Advertisement

Mechanisms of Transcriptional Activation in Eukaryotes

  • F. J. Herrera
  • D. D. Shooltz
  • S. J. Triezenberg
Part of the Handbook of Experimental Pharmacology book series (HEP, volume 166)

Abstract

Eukaryotic cells respond to growth, developmental and environmental cues in large part by regulating the expression of specific sets of genes. Befitting the wide range of these signals and the proper gene regulatory response, mechanisms of transcriptional activation in eukaryotes are impressively diverse. These mechanisms are built on the modular design of cis-acting DNA regulatory sequences and of trans-acting regulatory proteins, coupled with flexibility and diversity in the protein:protein interactions linking activators to chromatin-modifying enzymes and general transcription factors. This review summarizes and illustrates these principles of modular design and combinatorial logic underlying transcriptional activation in eukaryotes.

Keywords

Gene regulation Transcription RNA polymerase II Chromatin Enhancer 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Alexeev A, Mazin A, Kowalczykowski SC (2003) Rad54 protein possesses chromatin-remodeling activity stimulated by the Rad51-ssDNA nucleoprotein filament. Nat Struct Biol 10:182–186PubMedCrossRefGoogle Scholar
  2. Almlof T, Wallberg AE, Gustafsson JA, Wright AP (1998) Role of important hydrophobic amino acids in the interaction between the glucocorticoid receptor ψ 1-core activation domain and target factors. Biochemistry 37:9586–9594PubMedCrossRefGoogle Scholar
  3. Anest V, Hanson JL, Cogswell PC, Steinbrecher KA, Strahl BD, Baldwin AS (2003) A nucleosomal funct ion for IκB kinase-α in Nli-κB-dependent gene expression. Nature 423:659–663PubMedCrossRefGoogle Scholar
  4. Auboeuf D, Honig A, Berget SM, O’Malley BW (2002) Coordinate regulation of transcription and splicing by steroid receptor coregulators. Science 298:416–419PubMedCrossRefGoogle Scholar
  5. Bajic VB, Tan SL, Chong A, Tang S, Strom A, Gustafsson JA, Lin CY, Liu ET (2003) Dragon ERE Finder version 2: A tool for accurate detection and analysis of estrogen response elements in vertebrate genomes. Nucl Acids Res 31:3605–3607PubMedCrossRefGoogle Scholar
  6. Bannister AJ, Schneider R, Kouzarides T (2002) Histone methylation: dynamic or static? Cell 109:801–806PubMedCrossRefGoogle Scholar
  7. Barboric M, Nissen RM, Kanazawa S, Jabrane-Ferrat N, Peterlin BM (2001) NF-κB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II. Mol Cell 8:327–337PubMedCrossRefGoogle Scholar
  8. Beerli RR, Barbas CF, 3rd (2002) Engineering polydactyl zinc-finger transcription factors. Nat Biotechnol 20:135–141PubMedCrossRefGoogle Scholar
  9. Berger SL (2002) Histone modifications in transcriptional regulation. Curr Opin Genet Dev 12:142–148PubMedCrossRefGoogle Scholar
  10. Boardman PE, Oliver SG, Hubbard SJ (2003) SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences. Nucl Acids Res 31:3572–3575PubMedCrossRefGoogle Scholar
  11. Boube M, Joulia L, Cribbs DL, Bourbon HM (2002) Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man. Cell 110:143–151PubMedCrossRefGoogle Scholar
  12. Brooks CL, Gu W (2003) Ubiquitination, phosphorylation and acetylation: the molecular basis for p53 regulation. Curr Opin Cell Biol 15:164–171PubMedCrossRefGoogle Scholar
  13. Brown SA, Imbalzano AN, Kingston RE (1996) Activator-dependent regulation of transcriptional pausing on nucleosomal templates. Genes Dev 10:1479–1490PubMedCrossRefGoogle Scholar
  14. Brown SA, Weirich CS, Newton EM, Kingston RE (1998) Transcriptional activation domains stimulate initiation and elongation at different times and via different residues. EMBOJ 17:3146–3154CrossRefGoogle Scholar
  15. Brownell JE, Zhou J, Ranalli T, Kobayashi R, Edmondson DG, Roth SY, Allis CD (1996) Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84:843–851PubMedCrossRefGoogle Scholar
  16. Bultman S, Gebuhr T, Yee D, La Mantia C, Nicholson J, Gilliam A, Randazzo F, Metzger D, Chambon P, Crabtree G, Magnuson T (2000) A Brg1 null mutation in the mouse reveals functional differences among mammalian SWI/SNF complexes. Mol Cell 6:1287–1295PubMedCrossRefGoogle Scholar
  17. Buratowski S, Hahn S, Guarente L, Sharp PA (1989) Five intermediate complexes in transcription initiation by RNA polymerase II. Cell 56:549–561PubMedCrossRefGoogle Scholar
  18. Burley SK, Roeder RG (1996) Biochemistry and structural biology of transcription factor IID (TFIID). Annu Rev Biochem 65:769–799PubMedCrossRefGoogle Scholar
