Inhibition of TATA-Binding Protein Function by SAGA Subunits Spt3 and Spt8 at Gcn4-Activated Promoters

REFERENCES

• Ausubel, F. M., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A., and Struhl, K.. 1994. Current protocols in molecular biology. John Wiley & Sons, Inc., New York, N.Y
   Google Scholar
• Bannister, A. J., and Kouzarides, T.. 1996. The CBP co-activator is a histone acetyltransferase. Nature 384:641–643
   PubMed Web of Science ®Google Scholar
• 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. 270:19337–19344
   PubMedGoogle Scholar
• Berger, S. L., Piña, B., Silverman, N., Marcus, G. A., Agapite, J., Regier, J. L., Triezenberg, S. J., and Guarente, L.. 1992. Genetic isolation of ADA2: a potential transcriptional adaptor required for function of certain acidic activation domains. Cell 70:251–265
   PubMed Web of Science ®Google Scholar
• Birck, C., Poch, O., Romier, C., Ruff, M., Mengus, G., Lavigne, A.-C., Davidson, I., and Moras, D.. 1998. Human TAFII28 and TAFII18 interact through a canonical histone fold encoded by atypical evolutionary conserved sequence motifs also found in the SPT3 TAFII family. Cell 94:239–249
   PubMed Web of Science ®Google Scholar
• Brandl, C., Furlanetto, A., Martens, J., and Hamilton, K.. 1993. Characterization of NGG1, a novel yeast gene required for glucose repression of GAL4p-regulated transcription. EMBO J. 12:5255–5265
   PubMedGoogle Scholar
• Brownell, J. E., Zhou, J., Ranalli, T., Kobayashi, R., Edmondson, D. G., Roth, S. Y., and Allis, C. D.. 1996. Tetrahymena histone acetyltransferase A: a transcriptional co-activator linking gene expression to histone acetylation. Cell 84:843–851
   PubMed Web of Science ®Google Scholar
• Burley, S. K., and Roeder, R. G.. 1996. Biochemistry and structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem. 65:769–799
   PubMed Web of Science ®Google Scholar
• Burley, S. K., and Roeder, R. G.. 1998. TATA box mimicry by TFIID: autoinhibition of PolII transcription. Cell 94:551–553
   PubMedGoogle Scholar
• Candau, R., and Berger, S. L.. 1996. Structural and functional analysis of yeast putative adaptors: evidence for an adaptor complex in vivo. J. Biol. Chem. 271:5237–5245
   PubMedGoogle Scholar
• Candau, R., Moore, P. A., Wang, L., Barlev, N., Ying, C. Y., Rosen, C. A., and Berger, S. L.. 1996. Identification of functionally conserved human homologues of the yeast adaptors ADA2 and GCN5. Mol. Cell. Biol. 16:593–602
   PubMedGoogle Scholar
• Chiang, Y. C., Komarnitsky, P., Chase, D., and Denis, C. L.. 1996. ADR1 activation domains contact the histone acetyltransferase GCN5 and the core transcriptional factor TFIIB. J. Biol. Chem. 271:32359–32365
   PubMedGoogle Scholar
• Collart, M. A.. 1996. The NOT, SPT3, and MOT1 genes functionally interact to regulate transcription at core promoters. Mol. Cell. Biol. 16:6668–6676
   PubMedGoogle Scholar
• Drysdale, C. M., Jackson, B. M., McVeigh, R., Klebanow, E. R., Bai, Y., Kokubo, T., Swanson, M., Nakatani, Y., Weil, P. A., and Hinnebusch, A. G.. 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
   PubMedGoogle Scholar
• Eisenmann, D. M., Arndt, K. M., Ricupero, S. L., Rooney, J. W., and Winston, F.. 1992. SPT3 interacts with TFIID to allow normal transcription in Saccharomyces cerevisiae. Genes Dev. 6:1319–1331
   PubMed Web of Science ®Google Scholar
• Eisenmann, D. M., Chapon, C., Roberts, S. M., Dollard, C., and Winston, F.. 1994. The Saccharomyces cerevisiae SPT8 gene encodes a very acidic protein that is functionally related to SPT3 and TATA-binding protein. Genetics 137:647–657
   PubMedGoogle Scholar
• Eisenmann, D. M., Dollard, C., and Winston, F.. 1989. SPT15, the gene encoding the yeast TATA binding factor TFIID, is required for normal transcription initiation in vivo. Cell 58:1183–1191
