Activation domains of gene-specific transcription factors: Are histones among their targets?

Biochemistry and Cell Biology

Volumn 82, Issue 4, 2004, Pages 453-459

  Erkine, Alexandre M ^a  

^a UNIVERSITY OF SOUTH DAKOTA   (United States)

Author keywords

Activation domain; Chromatin; Nucleosome; Transcription

Indexed keywords

AMINO ACIDS; BIOCHEMISTRY; CHEMICAL ACTIVATION; MOLECULAR STRUCTURE; PLANTS (BOTANY); PROTEINS;

ACTIVATION DOMAINS; GENE-SPECIFIC TRANSCRIPTION FACTORS; HISTONES;

GENES;

DNA BINDING PROTEIN; HISTONE; TRANSCRIPTION FACTOR;

ACETYLATION; AMINO ACID SEQUENCE; CHROMATIN STRUCTURE; CONFERENCE PAPER; EUKARYOTE; GENETIC TRANSCRIPTION; HYDROPHOBICITY; NONHUMAN; NUCLEOSOME; PHYLUM; PROMOTER REGION; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; TRANSCRIPTION INITIATION;

ANIMALS; CHROMATIN; DNA; HISTONES; HUMANS; MODELS, BIOLOGICAL; NUCLEOSOMES; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 4644222751     PISSN: 08298211     EISSN: None     Source Type: Journal    
DOI: 10.1139/o04-036     Document Type: Conference Paper

References (78)

