Getting into chromatin: How do transcription factors get past the histones?

Biochemistry and Cell Biology

Volumn 81, Issue 3, 2003, Pages 101-112

  Morse, Randall H ^a  

^a UNIVERSITY AT ALBANY   (United States)

Author keywords

Chromatin; Nucleosome; Saccharomyces cerevisiae; Transcriptional activation

Indexed keywords

BINDING ENERGY; DNA; PROTEINS;

TRANSCRIPTIONAL ACTIVATORS;

BIOCHEMISTRY;

DNA BINDING PROTEIN; HISTONE; TRANSCRIPTION FACTOR;

BINDING AFFINITY; BINDING SITE; CHROMATIN; CHROMATIN STRUCTURE; CONFERENCE PAPER; DNA BINDING; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOSOME; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE;

ANIMALS; BINDING SITES; CHROMATIN; DNA; HISTONES; HUMANS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; NUCLEOSOMES; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0042733700     PISSN: 08298211     EISSN: None     Source Type: Journal    
DOI: 10.1139/o03-039     Document Type: Conference Paper

References (92)

1. Adams, C.C., and Workman, J.L. 1995. Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Mol. Cell. Biol. 15: 1405-1421.
2. Agalioti, T., Lomvardas, S., Parekh, B., Yie, J., Maniatis, T., and Thanos, D. 2000. Ordered recruitment of chromatin modifying and general transcription factors to the IFN-beta promoter. Cell, 103: 667-678.
3. Ahmad, K., and Henikoff, S., 2001. Modulation of a transcription factor counteracts heterochromatic gene silencing in Drosophila. Cell, 104: 839-847.
4. Ahmad, K., and Henikoff, S. 2002. Epigenetic consequences of nucleosome dynamics. Cell, 111: 281-284.
5. Alevizopoulos, A., Dusserre, Y., Tsai-Pflugfelder, M., von der Weid, T., Wahli, W., and Mermod, N. 1995. A proline-rich TGF-beta-responsive transcriptional activator interacts with histone H3. Genes Dev. 9: 3051-3066.
6. Almer, A., and Horz, W. 1986. Nuclease hypersensitive regions with adjacent positioned nucleosomes mark the gene boundaries of the PHO5/PHO3 locus in yeast. EMBO J. 5: 2681-2687.
7. Almer, A., Rudolph, H., Hinnen, A., and Horz, W. 1986. Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J. 5: 2689-2696.
8. Angermayr, M., Oechsner, U., Gregor, K., Schroth, G.P., and Bandlow, W. 2002. Transcription initiation in vivo without classical transactivators: DNA kinks flanking the core promoter of the housekeeping yeast adenylate kinase gene, AKY2, position nucleosomes and constitutively activate transcription. Nucleic Acids Res. 30: 4199-4207.
9. Aparicio, O.M., and Gottschling, D.E. 1994. Overcoming telomeric silencing: a trans-activator competes to establish gene expression in a cell cycle-dependent way. Genes Dev. 8: 1133-1146.
10. Arndt, K., and Fink, G.R. 1986. GCN4 protein, a positive transcription factor in yeast, binds general control promoters at all 5′ TGACTC 3′ sequences. Proc. Natl. Acad. Sci. U.S.A. 83: 8516-8520.
11. Axelrod, J.D., Reagan, M.S., and Majors, J. 1993. GAL4 disrupts a repressing nucleosome during activation of GALl transcription in vivo. Genes Dev. 7: 857-869.
12. Balasubramanian, B., and Morse, R.H. 1999. Binding of Gal4p and bicoid to nucleosomal sites in yeast in the absence of replication. Mol. Cell. Biol. 19: 2977-2985.
13. Bhaumik, S.R., and Green, M.R. 2001. SAGA is an essential in vivo target of the yeast acidic activator Gal4p. Genes Dev. 15: 1935-1945.