  19. Butler JE, Kadonaga JT (2001) Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev 15:2515–2519PubMedCrossRefGoogle Scholar
  20. Candau R, Moore PA, Wang L, Barlev N, Ying CY, Rosen CA, Berger SL (1996) Identification of human proteins functionally conserved with the yeast putative adaptors ADA2and GCN5. Mol Cell Biol 16:593–602PubMedGoogle Scholar
  21. Candau R, Scolnick DM, Darpino P, Ying CY, Halazonetis TD, Berger SL (1997) Two tandem and independent sub-activation domains in the amino terminus of p53 require the adaptor complex for activity. Oncogene 15:807–816PubMedCrossRefGoogle Scholar
  22. Carrozza MJ, Utley RT, Workman JL, Cote J (2003) The diverse functions of histone acetyltransferase complexes. Trends Genet 19:321–329PubMedCrossRefGoogle Scholar
  23. Cheung P, Tanner KG, Cheung WL, Sassone-Corsi P, Denu JM, Allis CD (2000) Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation. Mol Cell 5:905–915PubMedCrossRefGoogle Scholar
  24. Chiang CM, Roeder RG (1995) Cloning of an intrinsic human TFIID subunit that interacts with multiple transcriptional activators. Science 267:531–536PubMedCrossRefGoogle Scholar
  25. Cho EJ, Kobor MS, Kim M, Greenblatt J, Buratowski S (2001) Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNApolymerase II C-terminal domain. Genes Dev 15:3319–3329PubMedCrossRefGoogle Scholar
  26. Citterio E, Van Den Boom V, Schnitzler G, Kanaar R, Bonte E, Kingston RE, Hoeijmakers JH, Vermeulen W (2000) ATP-dependent chromatin remodeling by the Cockayne syndrome B DNA repair-transcription-coupling factor. Mol Cell Biol 20:7643–7653PubMedCrossRefGoogle Scholar
  27. Corbi N, Perez M, Maione R, Passananti C (1997) Synthesis of a new zinc finger peptide; comparison of its ‘code’ deduced and ‘CASTing’ derived binding sites. FEBS Lett 417:71–74PubMedCrossRefGoogle Scholar
  28. Cox JM, Hayward MM, Sanchez JF, Gegnas LD, van der Zee S, Dennis JH, Sigler PB, Schepartz A (1997) Bidirectional binding of the TATA box binding protein to the TATA box. Proc Natl Acad Sci USA 94:13475–13480PubMedCrossRefGoogle Scholar
  29. Cramer P, Pesce CG, Baralle FE, Kornblihtt AR (1997) Functional association between promoter structure and transcript alternative splicing. Proc Natl Acad Sci USA 94:11456–11460PubMedCrossRefGoogle Scholar
  30. Cress WD, Triezenberg SJ (1991) Critical structural elements of the VP16 transcriptional activation domain. Science 251:87–90PubMedCrossRefGoogle Scholar
  31. Dahlman-Wright K, Baumann H, McEwan IJ, Almlof T, Wright AP, Gustafsson JA, Hard T (1995) Structural characterization of a minimal functional transactivation domain from the human glucocorticoid receptor. Proc Natl Acad Sci USA 92:1699–1703PubMedCrossRefGoogle Scholar
  32. Dynlacht BD, Hoey T, Tjian R (1991) Isolation of coactivators associated with the TATA-binding protein that mediate transcriptional activation. Cell 66:563–576PubMedCrossRefGoogle Scholar
  33. Ebbert R, Birkmann A, Schuller HJ (1999) The product of the SNF2/SWI2 paralogue INO80 of Saccharomyces cerevisiae required for efficient expression of various yeast structural genes is part of a high-molecular-weight protein complex. Mol Microbiol 32:741–751PubMedCrossRefGoogle Scholar
  34. Eisen JA, Sweder KS, Hanawalt PC (1995) Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucl Acids Res 23:2715–2723PubMedCrossRefGoogle Scholar
  35. Emami KH, Navarre WW, Smale ST (1995) Core promoter specificities of the Sp1 and VP16 transcriptional activation domains. Mol Cell Biol 15:5906–5916PubMedGoogle Scholar
  36. Evans R, Fairley JA, Roberts SG (2001) Activator-mediated disruption of sequence-specific DNA contacts by the general transcription factor TFIIB. Genes Dev 15:2945–2949PubMedCrossRefGoogle Scholar
  37. Falke D, Juliano RL (2003) Selective gene regulation with designed transcription factors: implications for therapy. Curr Opin Mol Ther 5:161–166PubMedGoogle Scholar
  38. Felinski EA, Quinn PG (1999) The CREB constitutive activation domain interacts with TATA-binding protein-associated factor 110 (TAF110) through specific hydrophobic residues in one of the three subdomains required for both activation and TAF110 binding. J Biol Chem 274:11672–11678PubMedCrossRefGoogle Scholar
  39. Ferdous A, Kodadek T, Johnston SA (2002) A nonproteolytic function of the 19S regulatory subunit of the 26S proteasorne is required for efficient activated transcription by human RNA polymerase II. Biochemistry 41:12798–12805PubMedCrossRefGoogle Scholar
  40. Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CD, Khorasanizadeh S (2003) Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev 17:1870–1881PubMedCrossRefGoogle Scholar
