A multiplicity of coactivators is required by Gcn4p at individual promoters in vivo

Molecular and Cellular Biology

Volumn 23, Issue 8, 2003, Pages 2800-2820

  Swanson, Mark J ^a   Qiu, Hongfang ^a   Sumibcay, Laarni ^a   Krueger, Anna ^a   Kim, Soon ja ^a   Natarajan, Krishnamurthy ^a,b   Yoon, Sungpil ^a   Hinnebusch, Alan G ^a  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b JAWAHARLAL NEHRU UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; HOMOSERINE ACETYLTRANSFERASE; PROTEIN CCR4 NOT; PROTEIN PAF1; PROTEIN SW1; TRANSCRIPTION FACTOR SAGA; TRANSCRIPTION FACTOR SNF; UNCLASSIFIED DRUG;

AMINO ACID SYNTHESIS; ARTICLE; BIOSYNTHESIS; BUDDING; CHROMATIN; CHROMATIN STRUCTURE; COMPLEX FORMATION; CONTROLLED STUDY; FUNGAL GENE; GCN4P GENE; GENE ACTIVATION; GENE DELETION; GENE TARGETING; IMMUNOPRECIPITATION; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN INTERACTION; SACCHAROMYCES; STARVATION; TRANSCRIPTION INITIATION; YEAST CELL;

BASE SEQUENCE; BINDING SITES; CHROMATIN; DNA, FUNGAL; DNA-BINDING PROTEINS; GENE DELETION; GENES, FUNGAL; MACROMOLECULAR SUBSTANCES; MUTATION; NUCLEAR PROTEINS; PHENOTYPE; PLASMIDS; PROMOTER REGIONS (GENETICS); PROTEIN KINASES; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; RECOMBINANT PROTEINS; RIBONUCLEASES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANS-ACTIVATION (GENETICS); TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

SACCHAROMYCES; SACCHAROMYCETALES;

EID: 0037386056     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.23.8.2800-2820.2003     Document Type: Article

References (139)

1. Abrams, E., I. Neigeborn, and M. Carlson. 1986. Molecular analysis of SNF2 and SNF5, genes required for expression of glucose-repressible genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 6:3643-3651.
2. Adams, A., D. E. Gottschling, C. A. Kaiser, and T. Stearns. 1997. Methods in yeast genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
3. Aguilera, A., and H. L. Klein. 1988. Genetic control of intrachromosomal recombination in Saccharomyces cerevisiae. I. Isolation and genetic characterization of hyperrecombination mutations. Genetics 119:779-790.
4. Allard, S., R. T. Utley, J. Savard, A. Clarke, P. Grant, C. J. Brandl, L. Pillus, J. L. Workman, and J. Cote. 1999. NuA4, an essential transcription adaptor/histone H4 acetyltransferase complex containing Esa1p and the ATM-related cofactor Tra1p. EMBO J. 18:5108-5119.
5. Angus-Hill, M. L., A. Schlichter, D. Roberts, H. Erdjument-Bromage, P. Tempst, and B. R. Cairns. 2001. A Rsc3/Rsc30 zinc cluster dimer reveals novel roles for the chromatin remodeler RSC in gene expression and cell cycle control. Mol. Cell 7:741-751.
6. Badarinarayana, V., Y. C. Chiang, and C. L. Denis. 2000. Functional interaction of CCR4-NOT proteins with TATAA-binding protein (TBP) and its associated factors in yeast. Genetics 155:1045-1054.
7. Beelman, C. A., and R. Parker. 1995. Degradation of mRNA in eukaryotes. Cell 81:179-183.
8. Belotserkovskaya, R., D. E. Sterner, M. Deng, M. H. Sayre, P. M. Lieberman, and S. L. Berger. 2000. Inhibition of TATA-binding protein function by SAGA subunits Spt3 and Spt8 at Gcn4-activated promoters. Mol. Cell. Biol. 20:634-647.
9. Berger, S. L. 2002. Histone modifications in transcriptional regulation. Curr. Opin. Genet. Dev. 12:142-148.
10. Berger, S. L., B. Pina, N. Silverman, G. A. Marcus, J. Agapite, J. L. Regier, S. J. Triezenberg, and L. Guarente. 1992. Genetic isolation of ADA2: a potential transcription adaptor required for function of certain acidic activation domains. Cell 70:251-265.