14. Bresnick, E.H., Bustin, M., Marsaud, V., Richard-Foy, H., and Hager, G.L. 1992. The transcriptionally-active MMTV promoter is depleted of histone H1. Nucleic Acids Res. 20: 273-278.
15. Bunker, C.A., and Kingston, R.E. 1996. Activation domain-mediated enhancement of activator binding to chromatin in mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 93: 10 820-10 825.
16. Chasman, D.I., Lue, N.F., Buchman, A.R., LaPointe, J.W., Lorch, Y., and Kornberg, R.D. 1990. A yeast protein that influences the chromatin structure of UASG and functions as a powerful auxiliary gene activator. Genes Dev. 4: 503-514.
17. Cirillo, L.A., Lin, F.R., Cuesta, I., Friedman, D., Jarnik, M., and Zaret, K.S. 2002. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol. Cell 9: 279-289.
18. Cirillo, L.A., and Zaret, K.S. 1999. An early developmental transcription factor complex that is more stable on nucleosome core particles than on free DNA. Mol. Cell 4: 961-969.
19. Cosma, M.P. 2002. Ordered recruitment: gene-specific mechanism of transcription activation. Mol. Cell 10: 227-236.
20. Cosma, M.P., Tanaka, T., and Nasmyth, K. 1999. Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter. Cell, 97: 299-311.
21. Depew, D.E., and Wang, J.C. 1975. Conformational fluctuations of DNA helix. Proc. Natl. Acad. Sci. U.S.A. 72: 4275-4279.
22. Devlin, C., Tice-Baldwin, K., Shore, D., and Arndt, K.T. 1991. RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene. Mol. Cell. Biol. 11: 3642-3651.
23. Di Mauro, E., Kendrew, S.G., and Caserta, M. 2000. Two distinct nucleosome alterations characterize chromatin remodeling at the Saccharomyces cerevisiae ADH2 promoter. J. Biol. Chem. 275: 7612-7618.
24. Fascher, K.D., Schmitz, J., and Horz, W. 1993. Structural and functional requirements for the chromatin transition at the PHO5 promoter in Saccharomyces cerevisiae upon PHO5 activation. J. Mol. Biol. 231: 658-667.
25. Gaudreau, L., Keaveney, M., Nevado, J., Zaman, Z., Bryant, G.O., Struhl, K., and Ptashne, M. 1999. Transcriptional activation by artificial recruitment in yeast is influenced by promoter architecture and downstream sequences. Proc. Natl. Acad. Sci. U.S.A. 96: 2668-2673.
26. Gaudreau, L., Schmid, A., Blaschke, D., Ptashne, M., and Horz, W. 1997. RNA polymerase II holoenzyme recruitment is sufficient to remodel chromatin at the yeast PHO5 promoter. Cell, 89: 55-62.
27. Giardina, C., and Lis, J.T. 1993. DNA melting on yeast RNA polymerase II promoters. Science (Washington, D.C), 261: 759-762.
28. Godde, J.S., Nakatani, Y., and Wolffe, A.P. 1995. The amino-terminal tails of the core histones and the translational position of the TATA box determine TBP/TFIIA association with nucleosomal DNA. Nucleic Acids Res. 23: 4557-4564.
29. Granok, H., Leibovitch, B.A., Shaffer, C.D., and Elgin, S.C. 1995. Chromatin. Ga-ga over GAGA factor. Curr. Biol. 5: 238-241.
30. Grant, P.A., Duggan, L., Cote, J., Roberts, S.M., Brownell, J.E., Candau, R., Ohba, R., Owen-Hughes, T., Allis, C.D., Winston, F., Berger, S.L., and Workman, J.L. 1997. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 11: 1640-1650.
31. Gregory, P.D., Schmid, A., Zavari, M., Munsterkotter, M., and Horz, W. 1999. Chromatin remodelling at the PHO8 promoter requires SWI-SNF and SAGA at a step subsequent to activator binding. EMBO J. 18: 6407-6414.
32. Gross, D.S., Adams, C.C., Lee, S., and Stentz, B. 1993. A critical role for heat shock transcription factor in establishing a nucleosome-free region over the TATA-initiation site of the yeast HSP82 heat shock gene. EMBO J. 12: 3931-3945.