  41. Garvie CW, Wolberger C (2001) Recognition of specific DNA sequences. Mol Cell 8:937–946PubMedCrossRefGoogle Scholar
  42. Ge K, Guermah M, Yuan CX, Ito M, Wallberg AE, Spiegelman BM, Roeder RG (2002) Transcription coactivator TRAP220 is required for PPAR gamma 2-stimulated adipogenesis. Nature 417:563–567PubMedCrossRefGoogle Scholar
  43. Ghosh S, Karin M (2002) Missing pieces in the NF-κB puzzle. Cell 109 Suppl: S81-96Google Scholar
  44. Gill G, Pascal E, Tseng ZH, Tjian R (1994) A glutamine-rich hydrophobic patch in transcription factor Sp1 contacts the dTAFII110 component of the Drosophila TFIID complex and mediates transcriptional activation. Proc Natl Acad Sci USA 91:192–196PubMedCrossRefGoogle Scholar
  45. Gonzalez F, Delahodde A, Kodadek T, Johnston SA (2002) Recruitment of a 19S proteasome subcomplex to an activated promoter. Science 296:548–550PubMedCrossRefGoogle Scholar
  46. Goodrich JA, Hoey T, Thut CT, Admon A, Tjian R (1993) Drosophila TAFII40 interacts with both a VP16 activation domain and the basal transcription factor TFIIB. Cell 75:519–530PubMedCrossRefGoogle Scholar
  47. Gossen M, Bujard H (1992) Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc Natl Acad Sci USA 89:5547–5551PubMedCrossRefGoogle Scholar
  48. Gossen M, Bujard H (2002) Studying gene function in eukaryotes by conditional gene inactivation. Annu Rev Genet 36:153–173PubMedCrossRefGoogle Scholar
  49. Gossen M, Freundlieb S, Bender G, Muller G, Hillen W, Bujard H (1995) Transcriptional activation by tetracyclines in mammalian cells. Science 268:1766–1769PubMedCrossRefGoogle Scholar
  50. Grabe N (2002) AliBaba2: context specific identification of transcription factor binding sites. In Silico Biol 2:S1–15PubMedGoogle Scholar
  51. Grant PA, Schieltz D, Pray-Grant MG, Steger DJ, Reese JC, Yates JR, 3rd, Workman JL (1998) A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell 94:45–53PubMedCrossRefGoogle Scholar
  52. Hampsey M, Reinberg D (1999) RNA polymerase II as a control panel for multiple coactivator complexes. Curr Opin Genet Dev 9:132–139PubMedCrossRefGoogle Scholar
  53. Hampsey M, Reinberg D (2003) Tails of intrigue: phosphorylation of RNA polymerase II mediates histone methylation. Cell 113:429–432PubMedCrossRefGoogle Scholar
  54. Hassan AH, Prochasson P, Neely KE, Galasinski SC, Chandy M, Carrozza MJ, Workman JL (2002) Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111:369–379PubMedCrossRefGoogle Scholar
  55. Hayashi F, Ishima R, Liu D, Tong KI, Kim S, Reinberg D, Bagby S, Ikura M (1998) Human general transcription factor TFIIB: conformational variability and interaction with VP16 activation domain. Biochemistry 37:7941–7951PubMedCrossRefGoogle Scholar
  56. Heery DM, Kalkhoven E, Hoare S, Parker MG (1997) A signature motif in transcriptional co-activators mediates binding to nuclear receptors. Nature 387:733–736PubMedCrossRefGoogle Scholar
  57. Hengartner CT, Thompson CM, Zhang J, Chao DM, Liao SM, Koleske AJ, Okamura S, Young RA (1995) Association of an activator with an RNA polymerase II holoenzyme. Genes Dev 9:897–910PubMedCrossRefGoogle Scholar
  58. Henry KW, Wyce A, Lo WS, Duggan LJ, Emre NC, Kao CF, Pillus L, Shilatifard A, Osley MA, Berger SL (2003) Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev 17:2648–2663PubMedCrossRefGoogle Scholar
  59. Hudson BP, Martinez-Yamout MA, Dyson HJ, Wright PE (2000) Solution structure and acetyl-lysine binding activity of the GCN5 bromodomain. J Mol Biol 304:355–370PubMedCrossRefGoogle Scholar
  60. Iizuka M, Smith MM (2003) Functional consequences of histone modifications. Curr Opin Genet Dev 13:154–160PubMedCrossRefGoogle Scholar
  61. Ingles CT, Shales M, Cress WD, Triezenberg SJ, Greenblatt J (1991) Reduced binding of TFIID to transcriptionally compromised mutants of VP16. Nature 351:588–590PubMedCrossRefGoogle Scholar
  62. Ito M, Yuan CX, Malik S, Gu W, Fondell JD, Yamamura S, Fu ZY, Zhang X, Qin J, Roeder RG (1999) Identity between TRAP and SMCC complexes indicates novel pathways for the function of nuclear receptors and diverse mammalian activators. Mol Cell 3:361–370PubMedCrossRefGoogle Scholar
  63. Jackson BM, Drysdale CM, Natarajan K, Hinnebusch AG (1996) Identification of seven hydrophobic clusters in GCN4 making redundant contributions to transcriptional activation. Mol Cell Biol 16:5557–5571PubMedGoogle Scholar
  64. Jeddeloh JA, Stokes TL, Richards EJ (1999) Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 22:94–97PubMedCrossRefGoogle Scholar