11. Bernstein, B. E., J. K. Tong, and S. L. Schreiber. 2000. Genome wide studies of histone deacetylase function in yeast. Proc. Natl. Acad. Sci. USA 97:13708-13713.
12. Bhaumik, S. R., and M. R. Green. 2001. SAGA is an essential in vivo target of the yeast acidic activator Ga14p. Genes Dev. 15:1935-1945.
13. Bjorklund, S., O. Buzaite, and M. Hallberg. 2001. The yeast mediator. Mol. Cells 11:129-136.
14. Bushman, J. L., M. Foiani, A. M. Cigan, C. J. Paddon, and A. G. Hinnebusch. 1993. Guanine nucleotide exchange factor for eIF-2 in yeast: genetic and biochemical analysis of interactions between essential subunits GCD2, GCD6, and GCD7 and regulatory subunit GCN3. Mol. Cell. Biol. 13:4618-4631.
15. Cairns, B. R., R. S. Levinson, K. R. Yamamoto, and R. D. Kornberg. 1996. Essential role of Swp73p in the function of yeast Swi/Snf complex. Genes Dev. 10:2131-2144.
16. Cairns, B. R., A. Schlichter, H. Erdjument-Bromage, P. Tempst, R. D. Kornberg, and F. Winston. 1999. Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. Mol. Cell 4:715-723.
17. Chang, M., D. French-Cornay, H. Y. Fan, H. Klein, C. L. Denis, and J. A. Jaehning. 1999. A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling. Mol. Cell. Biol. 19:1056-1067.
18. Chavez, S., and A. Aguilera. 1997. The yeast HPR1 gene has a functional role in transcriptional elongation that uncovers a novel source of genome instability. Genes Dev. 11:3459-3470.
19. Chavez, S., T. Beilharz, A. G. Rondon, H. Erdjument-Bromage, P. Tempst, J. Q. Svejstrup, T. Lithgow, and A. Aguilera. 2000. A protein complex containing Tho2, Hpr1, Mft1 and a novel protein, Thp2, connects transcription elongation with mitotic recombination in Saccharomyces cerevisiae. EMBO J. 19:5824-5834.
20. Chen, J., Y. C. Chiang, and C. L. Denis. 2002. CCR4, a 3′-5′ poly(A) RNA and ssDNA exonuclease, is the catalytic component of the cytoplasmic deadenylase. EMBO J. 21:1414-1426.
21. Chen, J., J. Rappsilber, Y. C. Chiang, P. Russell, M. Mann, and C. L. Denis. 2001. Purification and characterization of the 1.0 MDa CCR4-NOT complex identifies two novel components of the complex. J. Mol. Biol. 314:683-694.
22. Chi, Y., M. J. Huddleston, X. Zhang, R. A. Young, R. S. Annan, S. A. Carr, and R. J. Deshaies. 2001. Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev. 15:1078-1092.
23. Collart, M. A., and K. Struhl. 1994. NOT1(CDC39), NOT2(CDC36), NOT3, and NOT4 encode a global-negative regulator of transcription that differentially affects TATA-element utilization. Genes Dev. 8:525-537.
24. Cosma, M. P., T. Tanaka, and K. Nasmyth. 1999. Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter. Cell 97:299-311.
25. Denis, C. L., and T. Malvar. 1990. The CCR4 gene from Saccharomyces cerevisiae is required for both nonfermentative and SPT-mediated gene expression. Genetics 124:283-291.
26. Dimova, D., Z. Nackerdien, S. Furgeson, S. Eguchi, and M. A. Osley. 1999. A role for transcriptional repressors in targeting the yeast Swi/Snf complex. Mol. Cell 4:75-83.
27. Dotson, M. R., C. X. Yuan, R. G. Roeder, L. C. Myers, C. M. Gustafsson, Y. W. Jiang, Y. Li, R. D. Kornberg, and F. J. Asturias. 2000. Structural organization of yeast and mammalian mediator complexes. Proc. Natl. Acad. Sci. USA 97:14307-14310.
28. Driscoll-Penn, M., B. Galgoci, and H. Greer. 1983. Identification of AAS genes and their regulatory role in general control of amino acid biosynthesis in yeast. Proc. Natl. Acad. Sci. USA 80:2704-2708.