1. 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(4): 667-678.
2. Aki, T., Choy, H.E., and Adhya, S. 1996. Histone-like protein HU as a specific transcriptional regulator: co-factor role in repression of gal transcription by GAL repressor. Genes Cells 1(2): 179-188.
3. 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(24): 3051-3066.
4. Altmann, H., Wendler, W., and Winnacker, E.L. 1994. Transcriptional activation by CTF proteins is mediated by a bipartite low-proline domain. Proc. Natl. Acad. Sci. U.S.A. 91(9): 3901-3905.
5. Amin, J., Ananthan, J., and Voellmy, R. 1988. Key features of heat shock regulatory elements. Mol. Cell Biol. 8(9): 3761-3769.
6. Barbaric, S., Walker, J., Schmid, A., Svejstrup, J.Q., and Horz, W. 2001. Increasing the rate of chromatin remodeling and gene activation - a novel role for the histone acetyltransferase Gcn5. EMBO J. 20(17): 4944-4951.
7. Barlev, N.A., Candau, R., Wang, L., Darpino, P., Silverman, N., and Berger, S.L. 1995. Characterization of physical interactions of the putative transcriptional adaptor, ADA2, with acidic activation domains and TATA-binding protein. J. Biol. Chem. 270(33): 19 337-19 344.
8. Bhaumik, S.R., and Green, M.R. 2001. SAGA is an essential in vivo target of the yeast acidic activator Ga14p. Genes Dev. 15(15): 1935-1945.
9. Birck, C., Poch, O., Romier, C., Ruff, M., Mengus, G., Lavigne, A.C., et al. 1998. Human TAF(II)28 and TAF(II)18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family. Cell, 94(2): 239-249.
10. Brown, C.E., Lechner, T., Howe, L., and Workman, J.L. 2000. The many HATs of transcription coactivators. Trends Biochem. Sci. 25(1): 15-19.
11. Brown, C.E., Howe, L., Sousa, K., Alley, S.C., Carrozza, M.J., Tan, S., and Workman, J.L. 2001. Recruitment of HAT complexes by direct activator interactions with the ATM-related Tra1 subunit. Science (Washington, D.C.), 292(5525): 2333-2337.
12. Buschmann, T., Fuchs, S.Y., Lee, C.G., Pan, Z.Q., and Ronai, Z. 2000. SUMO-1 modification of Mdm2 prevents its self-ubiquitination and increases Mdm2 ability to ubiquitinate p53. Cell, 101(7): 753-762.
13. Cho, H.S., Liu, C.W., Damberger, F.F., Pelton, J.G., Nelson, H.C., and Wemmer, D.E. 1996. Yeast heat shock transcription factor N-terminal activation domains are unstructured as probed by heteronuclear NMR spectroscopy. Protein Sci. 5(2): 262-269.
14. Cho, H., Orphanides, G., Sun, X., Yang, X.J., Ogryzko, V., Lees, E., et al. 1998. A human RNA polymerase II complex containing factors that modify chromatin structure. Mol. Cell Biol. 18(9): 5355-5363.
15. Chou, S., Chatterjee, S., Lee, M., and Struhl, K. 1999. Transcriptional activation in yeast cells lacking transcription factor IIA. Genetics, 153(4): 1573-1581.
16. 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(2): 279-289.
17. Clark-Adams, C.D., Norris, D., Osley, M.A., Fassler, J.S., and Winston, F. 1988. Changes in histone gene dosage alter transcription in yeast. Genes Dev. 2(2): 150-159.
18. Corona, D.F., Eberharter, A., Budde, A., Deuring, R., Ferrari, S., Varga-Weisz, P., et al. 2000. Two histone fold proteins, CHRAC-14 and CHRAC-16, are developmentally regulated subunits of chromatin accessibility complex (CHRAC). EMBO J. 19(12): 3049-3059.
19. 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(3): 299-311.
20. Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., and Richmond, T.J. 2002. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol. 319(5): 1097-1113.
21. Dhalluin, C., Carlson, J.E., Zeng, L., He, C., Aggarwal, A.K., and Zhou, M.M. 1999. Structure and ligand of a histone acetyltransferase bromodomain. Nature (London), 399(6735): 491-496.
22. 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(11): 7612-7618.
23. Drysdale, C.M., Duenas, E., Jackson, B.M., Reusser, U., Braus, G.H., and Hinnebusch, A.G. 1995. The transcriptional activator GCN4 contains multiple activation domains that are critically dependent on hydrophobic amino acids. Mol. Cell Biol. 15(3): 1220-1233.
24. Edmondson, D.G., Smith, M.M., and Roth, S.Y. 1996. Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4. Genes Dev. 10(10): 1247-1259.
25. Erkine, A.M., and Gross, D.S. 2003. Dynamic chromatin alterations triggered by natural and synthetic activation domains. J. Biol. Chem. 278(10): 7755-7764.
26. Escher, D., Bodmer-Glavas, M., Barberis, A., and Schaffner, W. 2000. Conservation of glutamine-rich transactivation function between yeast and humans. Mol. Cell Biol. 20(8): 2774-2782.
27. Gasser, S.M., and Cockell, M.M. 2001. The molecular biology of the SIR proteins. Gene, 279(1): 1-16.
