nucleosomes. Nature 1998, 394:498-502. Yeast SAGA and NuA4 multiprotein histone acetylase complexes were shown to bind to VP16 and Gcn4 activation domains, to target histone acetylation to nucleosomes with activator binding sites in vitro, and to stimulate in vitro activated transcription from nucleosomal templates.
43. Ogryzko VV, Kotani T, Zhang X, Schiltz 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. A mammalian PCAF multisubunit histone acetylase complex was purified. Like the yeast SAGA complex [26••], the PCAF and related hGCN5 complexes were shown to contain several TAFIIs, including those with histone-like folds.
44. Kuo MH, Zhuo J, Jambeck P, Churchill MEA, Allis CD: Histone acetyltransferase activity of yeast gcn5 is required for the activation of target genes in vivo. Genes Dev 1998,12:627-639. Gcn5 was shown to induce localized histone H3 acetylation of nucleosomes neighboring an activator binding site and this activity was correlated with transcriptional stimulation through the analysis of a large set of Gcn5 mutants.
45. Parekh BS, Maniatis T: Virus infection leads to localized hyperacetylation of histones H3 and H4 at the IFN-β promoter. Mol Cell 1999, 3:125-129. H3 and H4 histones were shown to be hyperacetylated in the region of the enhancer and promoter of two mammalian genes activated by viral infection.
46. Gregory PD, Schmid A, Zavari M, Liu L, Berger SL, Horz W: Absence of gcn5 HAT activity defines a novel state in opening of chromatin at the PHO5 promoter in yeast. Mol Cell 1998, 1:495-505. The influence of Gcn5 histone acetylation on chromatin structure was analyzed in the yeast PHO5 promoter where an ordered nucleosomal array places the TATA-box and one of two Pho4 activator binding sites within neighboring nucleosomes in the uninduced promoter. In the absence of Gcn5 histone acetylation, the nucleosomal template appeared more stable and partially resisted the nucleosome-disrupting activity of Pho4. As additional Pho4 binding sites largely compensated for a gcn5 deletion, it appears that there is a fine balance between the association of nucleosomes with the promoter region and their disruption by an activator, and that transcription factor binding is favored when histone amino termini are acetylated.
47. Chang M, French-Cornay D, Fan HY, Klein H, Denis CL, Jaehning JA: A complex containing RNA pol II, Paf1p, Cdc73p, Hpr1p and Ccr4p plays a role in protein kinase C signalling. Mol Cell Biol 1999, 19:1056-1067.
48. Boyer TJ, Martin MED, Lees M, Ricciardi RP, Berk AJ: Mammalian SPB/mediator complex is targeted by adenovirus E1A protein. Nature 1999, in press.
49. Rachez C, Lemon BD, Suldan Z, Bromleigh V, Gamble M, Naar AM, Erdjument-Bromage H, Tempst P, Freedman LP: Ligand dependent transcription activation by nuclear receptors requires the DRIP complex. Nature 1999, 398:824-828.
50. Naar AM, Beaurang PA, Zhou S, Abraham S, Solomon W, Tijan R: Composite co-activator ARC mediates chromatin-directed transcriptional activation. Nature 1999, 398:828-832.
51. Ito M, Yuan CX, Malik S, Gu W, Fondell JD, Yamamura S, Fu ZY, Zhang X, Qin J, Roeder RG: Identity between TRAP and SMCC complexes indicates novel pathways for the function of nuclear receptors and diverse mammalian activators. Mol Cell 1999, 3:361-370.