33. Imbalzano, A.N., Kwon, H., Green, M.R., and Kingston, R.E. 1994. Facilitated binding of TATA-binding protein to nucleosomal DNA [see comments]. Nature (London), 370: 481-485.
34. Iyer, V., and Struhl, K. 1995. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 14: 2570-2579.
35. Krebs, J.E., Fry, C.J., Samuels, M.L., and Peterson, C.L. 2000. Global role for chromatin remodeling enzymes in mitotic gene expression. Cell, 102: 587-598.
36. Larschan, E., and Winston, F. 2001. The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev. 15: 1946-1956.
37. Laybourn, P.J., and J.T. Kadonaga. 1991. Role of nucleosomal cores and histone H1 in regulation of transcription by RNA polymerase II. Science (Washington, D.C.), 254: 238-245.
38. Lieb, J.D., Liu, X., Botstein, D., and Brown, P.O. 2001. Promoter-specific binding of Rap l revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28: 327-334.
39. Lohr, D., and Hopper, J.E. 1985. The relationship of regulatory proteins and DNase I hypersensitive sites in the yeast GAL1-10 genes. Nucleic Acids Res. 13: 8409-8423.
40. Lohr, D., and Lopez, J. 1995. GAL4/GAL80-dependent nucleosome disruption/deposition on the upstream regions of the yeast GAL1-10 and GAL80 genes. J. Biol. Chem. 270: 27 671-27 678.
41. Lomvardas, S., and Thanos, D. 2001. Nucleosome sliding via TBP DNA binding in vivo. Cell, 106: 685-696.
42. Lomvardas, S., and Thanos, D. 2002. Modifying gene expression programs by altering core promoter chromatin architecture. Cell, 110: 261-271.
43. Lundgren, M., Chow, C.M., Sabbattini, P., Georgiou, A., Minaee, S., and Dillon, N. 2000. Transcription factor dosage affects changes in higher order chromatin structure associated with activation of a heterochromatic gene. Cell, 103: 733-743.
44. Mager, W.H., and Planta, R.J. 1990. Multifunctional DNA-binding proteins mediate concerted transcription activation of yeast ribosomal protein genes. Biochim. Biophys. Acta, 1050: 351-355.
45. McAndrew, P.C., Svaren, J., Martin, S.R., Horz, W., and Goding, C.R. 1998. Requirements for chromatin modulation and transcription activation by the Pho4 acidic activation domain. Mol. Cell. Biol. 18: 5818-5827.
46. Moreira, J.M., and Holmberg, S. 1998. Nucleosome structure of the yeast CHA1 promoter: analysis of activation- dependent chromatin remodeling of an RNA-polymerase-II-transcribed gene in TBP and RNA pol II mutants defective in vivo in response to acidic activators. EMBO J. 17: 6028-6038.
47. Morse, R.H. 1989. Nucleosomes inhibit both transcriptional initiation and elongation by RNA polymerase III in vitro. EMBO J. 8: 2343-2351.
48. Morse, R.H. 1991. Topoisomer heterogeneity of plasmid chromatin in living cells. J. Mol. Biol. 222: 133-137.
49. Morse, R.H. 1993. Nucleosome disruption by transcription factor binding in yeast. Science (Washington, D.C.), 262: 1563-1566.
50. Morse, R.H. 2000. RAP, RAP, open up! new wrinkles for RAP1 in yeast. Trends Genet. 16: 51-53.
51. Morse, R.H., Roth, S.Y., and Simpson, R.T. 1992. A transcriptionally active tRNA gene interferes with nucleosome positioning in vivo. Mol. Cell. Biol. 12: 4015-4025.
52. Muro-Pastor, M.I., Gonzalez, R., Strauss, J., Narendja, F., and Scazzocchio, C. 1999. The GATA factor AreA is essential for chromatin remodelling in a eukaryotic bidirectional promoter. EMBO J. 18: 1584-1597.