  65. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080PubMedCrossRefGoogle Scholar
  66. Joliot V, Demma M, Prywes R (1995) Interaction with RAP74 subunit of TFIIF is required for transcriptional activation by serum response factor. Nature 373:632–635PubMedCrossRefGoogle Scholar
  67. Kadonaga JT (2002) The DPE, a core promoter element for transcription by RNA polymerase II. Exp Mol Med 34:259–264PubMedGoogle Scholar
  68. Kamiuchi T, Abe E, Imanishi M, Kaji T, Nagaoka M, Sugiura Y (1998) Artificial nine zinc-finger peptide with 30 base pair binding sites. Biochemistry 37:13827–13834PubMedCrossRefGoogle Scholar
  69. Kanazawa S, Okamoto T, Peterlin BM (2000) Tat competes with CIITA for the binding to P-TEFb and blocks the express ion of MHC class II genes in HIV infection. Immunity 12:61–70PubMedCrossRefGoogle Scholar
  70. Kanazawa S, Soucek L, Evan G, Okamoto T, Peterlin BM (2003) c-Myc recruits P-TEFb for transcription, cellular proliferation and apoptosis. Oncogene 22:5707–5711PubMedCrossRefGoogle Scholar
  71. Kays AR, Schepartz A (2002) Ga14-VP16 and GaI4-AH increase the orientational and axial specificity of TATA box recognition by TATA box binding protein. Biochemistry 41:3147–3155PubMedCrossRefGoogle Scholar
  72. Kel AE, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E (2003) MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucl Acids Res 31:3576–3579PubMedCrossRefGoogle Scholar
  73. Kim J, Sif S, Jones B, Jackson A, Koipally J, Heller E, Winandy S, Viel A, Sawyer A, Ikeda T, Kingston R, Georgopoulos K (1999) Ikaros DNA-binding proteins direct formation of chromatin remodeling complexes in lymphocytes. Immunity 10:345–355PubMedCrossRefGoogle Scholar
  74. Kim LJ, Seto AG, Nguyen TN, Goodrich JA (2001) Human Taf(II)130 is a coactivator for NFATp. Mol Cell Biol 21:3503–3513PubMedCrossRefGoogle Scholar
  75. Kim YJ, Bjorklund S, Li Y, Sayre MH, Kornberg RD (1994) A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77:599–608PubMedCrossRefGoogle Scholar
  76. Klemm RD, Goodrich JA, Zhou S, Tjian R (1995) Molecular cloning and express ion of the 32-kDa subunit of human TFIID reveals interactions with VP16 and TFIIB that mediate transcriptional activation. Proc Natl Acad Sci USA 92:5788–5792PubMedCrossRefGoogle Scholar
  77. Kobayashi N, Boyer TG, Berk AJ (1995) A class of activation domains interacts directly with TFIIA and stimulates TFIIA-TFIID-promoter complex assembly. Mol Cell Biol 15:6465–6473PubMedGoogle Scholar
  78. Kobayashi N, Horn PJ, Sullivan SM, Triezenberg SJ, Boyer TG, Berk AJ (1998) DA-complex assembly activity required for VP16C transcriptional activation. Mol Cell Biol 18:4023–4031PubMedGoogle Scholar
  79. Kokubo T, Gong DW, Yamashita S, Horikoshi M, Roeder RG, Nakatani Y (1993) Drosophila 230-kD TFIID subunit, a functional homolog of the human cell cycle gene product, negatively regulates DNA binding of the TATA box-binding subunit of TFIID. Genes Dev 7:1033–1046PubMedCrossRefGoogle Scholar
  80. Kokubo T, Swanson MJ, Nishikawa JI, Hinnebusch AG, Nakatani Y (1998) The yeast TAF145 inhibitory domain and TFIIA competitively bind to TATA-binding protein. Mol Cell Biol 18:1003–1012PubMedGoogle Scholar
  81. Koleske AJ, Young RA (1994) An RNA polymerase II holoenzyme responsive to activators. Nature 368:466–469PubMedCrossRefGoogle Scholar
  82. Kotani T, Banno K, Ikura M, Hinnebusch AG, Nakatani Y, Kawaichi M, Kokubo T (2000) A role of transcriptional activators as antirepressors for the autoinhibitory activity of TATA box binding of transcription factor IID. Proc Natl Acad Sci USA 97:7178–7183PubMedCrossRefGoogle Scholar
  83. Kotani T, Miyake T, Tsukihashi Y, Hinnebusch AG, Nakatani Y, Kawaichi M, Kokubo T (1998) Identification of highly conserved amino-terminal segments of dTAFII230 and yTAFII145 that are functionally interchangeable for inhibiting TBP-DNA interactions in vitro and in promoting yeast cell growth in vivo. J Biol Chem 273:32254–32264PubMedCrossRefGoogle Scholar
  84. Kouzarides T (2002) Histone methylation in transcriptional control. Curr Opin Genet Dev 12:198–209PubMedCrossRefGoogle Scholar
  85. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C, Shilatifard A, Buratowski S, Greenblatt J (2003) Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol 23:4207–4218PubMedCrossRefGoogle Scholar
  86. Kulkarni MM, Arnosti DN (2003) Information display by transcriptional enhancers. Development 130:6569–6575PubMedCrossRefGoogle Scholar