29. Drysdale, C. M., E. Dueñas, B. M. Jackson, U. Reusser, G. H. Braus, and A. G. Hinnebusch. 1995. The transcriptional activator GCN4 contains multiple activation domains that are critically dependent on hydrophobic amino acids. Mol. Cell. Biol. 15:1220-1233.
30. Drysdale, C. M., B. M. Jackson, R. McVeigh, E. R. Klebanow, Y. Bai, T. Kokubo, M. Swanson, Y. Nakatani, P. A. Weil, and A. G. Hinnebusch. 1998. The Gcn4p activation domain interacts specifically in vitro with RNA polymerase II holoenzyme, TFIID, and the Adap-Gcn5p coactivator complex. Mol. Cell. Biol. 18:1711-1724.
31. Dudley, A. M., C. Rougeulle, and F. Winston. 1999. The Spt components of SAGA facilitate TBP binding to a promoter at a post-activator-binding step in vivo. Genes Dev. 13:2940-2945.
32. Eberharter, A., D. E. Sterner, D. Schieltz, A. Hassan, J. R. Yates, S. L. Berger, and J. L. Workman. 1999. The ADA complex is a distinct histone acetyltransferase complex in Saccharomyces cerevisiae. Mol. Cell. Biol. 19: 6621-6631.
33. Eisen, A., R. T. Utley, A. Nourani, S. Allard, P. Schmidt, W. S. Lane, J. C. Lucchesi, and J. Cotes. 2001. The yeast NuA4 and Drosophila MSL complexes contain homologous subunits important for transcription regulation. J. Biol. Chem. 276:3484-3491.
34. Eisenmann, D. M., K. M. Arndt, S. L. Ricupero, J. W. Rooney, and F. Winston. 1992. SPT3 interacts with TFIID to allow normal transcription in Saccharomyces cerevisiae. Genes Dev. 6:1319-1331.
35. Estruch, F., and M. Carlson. 1990. SNF6 encodes a nuclear protein that is required for expression of many genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 10:2544-2553.
36. Evangelista, C. C. J., A. M. Rodriguez-Torres, M. P. Limbach, and R. S. Zitomer. 1996. Rox3 and Rts1 function in the global stress response pathway in baker's yeast. Genetics 142:1083-1093.
37. Fassler, J. S., and F. Winston. 1989. The Saccharomyces cerevisiae SPT13/ GAL11 gene has both positive and negative regulatory roles in transcription. Mol. Cell. Biol. 9:5602-5609.
38. Fazzio, T. G., C. Kooperberg, J. P. Goldmark, C. Neal, R. Basom, J. Delrow, and T. Tsukiyama. 2001. Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol. Cell. Biol. 21:6450-6460.
39. Featherstone, M. 2002. Coactivators in transcription initiation: here are your orders. Curr. Opin. Genet. Dev. 12:149-155.
40. Georgakopoulos, T., and G. Thireos. 1992. Two distinct yeast transcriptional activators require the function of the GCN5 protein to promote normal levels of transcription. EMBO J. 11:4145-4152.
41. Gietz, R. D., and A. Sugino. 1988. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74:527-534.
42. Grant, P. A., L. Duggan, J. Cote, S. M. Roberts, J. E. Brownell, R. Candau, R. Ohba, T. Owen-Hughes, C. D. Allis, F. Winston, S. L. Berger, and J. L. Workman. 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.
43. Grant, P. A., A. Eberharter, S. John, R. G. Cook, B. M. Turner, and J. L. Workman. 1999. Expanded lysine acetylation specificity of Gcn5 in native complexes. J. Biol. Chem. 274:5895-5900.
44. Han, S. J., J. S. Lee, J. S. Kang, and Y. J. Kim. 2001. Med9/Cse2 and Gal11 modules are required for transcriptional repression of distinct groups of genes. J. Biol. Chem. 276:37020-37026.
45. Hassan, A. H., K. E. Neely, and J. L. Workman. 2001. Histone acetyltransferase complexes stabilize SWI/SNF binding to promoter nucleosomes. Cell 104:817-827.
46. Hata, H., H. Mitsui, H. Liu, Y. Bai, C. L. Denis, Y. Simizu, and A. Sakai. 1998. Dhh1p, a putative RNA helicase, associates with the general transcription factors Pop2p and Ccr4p from Saccharomyces cerevisiae. Genetics 148:571-579.