   PubMed Web of Science ®Google Scholar
• Feaver, W. J., Henry, N. L., Bushnell, D. A., Sayre, M. H., Brickner, J. H., Gileadi, O., and Kornberg, R. D.. 1994. Yeast TFIIE: cloning, expression and homology to vertebrate proteins. J. Biol. Chem. 269:27549–27553
   PubMedGoogle Scholar
• Gansheroff, L. J., Dollard, C., Tan, P., and Winston, F.. 1995. The Saccharomyces cerevisiae SPT7 gene encodes a very acidic protein important for transcription in vivo. Genetics 139:523–536
   PubMedGoogle Scholar
• Georgakopoulos, T., and Thireos, G.. 1992. Two distinct yeast transcriptional activators require the function of the GCN5 protein to promote normal levels of transcription. EMBO J. 11:4145–4152
   PubMed Web of Science ®Google Scholar
• Goppelt, A., Stelzer, G., Lottspeich, F., and Meisterernst, M.. 1996. A mechanism for repression of class II gene transcription through specific binding of NC2 to TPB-promoter complexes via heterodimeric histone fold domains. EMBO J. 15:3105–3116
   PubMed Web of Science ®Google Scholar
• Grant, P. A., Duggan, L., Côté, 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
   PubMed Web of Science ®Google Scholar
• Grant, P. A., Schieltz, D., Pray-Grant, M. G., Steger, D. J., Reese, J. C., Yates, J. R.III, and Workman, J. L.. 1998. A subset of TAFIIs are integral components of the SAGA complex required for nucleosome acetylation and transcription stimulation. Cell 94:45–53
   PubMedGoogle Scholar
• Grant, P. A., Sterner, D. E., Duggan, L. J., Workman, J. L., and Berger, S. L.. 1998. The SAGA unfolds: convergence of transcription regulators in chromatin-modifying complexes. Trends Cell Biol. 8:193–197
   PubMed Web of Science ®Google Scholar
• Gregory, P. D., Schmid, A., Zavari, M., Liu, L., Berger, S. L., and Hörz, W.. 1998. Absence of Gcn5 HAT activity defines a novel state in the opening of chromatin at the PHO5 promoter in yeast. Mol. Cell 1:495–505
   PubMedGoogle Scholar
• Hahn, S., Buratowski, S., Sharp, P. A., and Guarente, L.. 1989. Isolation of the gene encoding the yeast TATA binding protein TFIID: a gene identical to the SPT15 suppressor of Ty element insertions. Cell 58:1173–1181
   PubMedGoogle Scholar
• Harlow, E., and Lane, I.. 1988. Antibodies: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
   Google Scholar
• Hoffmann, A., Chiang, C.-M., Oelgeschläger, T., Xie, X., Burley, S. K., Nakatani, Y., and Roeder, R. G.. 1996. A histone octamer-like structure within TFIID. Nature 380:356–359
   PubMedGoogle Scholar
• Horiuchi, J., Silverman, N., Marcus, G. A., and Guarente, L.. 1995. ADA3, a putative transcriptional adaptor, consists of two separable domains and interacts with ADA2 and GCN5 in a trimeric complex. Mol. Cell. Biol. 15:1203–1209
   PubMed Web of Science ®Google Scholar
• Horiuchi, J., Silverman, N., Piña, B., Marcus, G. A., and Guarente, L.. 1997. ADA1, a novel component of the ADA/GCN5 complex, has broader effects than GCN5, ADA2, or ADA3. Mol. Cell. Biol. 17:3220–3228
   PubMedGoogle Scholar
• Inostroza, J. A., Mermelstein, F. H., Ha, I., Lane, W. S., and Reinberg, D.. 1992. Dr1, a TATA-binding protein–associated phosphoprotein and inhibitor of class II gene transcription. Cell 70:477–489
   PubMedGoogle Scholar
• Iyer, V., and Struhl, K.. 1996. Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 93:5208–5212
   PubMed Web of Science ®Google Scholar
• Kokubo, T., Yamashita, S., Horikoshi, M., Roeder, R. G., and Nakatani, Y.. 1994. Interaction between the N-terminal domain of the 230-kDa subunit and the TATA box-binding subunit of TFIID negatively regulates TATA-box binding. Proc. Natl. Acad. Sci. USA 91:3520–3524
   PubMedGoogle Scholar
• Kuo, M.-H., Zhou, J., Jambeck, P., Churchill, M. E. A., and Allis, C. D.. 1998. Histone acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in vivo. Genes Dev. 12:627–639