53. Owen-Hughes, T., and Workman, J.L. 1994. Experimental analysis of chromatin function in transcription control. Crit. Rev. Eukaryot. Gene Expr. 4: 403-441.
54. Pederson, D.S., and Morse, R.H. 1990. Effect of transcription of yeast chromatin on DNA topology in vivo. EMBO J. 9: 1873-1881.
55. Pederson, D.S., Venkatesan, M., Thoma, F., and Simpson, R.T. 1986. Isolation of an episomal yeast gene and replication origin as chromatin. Proc. Natl. Acad. Sci. U.S.A. 83: 7206-7210.
56. Perlmann, T., and Wrange, O. 1988. Specific glucocorticoid receptor binding to DNA reconstituted in a nucleosome. EMBO J. 7: 3073-3079.
57. Peterson, C.L., and Workman, J.L. 2000. Promoter targeting and chromatin remodeling by the SWI/SNF complex. Curr. Opin. Genet. Dev. 10: 187-192.
58. Polach, K.J., and Widom, J. 1995. Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation. J. Mol. Biol. 254: 130-149.
59. Polach, K.J., and Widom, J. 1996. A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites. J. Mol. Biol. 258: 800-812.
60. Ptashne, M., and Gann, A. 1997. Transcriptional activation by recruitment. Nature (London), 386: 569-577.
61. Ramsay, N., Felsenfeld, G., Rushton, B.M., and McGhee, J.D. 1984. A 145-base pair DNA sequence that positions itself precisely and asymmetrically on the nucleosome core. EMBO J. 3: 2605-2611.
62. Richard-Foy, H., and Hager, G.L. 1987. Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter. EMBO J. 6: 2321-2328.
63. Ryan, M.P., Jones, R., and Morse, R.H. 1998. SWI-SNF complex participation in transcriptional activation at a step subsequent to activator binding. Mol. Cell. Biol. 18: 1774-1782.
64. Ryan, M.P., Stafford, G.A., Yu, L., and Morse, R.H. 2000. Artificially recruited TATA-binding protein fails to remodel chromatin and does not activate three promoters that require chromatin remodeling. Mol. Cell. Biol. 20: 5847-5857.
65. Schmid, A., Fascher, K.D., and Horz, W. 1992. Nucleosome disruption at the yeast PHO5 promoter upon PHO5 induction occurs in the absence of DNA replication. Cell, 71: 853-864.
66. Sheldon, L.A., Becker, M., and Smith, C.L. 2001. Steroid hormone receptor-mediated histone deacetylation and transcription at the mouse mammary tumor virus promoter. J. Biol. Chem. 276: 32 423-32 426.
67. Simpson, R.T. 1990. Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature (London), 343: 387-389.
68. Simpson, R.T., and Stafford, D.W. 1983. Structural features of a phased nucleosome core particle. Proc. Natl. Acad. Sci. U.S.A. 80: 51-55.
69. Soutoglou, E., and Talianidis, I. 2002. Coordination of PIC assembly and chromatin remodeling during differentiation-induced gene activation. Science (Washington, D.C.), 295: 1901-1904.
70. Stafford, G.A., and Morse, R.H. 1997. Chromatin remodeling by transcriptional activation domains in a yeast episome. J. Biol. Chem. 272: 11 526-11 534.
71. Stafford, G.A., and Morse, R.H. 1998. Mutations in the AF-2/hormone-binding domain of the chimeric activator GAL4.estrogen receptor.VP16 inhibit hormone-dependent transcriptional activation and chromatin remodeling in yeast. J. Biol. Chem. 273: 34 240-34 246.
72. Stafford, G.A., and Morse, R.H. 2001. GCN5 dependence of chromatin remodeling and transcriptional activation by the GAL4 ad VP16 activation domains in budding yeast. Mol. Cell. Biol. 21: 4568-4578.
