Comparison of ABF1 and RAP1 in Chromatin Opening and Transactivator Potentiation in the Budding Yeast Saccharomyces cerevisiae

REFERENCES

• Barbaric, S., Munsterkotter M., Goding C., and Horz W.. 1998. Cooperative Pho2-Pho4 interactions at the PHO5 promoter are critical for binding of Pho4 to UASp1 and for efficient transactivation by Pho4 at UASp2. Mol. Cell. Biol. 18:2629–2639.
   PubMedGoogle Scholar
• Bodmer-Glavas, M., Edler K., and Barberis A.. 2001. RNA polymerase II and III transcription factors can stimulate DNA replication by modifying origin chromatin structures. Nucleic Acids Res. 29:4570–4580.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• Diffley, J. F., and Stillman B.. 1989. Similarity between the transcriptional silencer binding proteins ABF1 and RAP1. Science 246:1034–1038.
   PubMedGoogle Scholar
• Fourel, G., Miyake T., Defossez P. A., Li R., and Gilson E.. 2002. General regulatory factors (GRFs) as genome partitioners. J. Biol. Chem. 277:41736–41743.
   PubMedGoogle Scholar
• Gartenberg, M. R. 2000. The Sir proteins of Saccharomyces cerevisiae: mediators of transcriptional silencing and much more. Curr. Opin. Microbiol. 3:132–137.
   PubMedGoogle Scholar
• Goncalves, P. M., Griffioen G., Minnee R., Bosma M., Kraakman L. S., Mager W. H., and Planta R. J.. 1995. Transcription activation of yeast ribosomal protein genes requires additional elements apart from binding sites for Abf1p or Rap1p. Nucleic Acids Res. 23:1475–1480.
   PubMedGoogle Scholar
• Goncalves, P. M., Maurer K., van Nieuw Amerongen G., Bergkamp-Steffens K., Mager W. H., and Planta R. J.. 1996. C-terminal domains of general regulatory factors Abf1p and Rap1p in Saccharomyces cerevisiae display functional similarity. Mol. Microbiol. 19:535–543.
   PubMedGoogle Scholar
• Graham, I. R., Haw R. A., Spink K. G., Halden K. A., and Chambers A.. 1999. In vivo analysis of functional regions within yeast Rap1p. Mol. Cell. Biol. 19:7481–7490.
   PubMedGoogle Scholar
• Grunstein, M. 1997. Molecular model for telomeric heterochromatin in yeast. Curr. Opin. Cell Biol. 9:383–387.
   PubMed Web of Science ®Google Scholar
• Halfter, H., Kavety B., Vandekerckhove J., Kiefer F., and Gallwitz D.. 1989. Sequence, expression and mutational analysis of BAF1, a transcriptional activator and ARS1-binding protein of the yeast Saccharomyces cerevisiae. EMBO J. 8:4265–4272.
   PubMedGoogle Scholar
• Hardy, C. F. J., Sussel L., and Shore D.. 1992. Dissection of a carboxyl-terminal region of the yeast regulatory protein RAP1 with effects on both transcriptional activation and silencing. Mol. Cell. Biol. 12:1209–1217.
   PubMedGoogle Scholar
• Higuchi, R., Krummel B., and Saiki R. K.. 1988. A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions. Nucleic Acids Res. 16:7351–7367.
   PubMed Web of Science ®Google Scholar
• Hill, J., Donald K. A., Griffiths D. E., and Donald G.. 1991. DMSO-enhanced whole cell yeast transformation. Nucleic Acids Res. 19:5791. (Erratum, 19:6688.)
   PubMed Web of Science ®Google Scholar
• Hu, Y. F., Hao Z. L., and Li R.. 1999. Chromatin remodeling and activation of chromosomal DNA replication by an acidic transcriptional activation domain from BRCA1. Genes Dev. 13:637–642.
   PubMed Web of Science ®Google Scholar
• Kent, N. A., Bird L. E., and Mellor J.. 1993. Chromatin analysis in yeast using NP-40 permeabilised sphaeroplasts. Nucleic Acids Res. 21:4653–4654.
   PubMedGoogle Scholar
• Kurtz, S., and Shore D.. 1991. RAP1 protein activates and silences transcription of mating-type genes in yeast. Genes Dev. 5:616–628.