47. Hengartner, C. J., C. M. Thompson, J. Zhang, D. M. Chao, S. M. Liao, A. J. Koleske, S. Okamura, and R. A. Young. 1995. Association of an activator with an RNA polymerase II holoenzyme. Genes Dev. 9:897-910.
48. Hinnebusch, A. G. 1992. General and pathway-specific regulatory mechanisms controlling the synthesis of amino acid biosynthetic enzymes in Saccharomyces cerevisiae, p. 319-414. In J. R. Broach, E. W. Jones, and J. R. Pringle (ed.), The molecular and cellular biology of the yeast Saccharomyces: gene expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
49. Hinnebusch, A. G. 1996. Translational control of GCN4: gene-specific regulation by phosphorylation of eIF2, p. 199-244. In J. W. B. Hershey, M. B. Mathews, and N. Sonenberg (ed.), Translational control. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
50. Hinnebusch, A. G., G. Lucchini, and G. R. Fink. 1985. A synthetic HIS4 regulatory element confers general amino acid control on the cytochrome c gene CYC1 of yeast. Proc. Natl. Acad. Sci. USA 82:498-502.
51. Holstege, F. C., E. G. Jennings, J. J. Wyrick, T. I. Lee, C. J. Hengartner, M. R. Green, T. R. Golub, E. S. Lander, and R. A. Young. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95:717-728.
52. Horiuchi, J., N. Silverman, B. Pina, G. A. Marcus, and L. Guarente. 1997. ADA1, a novel component of the ADA/GCN5 complex, has broader effects than GCN5, ADA2, or ADA3. Mol. Cell. Biol. 17:3220-3228.
53. Howe, L., D. Auston, P. Grant, S. John, R. G. Cook, J. L. Workman, and L. Pillus. 2001. Histone H3 specific acetyltransferases are essential for cell cycle progression. Genes Dev. 15:3144-3154.
54. Jackson, B. M., C. M. Drysdale, K. Natarajan, and A. G. Hinnebusch. 1996. Identification of seven hydrophobic clusters in GCN4 making redundant contributions to transcriptional activation. Mol. Cell. Biol. 16:5557-5571.
55. Jia, M. H., R. A. Larossa, J. M. Lee, A. Rafalski, E. Derose, G. Gonye, and Z. Xue. 2000. Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl. Physiol. Genomics 3:83-92.
56. Jiang, Y. W., and D. J. Stillman. 1995. Regulation of HIS4 expression by the Saccharomyces cerevisiae SIN4 transcriptional regulator. Genetics 140:103-114.
57. John, S., L. Howe, S. T. Tafrov, P. A. Grant, R. Sternglanz, and J. L. Workman. 2000. The Something About Silencing protein, Sas3, is the catalytic subunit of NuA3, a yTAF(II)30-containing HAT complex that interacts with the Spt16 subunit of the yeast CP (Cdc68/Pob3)-FACT complex. Genes Dev. 14:1196-1208.
58. Jones, E. W., and G. R. Fink. 1982. Regulation of amino acid and nucleotide biosynthesis in yeast, p. 181-300. In J. N. Strathern, E. W. Jones, and J. R. Broach (ed.), The molecular biology of the yeast Saccharomyces: metabolism and gene expression. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
59. Klebanow, E. R., D. Poon, S. Zhou, and P. A. Weil. 1997. Cloning and characterization of an essential Saccharomyces cerevisiae gene, TAF40, which encodes yTAFII40 an RNA polymerase II-specific TATA-binding protein-associated factor. J. Biol. Chem. 272:9436-9442.
60. Koh, S. S., A. Z. Ansari, M. Ptashne, and R. A. Young. 1998. An activator target in the RNA polymerase II holoenzyme. Mol. Cell 1:895-904.
61. Krebs, J. E., C. J. Fry, M. L. Samuels, and C. L. Peterson. 2000. Global role for chromatin remodeling enzymes in mitotic gene expression. Cell 102: 587-598.
62. Kuo, M. H., and C. D. Allis. 1999. In vivo cross-linking and immunoprecipitation for studying dynamic protein:DNA associations in a chromatin environment. Methods 19:425-433.
63. Kuo, M. H., E. V. Baur, K. Struhl, and C. D. Allis. 2000. Gcn4 activator targets Gcn5 histone acetyltransferase to specific promoters independently of transcription. Mol. Cell 6:1309-1320.