73. Stargell, L.A., and Struhl, K. 1996. A new class of activation-defective TATA-binding protein mutants: evidence for two steps of transcriptional activation in vivo. Mol. Cell. Biol. 16: 4456-4464.
74. Steger, D.J., Haswell, E.S., Miller, A.L., Wente, S.R., and O'Shea, E.K. 2003. Regulation of chromatin remodeling by inositol polyphosphates. Science (Washington, D.C.), 299: 114-116.
75. Straka, C., and Horz, W. 1991. A functional role for nucleosomes in the repression of a yeast promoter. EMBO J. 10: 361-368.
76. Svaren, J., and Horz, W. 1997. Transcription factors vs. nucleosomes: regulation of the PHO5 promoter in yeast. Trends Biochem. Sci. 22: 93-97.
77. Svaren, J., Schmitz, J., and Horz, W. 1994. The transactivation domain of Pho4 is required for nucleosome disruption at the PHO5 promoter. EMBO J. 13: 4856-4862.
78. Tanaka, M. 1996. Modulation of promoter occupancy by cooperative DNA binding and activation-domain function is a major determinant of transcriptional regulation by activators in vivo. Proc. Natl. Acad. Sci. U.S.A. 93: 4311-4315.
79. Thomas, G.H., and Elgin, S.C. 1988. Protein/DNA architecture of the DNase I hypersensitive region of the Drosophila hsp26 promoter. EMBO J. 7: 2191-2201.
80. Vashee, S., and Kodadek, T. 1995. The activation domain of GAL4 protein mediates cooperative promoter binding with general transcription factors in vivo. Proc. Natl. Acad. Sci. U.S.A. 92: 10 683-10 687.
81. Venter, U., Svaren, J., Schmitz, J., Schmid, A., and Horz, W. 1994. A nucleosome precludes binding of the transcription factor Pho4 in vivo to a critical target site in the PHO5 promoter. EMBO J. 13: 4848-4855.
82. Venturi, C.B., Erkine, A.M., and Gross, D.S. 2000. Cell cycle-dependent binding of yeast heat shock factor to nucleosomes. Mol. Cell. Biol. 20: 6435-6448.
83. Verdone, L., Camilloni, G., Di E., Mauro, and Caserta, M. 1996. Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation. Mol. Cell. Biol. 16: 1978-1988.
84. Verdone, L., Cesari, F., Denis, C.L., Di Mauro, E., and Caserta, M. 1997. Factors affecting Saccharomyces cerevisiae ADH2 chromatin remodeling and transcription. J. Biol. Chem. 272: 30 828-30 834.
85. Wong, J., Shi, Y.B., and Wolffe, A.P. 1995. A role for nucleosome assembly in both silencing and activation of the Xenopus TR beta A gene by the thyroid hormone receptor. Genes Dev. 9: 2696-2711.
86. Workman, J.L., and Buchman, A.R. 1993. Multiple functions of nucleosomes and regulatory factors in transcription. Trends Biochem. Sci. 18: 90-95.
87. Woychik, N.A., and Hampsey, M. 2002. The RNA polymerase II machinery: structure illuminates function. Cell, 108: 453-463.
88. Wu, Y., Reece, R.J., and Ptashne, M. 1996. Quantitation of putative activator-target affinities predicts transcriptional activating potentials. EMBO J. 15: 3951-3963.
89. Xu, M., Simpson, R.T., and Kladde, M.P. 1998. Gal4p-mediated chromatin remodeling depends on binding site position in nucleosomes but does not require DNA replication. Mol. Cell. Biol. 18: 1201-1212.
90. Yu, L., and Morse, R.H. 1999. Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 19: 5279-5288.
91. Yu, L., Sabet, N., Chambers, A., and Morse, R.H. 2001. The N-terminal and C-terminal domains of RAP1 are dispensable for chromatin opening and GCN4-mediated HIS4 activation in budding yeast. J. Biol. Chem. 276: 33 257-33 264.
92. Zhu, Z., and Thiele, D.J. 1996. A specialized nucleosome modulates transcription factor access to a C. glabrata metal responsive promoter. Cell, 87: 459-470.