  87. Kumar KP, Akoulitchev S, Reinberg D (1998) Promoter-proximal stalling results from the inability to recruit transcription factor IIH to the transcription complex and is a regulated event. Proc Natl Acad Sci USA95:9767–9772Google Scholar
  88. Kuo MH, Zhou J, Iambeck P, Churchill ME, Allis CD (1998) Histone acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in vivo. Genes Dev 12:627–639PubMedCrossRefGoogle Scholar
  89. Kusch T, Guelman S, Abmayr SM, Workman JL (2003) Two Drosophila Ada2 homologues function in different multiprotein complexes. Mol Cell Biol 23:3305–3319PubMedCrossRefGoogle Scholar
  90. Kussie PH, Gorina S, Marechal V, Elenbaas B, Moreau J, Levine AJ, Pavletich NP (1996) Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274:948–953PubMedCrossRefGoogle Scholar
  91. Lachner M, Jenuwein T (2002) The many faces of histone lysine methylation. Curr Opin Cell Biol 14:286–298PubMedCrossRefGoogle Scholar
  92. Larschan E, Winston F (2001) The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev 15:1946–1956PubMedCrossRefGoogle Scholar
  93. Lau JF, Nusinzon I, Burakov D, Freedman LP, Horvath CM (2003) Role of metazoan mediator proteins in interferon-responsive transcription. Mol Cell Biol 23:620–628PubMedCrossRefGoogle Scholar
  94. Lee C, Chang JH, Lee HS, Cho Y (2002) Structural basis for the recognition of the E2F transactivation domain by the retinoblastoma tumor suppressor. Genes Dev 16:3199–3212PubMedCrossRefGoogle Scholar
  95. Lieberman PM, Berk AJ (1994) A mechanism for TAFs in transcriptional activation: activation domain enhancement of TFIID-TFIIA-promoter DNA complex formation. Genes Dev 8:995–1006PubMedCrossRefGoogle Scholar
  96. Lin Q, Barbas CF, 3rd, Schultz PG (2003) Small-molecule switches for zinc finger transcription factors. J Am Chem Soc 125:612–613PubMedCrossRefGoogle Scholar
  97. Lin YS, Ha I, Maldonado E, Reinberg D, Green MR (1991) Binding of general transcription factor TFIIB to an acidic activating region. Nature 353:569–571PubMedCrossRefGoogle Scholar
  98. Lipford JR, Deshaies RJ (2003) Diverse roles for ubiquitin-dependent proteolysis in transcriptional activation. Nat Cell Biol 5:845–850PubMedCrossRefGoogle Scholar
  99. Liu PQ, Rebar EJ, Zhang L, Liu Q, Jamieson AC, Liang Y, Qi H, Li PX, Chen B, Mendel MC, Zhong X, Lee YL, Eisenberg SP, Spratt SK, Case CC, Wolffe AP (2001) Regulation of an endogenous locus using a panel of designed zinc finger proteins targeted to accessible chromatin regions. Activation of vascular endothelial growth factor A. J Biol Chem 276:11323–11334PubMedCrossRefGoogle Scholar
  100. Lo WS, Duggan L, Tolga NC, Emre, Belotserkovskya R, Lane WS, Shiekhattar R, Berger SL (2001) Snf1-a histone kinase that works in concert with the histone acetyltransferase Gcn5 to regulate transcription. Science 293:1142–1146PubMedCrossRefGoogle Scholar
  101. Lo WS, Trievel RC, Rojas JR, Duggan L, Hsu JY, Allis CD, Marmorstein R, Berger SL (2000) Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14. Mol Cell 5:917–926PubMedCrossRefGoogle Scholar
  102. Luscombe NM, Thornton JM (2002) Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J Mol Biol 320:991–1009PubMedCrossRefGoogle Scholar
  103. Lusser A, Kadonaga JT (2003) Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25:1192–1200PubMedCrossRefGoogle Scholar
  104. Malik S, Roeder RG (2000) Transcriptional regulation through Mediator-like coactivators in yeast and metazoan cells. Trends Biochem Sci 25:277–283PubMedCrossRefGoogle Scholar
  105. Maniatis T, Reed R (2002) An extensive network of coupling among gene expression machines. Nature 416:499–506PubMedCrossRefGoogle Scholar
  106. Marcus GA, Horiuchi J, Silverman N, Guarente L (1996) ADA5/SPT20 links the ADA and SPT genes, which are involved in yeast transcription. Mol Cell Biol 16:3197–3205PubMedGoogle Scholar
  107. Marmorstein R, Fitzgerald MX (2003) Modulation of DNA-binding domains for sequence-specific DNA recognition. Gene 304:1–12PubMedCrossRefGoogle Scholar
  108. Martel LS, Brown HJ, Berk AJ (2002) Evidence that TAF-TATA box-binding protein interactions are required for activated transcription in mammalian cells. Mol Cell Biol 22:2788–2798PubMedCrossRefGoogle Scholar
  109. Martin ML, Lieberman PM, Curran T (1996) Fos-Jun dimerization promotes interaction of the basic region with TFIIE-34 and TFIIF. Mol Cell Biol 16:2110–2118PubMedGoogle Scholar
  110. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucl Acids Res 31:374–378PubMedCrossRefGoogle Scholar