64. Kuo, M. H., J. Zhou, P. Jambeck, M. E. Churchill, and C. D. Allis. 1998. Histone acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in vivo. Genes Dev. 12:627-639.
65. LaRossa, R. A., and J. V. Schloss. 1984. The sulfonylurea herbicide sulfometuron methyl is an extremely potent and selective inhibitor of acetolactate synthase in Salmonella typhimurium. J. Biol. Chem. 259:8753-8757.
66. Larschan, E., and F. Winston. 2001. The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Ga14. Genes Dev. 15:1946-1956.
67. Lee, T. I., H. C. Causton, F. C. Holstege, W. C. Shen, N. Hannett, E. G. Jennings, F. Winston, M. R. Green, and R. A. Young. 2000. Redundant roles for the TFIID and SAGA complexes in global transcription. Nature 405:701-704.
68. Lee, T. I., N. J. Rinaldi, F. Robert, D. T. Odom, Z. Bar-Joseph, G. K. Gerber, N. M. Hannett, C. T. Harbison, C. M. Thompson, I. Simon, J. Zeitlinger, E. G. Jennings, H. L. Murray, D. B. Gordon, B. Ren, J. J. Wyrick, J. B. Tagne, T. L. Volkert, E. Fraenkel, D. K. Gifford, and R. A. Young. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804.
69. Lee, T. I., J. J. Wyrick, S. S. Koh, E. G. Jennings, E. L. Gadbois, and R. A. Young. 1998. Interplay of positive and negative regulators in transcription initiation by RNA polymerase II holoenzyme. Mol. Cell. Biol. 18:4455-4462.
70. Lee, T. I., and R. A. Young. 2000. Transcription of eukaryotic proteincoding genes. Annu. Rev. Genet 34:77-137.
71. Lee, Y. C., J. M. Park, S. Min, S. J. Han, and Y. J. Kim. 1999. An activator binding module of yeast RNA polymerase II holoenzyme. Mol. Cell. Biol. 19:2967-2976.
72. Lei, E. P., H. Krebber, and P. A. Silver. 2001. Messenger RNAs are recruited for nuclear export during transcription. Genes Dev. 15:1771-1782.
73. Lemaire, M., and M. A. Collart. 2000. The TATA-binding protein-associated factor yTAFII19p functionally interacts with components of the global transcriptional regulator Ccr4-Not complex and physically interacts with the Not5 subunit. J. Biol. Chem. 275:26925-26934.
74. Liu, H. Y., V. Badarinarayana, D. C. Audino, J. Rappsilber, M. Mann, and C. L. Denis. 1998. The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively. EMBO J. 17:1096-1106.
75. Liu, H. Y., Y. C. Chiang, J. Pan, J. Chen, C. Salvadore, D. C. Audino, V. Badarinarayana, V. Palaniswamy, B. Anderson, and C. L. Denis. 2001. Characterization of CAF4 and CAF16 reveals a functional connection between the CCR4-NOT complex and a subset of SRB proteins of the RNA polymerase II holoenzyme. J. Biol. Chem. 276:7541-7548.
76. Liu, Y., J. A. Ranish, R. Aebersold, and S. Hahn. 2001. Yeast nuclear extract contains two major forms of RNA polymerase II mediator complexes. J. Biol. Chem. 276:7169-7175.
77. Longtine, M. S., A. McKenzie III, D. J. Demarini, N. G. Shah, A. Wach, A. Brachat, P. Philippsen, and J. R. Pringle. 1998. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14:953-961.
78. Madison, J. M., and F. Winston. 1997. Evidence that Spt3 functionally interacts with Mot1, TFIIA, and TATA-binding protein to confer promoter-specific transcriptional control in Saccharomyces cerevisiae. Mol. Cell. Biol. 17:287-295.
79. Maniatis, T., and R. Reed. 2002. An extensive network of coupling among gene expression machines. Nature 416:499-506.
80. Marcus, G. A., J. Horiuchi, N. Silverman, and L. Guarente, 1996. ADA5/SPT20 links the ADA and SPT genes, which are involved in yeast transcription. Mol. Cell. Biol. 16:3197-3205.
81. Marcus, G. A., N. Silverman, S. L. Berger, J. Horiuchi, and L. Guarente. 1994. Functional similarity and physical association between GCN5 and ADA2: putative transcriptional adaptors. EMBO J. 13:4807-4815.