28. 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(1): 55-62.
29. Gerber, H.P., Seipel, K., Georgiev, O., Hofferer, M., Hug, M., Rusconi, S., and Schaffner, W. 1994. Transcriptional activation modulated by homopolymeric glutamine and proline stretches. Science (Washington, D.C.), 263(5148): 808-811.
30. Ha, N., Hellauer, K., and Turcotte, B. 2000. Fusions with histone H3 result in highly specific alteration of gene expression. Nucleic Acids Res. 28(4): 1026-1035.
31. Hassan, A.H., Neely, K.E., Vignali, M., Reese, J.C., and Workman, J.L. 2001a. Promoter targeting of chromatin-modifying complexes. Front Biosci. 6: D1054-D1064.
32. Hassan, A.H., Neely, K.E., and Workman, J.L. 2001b. Histone Acetyltransferase Complexes Stabilize SWI/SNF Binding to Promoter Nucleosomes. Cell, 104(6): 817-827.
33. Hassan, A.H., Prochasson, P., Neely, K.E., Galasinski, S.C., Chandy, M., Carrozza, M.J., and Workman, J.L. 2002. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell, 111(3): 369-379.
34. Haynes, S.R., Dollard, C., Winston, F., Beck, S., Trowsdale, J., and Dawid, I.B. 1992. The bromodomain: a conserved sequence found in human, Drosophila and yeast proteins. Nucleic Acids Res. 20(10): 2603.
35. Henriksson, A., Almlof, T., Ford, J., McEwan, I.J., Gustafsson, J.A., and Wright, A.P. 1997. Role of the Ada adaptor complex in gene activation by the glucocorticoid receptor. Mol. Cell. Biol. 17(6): 3065-3073.
36. Hoeck, W., and Groner, B. 1990. Hormone-dependent phosphorylation of the glucocorticoid receptor occurs mainly in the amino-terminal transactivation domain. J. Biol. Chem. 265(10): 5403-5408.
37. Hollstein, M., Hergenhahn, M., Yang, Q., Bartsch, H., Wang, Z.Q., and Hainaut, P. 1999. New approaches to understanding p53 gene tumor mutation spectra. Mutat. Res. 431(2): 199-209.
38. Jackson, B.M., Drysdale, C.M., Natarajan, K., and Hinnebusch, A.G. 1996. Identification of seven hydrophobic clusters in GCN4 making redundant contributions to transcriptional activation. Mol. Cell Biol. 16(10): 5557-5571.
39. Kadonaga, J.T. 1998. Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines. Cell, 92(3): 307-313.
40. Katan-Khaykovich, Y., and Struhl, K. 2002. Dynamics of global histone acetylation and deacetylation in vivo: rapid restoration of normal histone acetylation status upon removal of activators and repressors. Genes Dev. 16(6): 743-752.
41. Kaufmann, J., Verrijzer, C.P., Shao, J., and Smale, S.T. 1996. CIF, an essential cofactor for TFIID-dependent initiator function. Genes Dev. 10(7): 873-886.
42. Kingston, R.E., and Narlikar, G.J. 1999. ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes Dev. 13(18): 2339-2352.
43. Klemm, R.D., Goodrich, J.A., Zhou, S., and Tjian, R. 1995. Molecular cloning and expression of the 32-kDa subunit of human TFIID reveals interactions with VP16 and TFIIB that mediate transcriptional activation. Proc. Natl. Acad. Sci. U.S.A. 92(13): 5788-5792.
44. Koh, S.S., Ansari, A.Z., Ptashne, M., and Young, R.A. 1998. An activator target in the RNA polymerase II holoenzyme. Mol. Cell 1(6): 895-904.
45. Larschan, E., and Winston, F. 2001. The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Ga14. Genes Dev. 15(15): 1946-1956.
46. Liu, X.D., and Thiele, D.J. 1996. Oxidative stress induced heat shock factor phosphorylation and HSF-dependent activation of yeast metallothionein gene transcription. Genes Dev. 10(5): 592-603.
47. Logie, C., and Peterson, C.L. 1997. Catalytic activity of the yeast SWI/SNF complex on reconstituted nucleosome arrays. EMBO J. 16(22): 6772-6782.
48. Lu, X., Ansari, A.Z., and Ptashne, M. 2000. An artificial transcriptional activating region with unusual properties. Proc. Natl. Acad. Sci. U.S.A. 97(5): 1988-1992.
49. Luger, K., Mader, A.W., Richmond, R.K., Sargent, D.F., and Richmond, T.J. 1997. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature (London), 389(6648): 251-260.
50. Ma, J., and Ptashne, M. 1987. A new class of yeast transcriptional activators. Cell, 51(1): 113-119.
51. 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 H mutants defective in vivo in response to acidic activators. EMBO J. 17(20): 6028-6038.
52. Muller, J.M., Krauss, B., Kaltschmidt, C., Baeuerle, P.A., and Rupec, R.A. 1997. Hypoxia induces c-fos transcription via a mitogen-activated protein kinase-dependent pathway. J. Biol. Chem. 272(37): 23 435-23 439.
53. Natarajan, K., Jackson, B.M., Zhou, H., Winston, F., and Hinnebusch, A.G. 1999. Transcriptional activation by Gcn4p involves independent interactions with the SWI/SNF complex and the SRB/mediator. Mol. Cell 4(4): 657-664.