   PubMed Web of Science ®Google Scholar
• Lascaris, R. F., Groot E., Hoen P. B., Mager W. H., and Planta R. J.. 2000. Different roles for Abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene. Nucleic Acids Res. 28:1390–1396.
   PubMedGoogle Scholar
• Li, R., Yu D. S., Tanaka M., Zheng L., Berger S. L., and Stillman B.. 1998. Activation of chromosomal DNA replication in Saccharomyces cerevisiae by acidic transcriptional activation domains. Mol. Cell. Biol. 18:1296–1302.
   PubMedGoogle Scholar
• Lieb, J. D., Liu X., Botstein D., and Brown P. O.. 2001. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28:327–334.
   PubMed Web of Science ®Google Scholar
• Marahrens, Y., and Stillman B.. 1992. A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science 255:817–823.
   PubMed Web of Science ®Google Scholar
• Martens, J. A., and Brandl C. J.. 1994. GCN4p activation of the yeast TRP3 gene is enhanced by ABF1p and uses a suboptimal TATA element. J. Biol. Chem. 269:15661–15667.
   PubMedGoogle Scholar
• Mencia, M., Moqtaderi Z., Geisberg J. V., Kuras L., and Struhl K.. 2002. Activator-specific recruitment of TFIID and regulation of ribosomal protein genes in yeast. Mol. Cell 9:823–833.
   PubMed Web of Science ®Google Scholar
• Miller, J. A., and Widom J.. 2003. Collaborative competition mechanism for gene activation in vivo. Mol. Cell. Biol. 23:1623–1632.
   PubMed Web of Science ®Google Scholar
• Miyake, T., Loch C. M., and Li R.. 2002. Identification of a multifunctional domain in autonomously replicating sequence-binding factor 1 required for transcriptional activation, DNA replication, and gene silencing. Mol. Cell. Biol. 22:505–516.
   PubMedGoogle Scholar
• Morse, R. H. 2003. Getting into chromatin: how do transcription factors get past the histones? Biochem. Cell Biol. 81:101–112.
   PubMedGoogle Scholar
• Morse, R. H. 1993. Nucleosome disruption by transcription factor binding in yeast. Science 262:1563–1566.
   PubMedGoogle Scholar
• Morse, R. H. 2000. RAP, RAP, open up! New wrinkles for RAP1 in yeast. Trends Genet. 16:51–53.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• Pal, S., Cantor A. B., Johnson K. D., Moran T. B., Boyer M. E., Orkin S. H., and Bresnick E. H.. 2004. Coregulator-dependent facilitation of chromatin occupancy by GATA-1. Proc. Natl. Acad. Sci. USA 101:980–985.
   PubMed Web of Science ®Google Scholar
• Pilpel, Y., Sudarsanam P., and Church G. M.. 2001. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 29:153–159.
   PubMed Web of Science ®Google Scholar
• Pina, B., Fernandez-Larrea J., Garcia-Reyero N., and Idrissi F. Z.. 2003. The different (sur)faces of Rap1p. Mol. Genet. Genomics 268:791–798.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Pryde, F. E., and Louis E. J.. 1999. Limitations of silencing at native yeast telomeres. EMBO J. 18:2538–2550.
   PubMed Web of Science ®Google Scholar
• Reed, S. H., Akiyama M., Stillman B., and Friedberg E. C.. 1999. Yeast autonomously replicating sequence binding factor is involved in nucleotide excision repair. Genes Dev. 13:3052–3058.
   PubMedGoogle Scholar
• 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 Esa1 histone acetylase. Mol. Cell 6:1297–1307.
   PubMed Web of Science ®Google Scholar
• Rhode, P. R., Elsasser S., and Campbell J. L.. 1992. Role of multifunctional autonomously replicating sequence binding factor 1 in the initiation of DNA replication and transcriptional control in Saccharomyces cerevisiae. Mol. Cell. Biol. 12:1064–1077.
   PubMedGoogle Scholar
• Rhode, P. R., Sweder K. S., Oegema K. F., and Campbell J. L.. 1989. The gene encoding ARS-binding factor I is essential for the viability of yeast. Genes Dev. 3:1926–1939.