82. Martens, J. A., and F. Winston. 2002. Evidence that Swi/Snf directly represses transcription in S. cerevisiae. Genes Dev. 16:2231-2236.
83. Moehle, C. M., and A. G. Hinnebusch. 1991. Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:2723-2735.
84. Moqtaderi, Z., J. D. Yale, K. Struhl, and S. Buratowski. 1996. Yeast homologues of higher eukaryotic TFIID subunits. Proc. Natl. Acad. Sci. USA 93:14654-14658.
85. Moreira, J. M., and S. Holmberg. 1999. Transcriptional repression of the yeast CHA1 gene requires the chromatin-remodeling complex RSC. EMBO J. 18:2836-2844.
86. Mueller, C. L., and J. A. Jaehning. 2002. Ctr9, Rtfl, and Leo1 are components of the Paf1/RNA polymerase II complex. Mol. Cell. Biol. 22:1971-1980.
87. Myers, L. C., C. M. Gustafsson, D. A. Bushnell, M. Lui, H. Erdjument-Bromage, P. Tempst, and R. D. Kornberg. 1998. The Med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain. Genes Dev. 12:45-54.
88. Myers, L. C., C. M. Gustafsson, K. C. Hayashibara, P. O. Brown, and R. D. Kornberg. 1999. Mediator protein mutations that selectively abolish activated transcription. Proc. Natl. Acad. Sci. USA 96:67-72.
89. Myers, L. C., and R. D. Kornberg. 2000. Mediator of transcriptional regulation. Annu. Rev. Biochem. 69:729-749.
90. Naar, A. M., B. D. Lemon, and R. Tjian. 2001. Transcriptional coactivator complexes. Annu. Rev. Biochem 70:475-501.
91. Narlikar, G. J., H. Y. Fan, and R. E. Kingston. 2002. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108: 475-487.
92. II61 has a general role in RNA polymerase II transcription and is required by Gcn4p to recruit the SAGA coactivator complex. Mol. Cell 2:683-692.
93. Natarajan, K., B. M. Jackson, H. Zhou, F. Winston, and A. G. Hinnebusch. 1999. Transcriptional activation by Gcn4p involves independent interactions with SWI/SNF complex and SRB/mediator. Mol. Cell 4:657-664.
94. Natarajan, K., M. R. Meyer, B. M. Jackson, D. Slade, C. Roberts, A. G. Hinnebusch, and M. J. Marton. 2001. Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast. Mol. Cell. Biol. 21:4343-4368.
95. Neely, K. E., A. H. Hassan, C. E. Brown, L. Howe, and J. L. Workman. 2002. Transcription activator interactions with multiple SWI/SNF subunits. Mol. Cell. Biol. 22:1615-1625.
96. Neely, K. E., A. H. Hassan, A. E. Wallberg, D. J. Steger, B. R. Cairns, A. P. Wright, and J. L. Workman. 1999. Activation domain-mediated targeting of the SWI/SNF complex to promoters stimulates transcription from nucleosome arrays. Mol. Cell 4:649-655.
97. Ng, H. H., F. Robert, R. A. Young, and K. Struhl. 2002. Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. Genes Dev. 16:806-819.
98. Park, J. M., H. S. Kim, S. J. Han, M. S. Hwang, Y. C. Lee, and Y. J. Kim. 2000. In vivo requirement of activator-specific binding targets of mediator. Mol. Cell. Biol. 20:8709-8719.
99. Peterson, C. L., A. Dingwall, and M. P. Scott. 1994. Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement. Proc. Natl. Acad. Sci. USA 91:2905-2908.
100. Pina, B., S. Berger, G. A. Marcus, N. Silverman, J. Agapite, and L. Guarente. 1993. ADA3: a gene, identified by resistance to GAL4-VP16, with properties similar to and different from those of ADA2. Mol. Cell. Biol. 13:5981-5989.
101. Piruat, J. I., S. Chavez, and A. Aguilera. 1997. The yeast HRS1 gene is involved in positive and negative regulation of transcription and shows genetic characteristics similar to SIN4 and GAL11. Genetics 147:1585-1594.
102. Pokholok, D. K., N. M. Hannett, and R. A. Young. 2002. Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol. Cell 9:799-809.
103. Poon, D., Y. Bai, A. M. Campbell, S. Bjorklund, Y. J. Kim, S. Zhou, R. D. Kornberg, and P. A. Weil. 1995. Identification and characterization of a TFIID-like multiprotein complex from Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 92:8224-8228.