54. Neely, K.E., Hassan, A.H., Wallberg, A.E., Steger, D.J., Cairns, B.R., Wright, A.P., and Workman, J.L. 1999. Activation domain-mediated targeting of the SWI/SNF complex to promoters stimulates transcription from nucleosome arrays. Mol. Cell 4(4): 649-655.
55. Neely, K.E., Hassan, A.H., Brown, C.E., Howe, L., and Workman, J.L. 2002. Transcription activator interactions with multiple SWI/SNF subunits. Mol. Cell Biol. 22(6): 1615-1625.
56. Nyanguile, O., Uesugi, M., Austin, D.J., and Verdine, G.L. 1997. A nonnatural transcriptional coactivator. Proc. Natl. Acad. Sci. U.S.A. 94(25): 13 402-13 406.
57. Ogryzko, V.V., Kotani, T., Zhang, X., Schlitz, R.L., Howard, T., Yang, X.J., Howard, B.H., Qin, J., and Nakatani, Y. 1998. Histone-like TAFs within the PCAF histone acetylase complex. Cell, 94(1): 35-44.
58. Parthun, M.R., and Jaehning, J.A. 1992. A transcriptionally active form of GAL4 is phosphorylated and associated with GAL80. Mol. Cell Biol. 12(11): 4981-4987.
59. Poot, R.A., Dellaire, G., Hulsmann, B.B., Grimaldi, M.A., Corona, D.F., Becker, P.B., Bickmore, W.A., and Varga-Weisz, P.D. 2000. HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins. EMBO J. 19(13): 3377-3387.
60. Prochasson, P., Neely, K.E., Hassan, A.H., Li, B., and Workman, J.L. 2003. Targeting activity is required for SWI/SNF function in vivo and is accomplished through two partially redundant activator-interaction domains. Mol. Cell 12(4): 983-990.
61. Ptashne, M., and Gann, A. 1997. Transcriptional activation by recruitment. Nature (London), 386(6625): 569-577.
62. Regier, J.L., Shen, F., and Triezenberg, S.J. 1993. Pattern of aromatic and hydrophobic amino acids critical for one of two subdomains of the VP16 transcriptional activator. Proc. Natl. Acad. Sci. U.S.A. 90(3): 883-887.
63. Reid, J.L., Iyer, V.R., Brown, P.O., and Struhl, K. 2000. Coordinate Regulation of Yeast Ribosomal Protein Genes Is Associated with Targeted Recruitment of Esal Histone Acetylase. Mol. Cell 6(6): 1297-1307.
64. Reinke, H., and Horz, W. 2003. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell 11(6): 1599-1607.
65. Saha, S., Ansari, A.Z., Jarrell, K.A., Ptashne, M., and Jarell, K.A. 2003. RNA sequences that work as transcriptional activating regions. Nucleic Acids Res. 31(5): 1565-1570.
66. Sauer, F., Fondell, J.D., Ohkuma, Y., Roeder, R.G., and Jackle, H. 1995. Control of transcription by Kruppel through interactions with TFIIB and TFIIE beta. Nature (London), 375(6527): 162-164.
67. Stafford, G.A., and Morse, R.H. 1997. Chromatin remodeling by transcriptional activation domains in a yeast episome. J. Biol. Chem. 272(17): 11 526-11 534.
68. Strahl, B.D., and Allis, C.D. 2000. The language of covalent histone modifications. Nature (London), 403(6765): 41-45.
69. 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(20): 4856-4862.
70. Swanson, M.J., Qiu, H., Sumibcay, L., Krueger, A., Kim, S.J., Natarajan, K., Yoon, S., and Hinnebusch, A.G. 2003. A multiplicity of coactivators is required by Gcn4p at individual promoters in vivo. Mol. Cell Biol. 23(8): 2800-2820.
71. Thut, C.J., Chen, J.L., Klemm, R., and Tjian, R. 1995. p53 transcriptional activation mediated by coactivators TAFII40 and TAFII60. Science (Washington, D.C.), 267(5194): 100-104.
72. Triezenberg, S.J. 1995. Structure and function of transcriptional activation domains. Curr. Opin. Genet. Dev. 5(2): 190-196.
73. Utley, R.T., Ikeda, K., Grant, P.A., Cote, J., Steger, D.J., Eberharter, A., John, S., and Workman, J.L. 1998. Transcriptional activators direct histone acetyltransferase complexes to nucleosomes. Nature (London), 394(6692): 498-502.
74. Vogelauer, M., Wu, J., Suka, N., and Grunstein, M. 2000. Global histone acetylation and deacetylation in yeast. Nature (London), 408(6811): 495-498.
75. Wenzelides, S., Altmann, H., Wendler, W., and Winnacker, E.L. 1996. CTF5 - a new transcriptional activator of the NFI/CTF family. Nucleic Acids Res. 24(12): 2416-2421.
76. Wilson, C.J., Chao, D.M., Imbalzano, A.N., Schnitzler, G.R., Kingston, R.E., and Young, R.A. 1996. RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell, 84(2): 235-244.
77. Yanagisawa, S. 2001. The transcriptional activation domain of the plant-specific Dof1 factor functions in plant, animal, and yeast cells. Plant Cell Physiol. 42(8): 813-822.
78. Yudkovsky, N., Logie, C., Hahn, S., and Peterson, C.L. 1999. Recruitment of the SWI/SNF chromatin remodeling complex by transcriptional activators. Genes Dev. 13(18): 2369-2374.