  111. McEwan IJ, Dahlman-Wright K, Ford J, Wright AP (1996) Functional interaction of the c-Myc transactivation domain with the TATA binding protein: evidence for an induced fit model of transactivation domain folding. Biochemistry 35:9584–9593PubMedCrossRefGoogle Scholar
  112. McKenna NJ, O’Malley BW (2002a) Combinatorial control of gene expression by nuclear receptors and coregulators. Cell 108:465–474PubMedCrossRefGoogle Scholar
  113. McKenna NJ, O’Malley BW (2002b) Minireview: nuclear receptor coactivators—an update. Endocrinology 143:2461–2465PubMedCrossRefGoogle Scholar
  114. Merika M, Thanos D (2001) Enhanceosomes. Curr Opin Genet Dev 11:205–208PubMedCrossRefGoogle Scholar
  115. Min J, Zhang Y, Xu RM (2003) Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev 17:1823–1828PubMedCrossRefGoogle Scholar
  116. Mitchell PJ, Tjian R (1989) Transcriptional regulation in mammalian cells by sequencespecific DNA binding proteins. Science 245:371–378PubMedCrossRefGoogle Scholar
  117. Mittler G, Stuhler T, Santolin L, Uhlmann T, Kremmer E, Lottspeich F, Berti L, Meisterernst M (2003) A novel docking site on Mediator is critical for activation by VP16 in mammalian cells. EMBOJ 22:6494–6504CrossRefGoogle Scholar
  118. Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, Wu C (2004) ATP-Driven Exchange of histone H2AZ variant catalyzed by SWRI chromatin remodeling complex. Science 303:343–348PubMedCrossRefGoogle Scholar
  119. Muratani M, Tansey WP (2003) How the ubiquitin-proteasome system controls transcription. Nat Rev Mol Cell Biol 4:192–201PubMedCrossRefGoogle Scholar
  120. Myers LC, Kornberg RD (2000) Mediator of transcriptional regulation. Annu Rev Biochem 69:729–749PubMedCrossRefGoogle Scholar
  121. Narlikar GJ, Fan HY, Kingston RE (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell 108:475–487PubMedCrossRefGoogle Scholar
  122. Ng HH, Robert F, Young RA, Struhl K (2002) Genome-wide location and regulated recruitment of the RSCnucleosome-remodeling complex. Genes Dev 16:806–819PubMedCrossRefGoogle Scholar
  123. Ng HH, Robert F, Young RA, Struhl K (2003) Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell 11:709–719PubMedCrossRefGoogle Scholar
  124. Nishikawa J, Kokubo T, Horikoshi M, Roeder RG, Nakatani Y (1997) Drosophila TAF(II)230 and the transcriptional activator VP16 bind competitively to the TATA box-binding domain of the TATA box-binding protein. Proc Natl Acad Sci USA 94:85–90PubMedCrossRefGoogle Scholar
  125. Nogues G, Kadener S, Cramer P, Bentley D, Kornblihtt AR (2002) Transcriptional activators differ in their abilities to control alternative splicing. J Biol Chem 277:43110–43114PubMedCrossRefGoogle Scholar
  126. Nowak SJ, Corces VG (2000) Phosphorylation of histone H3 correlates with transcriptionally active loci. Genes Dev 14:3003–3013PubMedCrossRefGoogle Scholar
  127. O’Hare P, Williams G (1992) Structural studies of the acidic transactivation domain of the Vmw65 protein of herpes simplex virus using 1H NMR. Biochemistry 31:4150–4156PubMedCrossRefGoogle Scholar
  128. Ottosen S, Herrera FJ, Triezenberg SJ (2002) Transcription. Proteasome parts at gene promoters. Science 296:479–481PubMedCrossRefGoogle Scholar
  129. Pascreau G, Arlot-Bonnemains Y, Prigent C (2003) Phosphorylation of histone and histone-like proteins by aurora kinases during mitosis. Prog Cell Cycle Res 5:369–374PubMedGoogle Scholar
  130. Pearson A, Greenblatt J (1997) Modular organization of the E2Fl activation domain and its interaction with general transcription factors TBP and TFIIH. Oncogene 15:2643–2658PubMedCrossRefGoogle Scholar
  131. Praz V, Perier R, Bonnard C, Bucher P (2002) The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucl Acids Res 30:322–324PubMedCrossRefGoogle Scholar
  132. Proudfoot NJ, Furger A, Dye MJ (2002) Integrating mRNA processing with transcription. Cell 108:501–512PubMedCrossRefGoogle Scholar
  133. Ptashne M, Gann A (1997) Transcriptional activation by recruitment. Nature 386:569–577PubMedCrossRefGoogle Scholar
  134. Pugh BF (2000) Control of gene expression through regulation of the TATA-binding protein. Gene 255:1–14PubMedCrossRefGoogle Scholar
  135. Rachez C, Freedman LP (2001) Mediator complexes and transcription. Curr Opin Cell Biol 13:274–280PubMedCrossRefGoogle Scholar
  136. Radhakrishnan I, Perez-Alvarado GC, Parker D, Dyson HJ, Montminy MR, Wright PE (1997) Solution structure of the KIX domain of CBP bound to the transactivation domain of CREB: a model for activator:coactivator interactions. Cell 91:741–752PubMedCrossRefGoogle Scholar
  137. Rawson RB (2003) The SREBP pathway-insights from Insigs and insects. Nat Rev Mol Cell Biol 4:631–640PubMedCrossRefGoogle Scholar