104. Pugh, B. F. 2000. Control of gene expression through regulation of the TATA-binding protein. Gene 255:1-14.
105. Reifsnyder, C., J. Lowell, A. Clarke, and L. Pillus. 1996. Yeast SAS silencing genes and human genes associated with AML and HIV-1 Tat interactions are homologous with acetyltransferases. Nat. Genet. 14:42-49.
106. Reinke, H., P. D. Gregory, and W. Horz. 2001. A transient histone hyperacetylation signal marks nucleosomes for remodeling at the PH08 promoter in vivo. Mol. Cell 7:529-538.
107. Ricci, A. R., J. Genereaux, and C. J. Brandl. 2002. Components of the SAGA histone acetyltransferase complex are required for repressed transcription of ARG1 in rich medium. Mol. Cell. Biol. 22:4033-4042.
108. Roberts, S. M., and F. Winston. 1996. SPT20/ADA5 encodes a novel protein functionally related to the TATA-binding protein and important for transcription in Saccharomyces cerevisiae. Mol. Cell. Biol. 16:3206-3213.
109. Roth, S. Y., J. M. Denu, and C. D. Allis. 2001. Histone acetyltransferases. Annu. Rev. Biochem 70:81-120.
110. Sachs, A. B., and G. Varani. 2000. Eukaryotic translation initiation: there are (at least) two sides to every story. Nat. Struct. Biol. 7:356-361.
111. Santos-Rosa, H., B. Clever, W. D. Heyer, and A. Aguilera. 1996. The yeast HRS1 gene encodes a polyglutamine-rich nuclear protein required for spontaneous and hpr1-induced deletions between direct repeats. Genetics 142:705-716.
112. Schneiter, R., C. E. Guerra, M. Lampl, G. Gogg, S. D. Kohlwein, and H. L. Klein. 1999. The Saccharomyces cerevisiae hyperrecombination mutant hpr1Δ is synthetically lethal with two conditional alleles of the acetyl coenzyme A carboxylase gene and causes a defect in nuclear export of polyadenylated RNA. Mol. Cell. Biol. 19:3415-3422.
113. Schurch, A., J. Miozzari, and R. Hutter. 1974. Regulation of tryptophan biosynthesis in Saccharomyces cerevisiae: mode of action of 5-methyltryptophan and 5-methyltryptophan-sensitive mutants. J. Bacteriol. 117:1131-1140.
114. Shi, X., M. Chang, A. J. Wolf, C. H. Chang, A. A. Frazer Abel, P. A. Wade, Z. F. Burton, and J. A. Jaehning. 1997. Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme. Mol. Cell. Biol. 17:1160-1169.
115. Sikorski, R. S., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19-27.
116. Spencer, V. A., and J. R. Davie. 1999. Role of covalent modifications of histones in regulating gene expression. Gene 240:1-12.
117. Squazzo, S. L., P. J. Costa, D. L. Lindstrom, K. E. Kumer, R. Simic, J. L. Jennings, A. J. Link, K. M. Arndt, and G. A. Hartzog. 2002. The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J. 21:1764-1774.
118. Sterner, D. E., and S. L. Berger. 2000. Acetylation of histones and transcription-related factors. Microbiol. Mol. Biol. Rev. 64:435-459.
119. Sterner, D. E., P. A. Grant, S. M. Roberts, L. J. Duggan, R. Belotserkovskaya, L. A. Pacella, F. Winston, J. L. Workman, and S. L. Berger. 1999. Functional organization of the yeast SAGA complex: distinct components involved in structural integrity, nucleosome acetylation, and TATA-binding protein interaction. Mol. Cell. Biol. 19:86-98.
120. Strahl, B. D., and C. D. Allis. 2000. The language of covalent histone modifications. Nature 403:41-45.
121. Straßer, K., M. S., P. Mason, P. J., M. Oppizzi, S. Rodriquez-Navarro, A. G. Rondonk, A. Aguilera, K. Struhl, R. Reed, and E. Hurt. 2002. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417:304-308.
122. Struhl, K. 1985. Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc. Natl. Acad. Sci. USA 82:8419-8423.
123. Sudarsanam, P., V. R. Iyer, P. O. Brown, and F. Winston. 2000. Wholegenome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 97:3364-3369.