   PubMed Web of Science ®Google Scholar
• Lieberman, P. M., and Berk, A. J.. 1991. The Zta trans-activator protein stabilizes TFIID association with promoter DNA by direct protein-protein interaction. Genes Dev. 5:2441–2454
   PubMedGoogle Scholar
• Liu, D., Ishima, R., Tong, K. I., Bagby, S., Kokubo, T., Muhandiram, D. R., Kay, L. E., Nakatani, Y., and Ikura, M.. 1998. Solution structure of a TBP-TAF(II)230 complex: protein mimicry of the minor groove surface of the TATA box unwound by TBP. Cell 94:573–583
   PubMedGoogle Scholar
• Longtine, M. S., McKenzie, A.III, Demarini, D. J., Shah, N. G., Wach, A., Brachat, A., Philippsen, P., and Pringle, J. R.. 1998. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14:953–961
   PubMed Web of Science ®Google Scholar
• Madison, J. M., and Winston, F.. 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
   PubMedGoogle Scholar
• Marcus, G. A., Horiuchi, J., Silverman, N., and Guarente, L.. 1996. ADA5/SPT20 links the ADA and SPT genes, which are involved in yeast transcription. Mol. Cell. Biol. 16:3197–3205
   PubMedGoogle Scholar
• Marcus, G. A., Silverman, N., Berger, S. L., Horiuchi, J., and Guarente, L.. 1994. Functional similarity and physical association between GCN5 and ADA2: putative transcriptional adaptors. EMBO J. 13:4807–4815
   PubMed Web of Science ®Google Scholar
• Meisterernst, M., and Roeder, R. G.. 1991. Family of proteins that interact with TFIID and regulate promoter activity. Cell 67:557–567
   PubMed Web of Science ®Google Scholar
• Mizzen, C. A., Yang, X.-J., Kokubo, T., Brownell, J. E., Bannister, A. J., Owen-Hughes, T., Workman, J., Wang, L., Berger, S. L., Kouzarides, T., Nakatani, Y., and Allis, C. D.. 1996. The TAF(II)250 subunit of TFIID has histone acetyltransferase activity. Cell 87:1261–1270
   PubMed Web of Science ®Google Scholar
• Ogryzko, V. V., Kotani, T., Zhang, X., Schiltz, 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 94:35–44
   PubMedGoogle Scholar
• Ogryzko, V. V., Schlitz, R. L., Russanova, V., Howard, B. H., and Nakatani, Y.. 1996. The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87:953–959
   PubMed Web of Science ®Google Scholar
• Ozer, J., Lezina, L. E., Ewing, J., Audi, S., and Lieberman, P. M.. 1998. Association of transcription factor IIA with TATA binding protein is required for transcriptional activation of a subset of promoters and cell cycle progression in Saccharomyces cerevisiae. Mol. Cell. Biol. 18:2559–2570
   PubMedGoogle Scholar
• Piña, B., Berger, S., Marcus, G. A., Silverman, N., Agapite, J., and Guarente, L.. 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
   PubMedGoogle Scholar
• Reese, J. C., Apone, L., Walker, S. S., Griffin, L. A., and Green, M. R.. 1994. Yeast TAFIIS in a multisubunit complex required for activated transcription. Nature 371:523–527
   PubMedGoogle Scholar
• Roberts, S. G., Choy, B., Walker, S. S., Lin, Y. S., and Green, M. R.. 1995. A role for activator-mediated TFIIB recruitment in diverse aspects of transcriptional regulation. Curr. Biol. 5:508–516
   PubMedGoogle Scholar
• Roberts, S. M., and Winston, F.. 1997. Essential functional interactions of SAGA, a Saccharomyces cerevisiae complex of Spt, Ada, and Gcn5 proteins, with the Snf/Swi and Srb/mediator complexes. Genetics 147:451–465
   PubMedGoogle Scholar
• Roberts, S. M., and Winston, F.. 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
   PubMedGoogle Scholar
• Rose, M. D., Winston, F., and Hieter, P.. 1990. Methods in yeast genetics: a laboratory course manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
   Google Scholar
• Rothstein, R. J.. 1983. One-step gene disruption in yeast. Methods Enzymol. 101:202–211
   PubMed Web of Science ®Google Scholar