  138. Ren B, Cam H, Takahashi Y, Volkert T, Terragni J, Young RA, Dynlacht BD (2002) E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev 16:245–256PubMedCrossRefGoogle Scholar
  139. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA (2000) Genome-wide location and function of DNA binding proteins. Science 290:2306–2309PubMedCrossRefGoogle Scholar
  140. Reyes JC, Barra J, Muchardt C, Camus A, Babinet C, Yaniv M (1998) Altered control of cellular proliferation in the absence of mammalian brahma (SNF2α). EMBO J 17:6979–6991aPubMedCrossRefGoogle Scholar
  141. Roberts SG, Green MR (1994) Activator-induced conformational change in general transcription factor TFIIB. Nature 371:717–720PubMedCrossRefGoogle Scholar
  142. Roberts SG, Ha I, Maldonado E, Reinberg D, Green MR (1993) Interaction between an acidic activator and transcription factor TFIIB is required for transcriptional activation. Nature 363:741–744PubMedCrossRefGoogle Scholar
  143. Rojo-Niersbach E, Furukawa T, Tanese N (1999) Genetic dissection of hTAF(II)130 defines a hydrophobic surface required for interaction with glutamine-rich activators. J Biol Chem 274:33778–33784PubMedCrossRefGoogle Scholar
  144. Roth SY, Denu JM, Allis CD (2001) Histone acetyltransferases. Annu Rev Biochem 70:81–120PubMedCrossRefGoogle Scholar
  145. Rougvie AE, Lis JT (1988) The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell 54:795–804PubMedCrossRefGoogle Scholar
  146. Sadowski I, Ma J, Triezenberg S, Ptashne M (1988) GAL4-VPI6 is an unusually potent transcriptional activator. Nature 335:563–564PubMedCrossRefGoogle Scholar
  147. Salghetti SE, Caudy AA, Chenoweth JG, Tansey WP (2001) Regulation of transcriptional activation domain function by ubiquitin. Science 293:1651–1653PubMedCrossRefGoogle Scholar
  148. Salghetti SE, Muratani M, Wijnen H, Futcher B, Tansey WP (2000) Functional overlap of sequences that activate transcription and signal ubiquitin-mediated proteolysis. Proc Natl Acad Sci USA 97:3118–3123PubMedGoogle Scholar
  149. Sauer F, Hansen SK, Tjian R (1995) Multiple TAFIIs directing synergistic activation of transcription. Science 270:1783–1788PubMedCrossRefGoogle Scholar
  150. Schmitz ML, dos Santos Silva MA, Altmann H, Czisch M, Holak TA, Baeuerle PA (1994) Structural and functional analysis of the NF-κ B p65 C terminus. An acidic and modular transactivation domain with the potential to adopt an α-helical conformation. J Biol Chem 269:25613–25620PubMedGoogle Scholar
  151. Schultz DC, Friedman JR, Rauscher FJ, 3rd (2001) Targeting histone deacetylase complexes via KRAB-zinc finger proteins: the PHD and bromodomains of KAP-1 form a cooperative unit that recruits a novel isoform of the Mi-2 subunit of NuRD. Genes Dev 15:428–443PubMedCrossRefGoogle Scholar
  152. Sera T, Uranga C (2002) Rational design of artificial zinc-finger proteins using a nondegenerate recognition code table. Biochemistry 41:7074–7081PubMedCrossRefGoogle Scholar
  153. Shen F, Triezenberg SJ, Hensley P, Porter D, Knutson JR (1996a) Critical amino acids in the transcriptional activation domain of the herpesvirus protein VP16 are solvent-exposed in highly mobile protein segments. An intrinsic fluorescence study. J Biol Chem 271:4819–4826PubMedCrossRefGoogle Scholar
  154. Shen F, Triezenberg SJ, Hensley P, Porter D, Knutson JR (1996b) Transcriptional activation domain of the herpesvirus protein VP16 becomes conformationally constrained upon interaction with basal transcription factors. J Biol Chem 271:4827–4837PubMedCrossRefGoogle Scholar
  155. Shen X, Mizuguchi G, Hamiche A, Wu C (2000) A chromatin remodelling complex involved in transcription and DNA processing. Nature 406:541–544PubMedCrossRefGoogle Scholar
  156. Smale ST, Kadonaga JT (2003) The RNA polymerase II core promoter. Annu Rev Biochem 72:449–479PubMedCrossRefGoogle Scholar
  157. Soloaga A, Thomson S, Wiggin GR, Rampersaud N, Dyson MH, Hazzalin CA, Mahadevan LC, Arthur JS (2003) MSK2 and MSKI mediate the mitogen-and stress-induced phosphorylation of histone H3 and HMG-14. EMBO J 22:2788–2797PubMedCrossRefGoogle Scholar
  158. Sterner DE, Berger SL (2000) Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev 64:435–459PubMedCrossRefGoogle Scholar
  159. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41–45PubMedCrossRefGoogle Scholar
  160. Sudarsanam P, Iyer VR, Brown PO, Winston F (2000) Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 97:3364–3369PubMedGoogle Scholar