124. Sudarsanam, P., and F. Winston. 2000. The Swi/Snf family nucleosome-remodeling complexes and transcriptional control. Trends Genet. 16:345-351.
125. Svejstrup, J. Q., Y. Li, J. Fellows, A. Gnatt, S. Bjorklund, and R. D. Kornberg. 1997. Evidence for a mediator cycle at the initiation of transcription. Proc. Natl. Acad. Sci. USA 94:6075-6078.
126. Syntichaki, P., I. Topalidou, and G. Thireos. 2000. The Gcn5 bromodomain co-ordinates nucleosome remodeling. Nature 404:414-417.
127. Takemaru, K., S. Harashima, H. Ueda, and S. Hirose. 1998. Yeast coactivator MBF1 mediates GCN4-dependent transcriptional activation. Mol. Cell. Biol. 18:4971-4976.
128. Thompson, C. M., A. J. Koleske, D. M. Chao, and R. A. Young. 1993. A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast. Cell 73:1361-1375.
129. Tran, H. G., D. J. Steger, V. R. Iyer, and A. D. Johnson. 2000. The chromo domain protein Chd1p from budding yeast is an ATP-dependent chromatin-modifying factor. EMBO J. 19:2323-2331.
130. Tucker, M., R. R. Staples, M. A. Valencia-Sanchez, D. Muhlrad, and R. Parker. 2002. Ccr4p is the catalytic subunit of a Ccr4p/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae. EMBO J. 21:1427-1436.
131. Tucker, M., M. A. Valencia-Sanchez, R. R. Staples, J. Chen, C. L. Denis, and R. Parker. 2001. The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell 104:377-386.
132. Utley, R. T., K. Ikeda, P. A. Grant, J. Cote, D. J. Steger, A. Eberharter, S. John, and J. L. Workman. 1998. Transcriptional activators direct histone acetyltransferase complexes to nucleosomes. Nature 394:498-502.
133. Wade, P. A., W. Werel, R. C. Fentzke, N. E. Thompson, J. F. Leykam, R. R. Burgess, J. A. Jaehning, and Z. F. Burton. 1996. A novel collection of accessory factors associated with yeast RNA polymerase II. Protein Expr. Purif. 8:85-90.
134. Wek, S. A., S. Zhu, and R. C. Wek. 1995. The histidyl-tRNA synthetase-related sequence in the eIF-2α protein kinase GCN2 interacts with tRNA and is required for activation in response to starvation for different amino acids. Mol. Cell. Biol. 15:4497-4506.
135. Winston, F., and C. D. Allis. 1999. The bromodomain: a chromatin-targeting module? Nat. Struct. Biol. 6:601-604.
136. Winzeler, E. A., A. Astromoff, H. Liang, K. Anderson, B. Andre, R. Bangham, R. Benito, J. D. Boeke, H. Bussey, A. M. Chu, C. Connelly, K. Davis, F. Dietrich, S. W. Dow, M. Bakkoury, F. Foury, S. H. Friend, E. Gentalen, G. Giaever, J. H. J. Hegemann, T., M. Laub, H. Liao, N. Liebundguth, D. J. Lockhart, A. Lucau-Danila, M. Lussier, N. M'Rabet, P. Menard, M. Mittmann, C. Pai, C. Rebischung, J. L. Revuelta, L. Riles, C. J. Roberts, P. Ross-McDonald, B. Scherens, M. Snyder, S. Sookhai-Mahadeo, R. K. Storms, S. Veronneau, M. Voet, G. Volckaert, T. R. Ward, R. Wysocki, G. S. Yen, K. Yu, K. Zimmermann, P. Philippsen, M. Johnston, and R. W. Davis. 1999. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901-906.
137. Wolfner, M., D. Yep, F. Messenguy, and G. R. Fink. 1975. Integration of amino acid biosynthesis into the cell cycle of Saccharomyces cerevisiae. J. Mol. Biol. 96:273-290.
138. Woontner, M., P. A. Wade, J. Bonner, and J. A. Jaehning. 1991. Transcriptional activation in an improved whole-cell extract from Saccharomyces cerevisiae. Mol. Cell. Biol. 11:4555-4560.
139. Yudkovsky, N., C. Logie, S. Hahn, and C. L. Peterson. 1999. Recruitment of the SWI/SNF chromatin remodeling complex by transcriptional activators. Genes Dev. 13:2369-2374.