• Saleh, A., Lang, V., Cook, R., and Brandl, C. J.. 1997. Identification of native complexes containing the yeast coactivator/repressor proteins NGG1/ADA3 and ADA2. J. Biol. Chem. 272:5571–5578
   PubMed Web of Science ®Google Scholar
• Saleh, A., Schieltz, D., Ting, N., McMahon, S. B., Litchfield, D. W., Yates, J. R.III, Lees-Miller, S. P., Cole, M. D., and Brandl, C. J.. 1998. Tra1p is a component of the yeast Ada.Spt transcriptional regulatory complexes. J. Biol. Chem. 273:26559–26565
   PubMedGoogle Scholar
• Sawadogo, M., and Roeder, R.. 1985. Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. Cell 43:165–175
   PubMed Web of Science ®Google Scholar
• Sayre, M. H., Tschochner, H., and Kornberg, R. D.. 1992. Reconstitution of transcription with five purified initiation factors and RNA polymerase II from Saccharomyces cerevisiae. J. Biol. Chem. 267:23376–23382
   PubMedGoogle Scholar
• Silverman, N., Agapite, J., and Guarente, L.. 1994. Yeast ADA2 protein binds to the VP16 protein activation domain and activates transcription. Proc. Natl. Acad. Sci. USA 91:11665–11668
   PubMedGoogle Scholar
• Stargell, L. A., and Struhl, K.. 1996. Mechanisms of transcriptional activation in vivo: two steps forward. Trends Genet. 12:311–315
   PubMedGoogle Scholar
• Sterner, D. E., Grant, P. A., Roberts, S. M., Duggan, L. J., Belotserkovskaya, R., Pacella, L. A., Winston, F., Workman, J. L., and Berger, S. L.. 1999. Functional organization of the yeast SAGA complex: distinct components involved in structural integrity, nucleosome acetylation, and TBP binding. Mol. Cell. Biol. 19:86–98
   PubMed Web of Science ®Google Scholar
• Struhl, K.. 1986. Constitutive and inducible Saccharomyces cerevisiae promoters: evidence for two distinct molecular mechanisms. Mol. Cell. Biol. 6:3847–3853
   PubMedGoogle Scholar
• Utley, R. T., Ikeda, K., Grant, P. A., Côté, J., Steger, D. J., Eberharter, A., John, S., and Workman, J. L.. 1998. Transcriptional activators direct histone acetyltransferase complexes to nucleosomes. Nature 394:498–502
   PubMed Web of Science ®Google Scholar
• Vassilev, A., Yamauchi, J., Kotani, T., Prives, C., Avantaggiati, M. L., Qin, J., and Nakatani, Y.. 1998. The 400 kDa subunit of the PCAF histone acetylase complex belongs to the ATM superfamily. Mol. Cell 2:869–875
   PubMedGoogle Scholar
• Wade, P. A., and Wolffe, A. P.. 1997. Histone acetyltransferases in control. Curr. Biol. 7:82–84
   PubMedGoogle Scholar
• Wang, L., Liu, L., and Berger, S. L.. 1998. Critical residues for histone acetylation by GCN5, functioning in Ada and SAGA complexes, are also required for transcriptional function in vivo. Genes Dev. 12:640–653
   PubMed Web of Science ®Google Scholar
• Winston, F.. 1992. Analysis of SPT genes: a genetic approach toward analysis of TFIID, histones, and other transcription factors of yeast Transcriptional regulation. McKnight, S. L., and Yamamoto, K. R. 1271–1293 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
   Google Scholar
• Winston, F., Dollard, C., and Ricupero-Hovasse, S. L.. 1995. Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C. Yeast 11:53–55
   PubMed Web of Science ®Google Scholar
• Winston, F., Durbin, K. J., and Fink, G. R.. 1984. The SPT3 gene is required for normal transcription of Ty elements in S. cerevisiae. Cell 39:675–682
   PubMed Web of Science ®Google Scholar
• Xie, X., Kokubo, T., Cohen, S. L., Mirza, U. A., Hoffmann, A., Chait, B. T., Roeder, R. G., Nakatani, Y., and Burley, S. K.. 1996. Structural similarity between TAFs and the heterotetrameric core of the histone octamer. Nature 380:316–322
   PubMed Web of Science ®Google Scholar
• Yang, X.-J., Ogryzko, V. V., Nishikawa, J., Howard, B. H., and Nakatani, Y.. 1996. A p300/CBP-associated factor that competes with the adenoviral E1A oncoprotein. Nature 382:319–324
   PubMed Web of Science ®Google Scholar