   PubMedGoogle Scholar
• Rolfes, R. J., Zhang F., and Hinnebusch A. G.. 1997. The transcriptional activators BAS1, BAS2, and ABF1 bind positive regulatory sites as the critical elements for adenine regulation of ADE5,7. J. Biol. Chem. 272:13343–13354.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• Sabet, N., Tong F., Madigan J. P., Volo S., Smith M. M., and Morse R. H.. 2003. Global and specific transcriptional repression by the histone H3 amino terminus in yeast. Proc. Natl. Acad. Sci. USA 100:4084–4089.
   PubMedGoogle Scholar
• Schroeder, S. C., and Weil P. A.. 1998. Genetic tests of the role of Abf1p in driving transcription of the yeast TATA box binding protein-encoding gene, SPT15. J. Biol. Chem. 273:19884–19891.
   PubMedGoogle Scholar
• Shore, D. 1994. RAP1: a protean regulator in yeast. Trends Genet. 10:408–412.
   PubMed Web of Science ®Google Scholar
• Simpson, R. T. 1991. Nucleosome positioning: occurrence, mechanisms, and functional consequences. Prog. Nucleic Acid Res. Mol. Biol. 40:143–184.
   Google Scholar
• Springer, C., Krappmann S., Kunzler M., Zmasek C., and Braus G. H.. 1997. Regulation of the yeast HIS7 gene by the global transcription factor Abf1p. Mol. Gen. Genet. 256:136–146.
   PubMedGoogle Scholar
• Springer, C., Kunzler M., Balmelli T., and Braus G. H.. 1996. Amino acid and adenine cross-pathway regulation act through the same 5′-TGACTC-3′ motif in the yeast HIS7 promoter. J. Biol. Chem. 271:29637–29643.
   PubMedGoogle Scholar
• Stafford, G. A., and Morse R. H.. 1997. Chromatin remodeling by transcriptional activation domains in a yeast episome. J. Biol. Chem. 272:11526–11534.
   PubMedGoogle Scholar
• Strahl-Bolsinger, S., Hecht A., Luo K., and Grunstein M.. 1997. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 11:83–93.
   PubMed Web of Science ®Google Scholar
• Thoma, F. 1992. Nucleosome positioning. Biochim. Biophys. Acta 1130:1–19.
   PubMed Web of Science ®Google Scholar
• Thoma, F., Bergman L. W., and Simpson R. T.. 1984. Nuclease digestion of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease-sensitive regions. J. Mol. Biol. 177:715–733.
   PubMed Web of Science ®Google Scholar
• Valerius, O., Brendel C., Wagner C., Krappmann S., Thoma F., and Braus G. H.. 2003. Nucleosome position-dependent and -independent activation of HIS7 expression in Saccharomyces cerevisiae by different transcriptional activators. Eukaryot. Cell 2:876–885.
   PubMedGoogle Scholar
• Venditti, P., Costanzo G., Negri R., and Camilloni G.. 1994. ABFI contributes to the chromatin organization of Saccharomyces cerevisiae ARS1 B-domain. Biochim. Biophys. Acta 1219:677–689.
   PubMedGoogle Scholar
• Wang, Y., Liu C. L., Storey J. D., Tibshirani R. J., Herschlag D., and Brown P. O.. 2002. Precision and functional specificity in mRNA decay. Proc. Natl. Acad. Sci. USA 99:5860–5865.
   PubMed Web of Science ®Google Scholar
• Wiltshire, S., Raychaudhuri S., and Eisenberg S.. 1997. An Abf1p C-terminal region lacking transcriptional activation potential stimulates a yeast origin of replication. Nucleic Acids Res. 25:4250–4256.
   PubMedGoogle 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
• Yu, L., and Morse R. H.. 1999. Chromatin opening and transactivator potentiation by RAP1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 19:5279–5288.
   PubMed Web of Science ®Google Scholar
• 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. 276:33257–33264.
   PubMedGoogle Scholar
• Yu, Q., Qiu R., Foland T. B., Griesen D., Galloway C. S., Chiu Y. H., Sandmeier J., Broach J. R., and Bi X.. 2003. Rap1p and other transcriptional regulators can function in defining distinct domains of gene expression. Nucleic Acids Res. 31:1224–1233.
   PubMed Web of Science ®Google Scholar