  161. Thomson S, Clayton AL, Mahadevan LC (2001) Independent dynamic regulation of histone phosphorylation and acetylation during immediate-early gene induction. Mol Cell 8:1231–1241PubMedCrossRefGoogle Scholar
  162. Triezenberg SJ (1995) Structure and function of transcriptional activation domains. Curr Opin Genet Dev 5:190–196PubMedCrossRefGoogle Scholar
  163. Uesugi M, Nyanguile O, Lu H, Levine AJ, Verdine GL (1997) Induced α helix in the VP16 activation domain upon binding to a human TAE Science 277:1310–1313PubMedCrossRefGoogle Scholar
  164. Van Hoy M, Leuther KK, Kodadek T, Johnston SA (1993) The acidic activation domains of the GCN4and GAL4 proteins are not α helical but form β sheets. Cell 72:587–594PubMedCrossRefGoogle Scholar
  165. Vlachonasios KE, Thomashow MF, Triezenberg SJ (2003) Disruption mutations of ADA2b and GCN5 transcriptional adaptor genes dramatically affect Arabidopsis growth, development, and gene expression. Plant Cell 15:626–638PubMedCrossRefGoogle Scholar
  166. Warnmark A, Treuter E, Wright AP, Gustafsson JA (2003) Activation functions 1 and 2 of nuclear receptors: molecular strategies for transcriptional activation. Mol Endocrinol 17:1901–1909PubMedCrossRefGoogle Scholar
  167. Warnmark A, Wikstrom A, Wright AP, Gustafsson JA, Hard T (2001) The N-terminal regions of estrogen receptor α and β are unstructured in vitro and show different TBP binding properties. J Biol Chem 276:45939–45944PubMedCrossRefGoogle Scholar
  168. Weinmann AS, Bartley SM, Zhang T, Zhang MQ, Farnham PJ (2001) Use of chromatin immunoprecipitation to clone novel E2F target promoters. Mol Cell Biol 21:6820–6832PubMedCrossRefGoogle Scholar
  169. Weinmann P, Gossen M, Hillen W, Bujard H, Gatz C (1994) A chimeric transactivator allows tetracycline-responsive gene expression in whole plants. Plant J 5:559–569PubMedCrossRefGoogle Scholar
  170. Wieczorek E, Brand M, Iacq X, Tora L (1998) Function of TAF(II)-containing complex without TBP in transcription by RNA polymerase II. Nature 393:187–191PubMedCrossRefGoogle Scholar
  171. Willy PJ, Kobayashi R, Kadonaga JT (2000) A basal trans cription factor that activates or represses transcription. Science 290:982–985PubMedCrossRefGoogle Scholar
  172. Wolfe SA, Ramm EI, Pabo CO (2000) Combining structure-based design with phage display to create new Cys(2)His(2) zinc finger dimers. Structure Fold Des 8:739–750PubMedCrossRefGoogle Scholar
  173. Wolstein O, Silkov A, Revach M, Dikstein R (2000) Specific interaction of TAFIIl05 with OCA-B is involved in activation of octamer-dependent transcription. J Biol Chem 275:16459–16465PubMedCrossRefGoogle Scholar
  174. Xiao H, Pearson A, Coulombe B, Truant R, Zhang S, Regier JL, Triezenberg SJ, Reinberg D, Flores O, Ingles CT, et al. (1994) Binding of basal transcription factor TFIIH to the acidic activation domains of VP16 and p53. Mol Cell Biol 14:7013–7024PubMedGoogle Scholar
  175. Xie Y, Denison C, Yang SH, Fancy DA, Kodadek T (2000a) Biochemical characterization of the TATA-binding protein-Gal4 activation domain complex. J Biol Chem 275:31914–31920PubMedCrossRefGoogle Scholar
  176. Xie Y, Sun L, Kodadek T (2000b) TATA-binding protein and the Gal4 transactivator do not bind to promoters cooperatively. J Biol Chem 275:40797–40803PubMedCrossRefGoogle Scholar
  177. XU J, Li Q (2003) Review of the in vivo functions of the p160 steroid receptor coactivator family. Mol Endocrinol 17:1681–1692PubMedCrossRefGoogle Scholar
  178. Xu W, Cho H, Evans RM (2003) Acetylation and methylation in nuclear receptor gene activation. Methods Enzymol 364:205–223PubMedGoogle Scholar
  179. Yamamoto Y, Verma UN, Prajapati S, Kwak YT, Gaynor RB (2003) Histone H3 phosphorylation by IKK-α is critical for cytokine-induced gene expression. Nature 423:655–659PubMedCrossRefGoogle Scholar
  180. Yankulov K, Blau J, Purton T, Roberts S, Bentley DL (1994) Transcriptional elongation by RNApolymerase II is stimulated by transactivators. Cell 77:749–759PubMedCrossRefGoogle Scholar
  181. Zhang L, Spratt SK, Liu Q, Johnstone B, Qi H, Raschke EE, Jamieson AC, Rebar EJ, Wolffe AP, Case CC (2000) Synthetic zinc finger transcription factor action at an endogenous chromosomal site. Activation of the human erythropoietin gene. J Biol Chem 275:33850–33860PubMedCrossRefGoogle Scholar
  182. Zhang Y (2003) Transcriptional regulation by histone ubiquitination and deubiquitination. Genes Dev 17:2733–2740PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • F. J. Herrera
    • 1
  • D. D. Shooltz
    • 1
  • S. J. Triezenberg
    • 1
  1. 1.Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUSA

Personalised recommendations