Preferential Accessibility of the Yeast his3 Promoter Is Determined by a General Property of the DNA Sequence, Not by Specific Elements

REFERENCES

• Axelrod, J. D., and Majors, J.. 1993. GAL4 disrupts a nucleosome to activate GAL1 transcription in vivo. Genes Dev. 7:857–869
   PubMedGoogle Scholar
• Chen, W., and Struhl, K.. 1985. Yeast mRNA initiation sites are determined primarily by specific sequences, not by the distance from the TATA element. EMBO J. 4:3273–3280
   PubMedGoogle Scholar
• Chen, W., and Struhl, K.. 1988. Saturation mutagenesis of a yeast his3 TATA element: genetic evidence for a specific TATA-binding protein. Proc. Natl. Acad. Sci. USA 85:2691–2695
   PubMed Web of Science ®Google Scholar
• Drew, H. R., and Travers, A. A.. 1985. DNA bending and its relation to nucleosome positioning. J. Mol. Biol. 186:773–790
   PubMed Web of Science ®Google Scholar
• Eibel, H., and Philippsen, P.. 1984. Preferential integration of yeast transposable element Ty into a promoter region. Nature 307:386–388
   PubMed Web of Science ®Google Scholar
• Erkine, A. M., Adams, C., Gao, M., and Gross, D. S.. 1995. Multiple protein-DNA interactions over the yeast HSC82 heat shock gene promoter. Nucleic Acids Res. 23:1822–1829
   PubMedGoogle Scholar
• 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
   PubMedGoogle Scholar
• Fedor, M. J., Lue, N. F., and Kornberg, R. D.. 1988. Statistical positioning of nucleosomes by specific protein binding to an upstream activating sequence in yeast. J. Mol. Biol. 204:109–127
   PubMedGoogle Scholar
• Felsenfeld, G.. 1996. Chromatin unfolds. Cell 86:13–19
   PubMed Web of Science ®Google Scholar
• Grunstein, M.. 1997. Histone acetylation in chromatin structure and transcription. Nature 389:349–352
   PubMed Web of Science ®Google Scholar
• Hill, D. E., Hope, I. A., Macke, J. P., and Struhl, K.. 1986. Saturation mutagenesis of the yeast HIS3 regulatory site: requirements for transcriptional induction and for binding by GCN4 activator protein. Science 234:451–457
   PubMedGoogle Scholar
• Hirschhorn, J. N., Brown, S. A., Clark, C. D., and Winston, F.. 1992. Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. Genes Dev. 6:2288–2298
   PubMed Web of Science ®Google Scholar
• Hope, I. A., Mahadevan, S., and Struhl, K.. 1988. Structural and functional characterization of the short acidic transcriptional activation region of yeast GCN4 protein. Nature 333:635–640
   PubMedGoogle Scholar
• Iyer, V., and Struhl, K.. 1995. Mechanism of differential utilization of the his3 TR and TC TATA elements. Mol. Cell. Biol. 15:7059–7066
   PubMedGoogle Scholar
• Iyer, V., and Struhl, K.. 1995. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic structure. EMBO J. 14:2570–2579
   PubMed Web of Science ®Google Scholar
• Kadosh, D., and Struhl, K.. 1997. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell 89:365–371
   PubMed Web of Science ®Google Scholar
• Kadosh, D., and Struhl, K.. 1998. Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol. Cell. Biol. 18:5121–5127
   PubMed Web of Science ®Google Scholar
• Kent, N. A., Tsang, J. S. H., Crowther, D. J., and Mellor, J.. 1994. Chromatin structure modulation in Saccharomyces cerevisiae by centromere and promoter factor 1. Mol. Cell. Biol. 14:5229–5241
   PubMedGoogle Scholar
• Kladde, M. P., Xu, M., and Simpson, R. T.. 1996. Direct study of DNA-protein interactions in repressed and active chromatin in living cells. EMBO J. 15:6290–6300
   PubMedGoogle Scholar
• Klein, C., and Struhl, K.. 1994. Increased recruitment of TATA-binding protein to the promoter by transcriptional activation domains in vivo. Science 266:280–282
   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
• Kuras, L., and Struhl, K.. 1999. Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme. Nature 389:609–612
   Google Scholar
• Lee, M. S., and Garrard, W. T.. 1992. Uncoupling gene activity from chromatin structure: promoter mutations can inactivate transcription of the yeast HSP82 gene without eliminating nucleosome-free regions. Proc. Natl. Acad. Sci. USA 89:9166–9170
   PubMedGoogle Scholar
• Li, X.-L., Virbasius, A., Zhu, X., and Green, M. R.. 1999. Enhancement of TBP binding by activators and general transcription factors. Nature 389:605–609
   Google Scholar
• Lohr, D.. 1984. Organization of the GAL1-GAL10 intergenic control region chromatin. Nucleic Acids Res. 12:8457–8474
   PubMed Web of Science ®Google Scholar
• Lorch, Y., Cairns, B. R., Zhang, M., and Kornberg, R. D.. 1998. Activated RSC-nucleosome complex and persistently altered form of the nucleosome. Cell 94:29–34
   PubMed Web of Science ®Google Scholar
• Losa, R., Omari, S., and Thoma, F.. 1990. Poly(dA) · poly(dT) rich sequences are not sufficient to exclude nucleosome formation in a constitutive yeast promoter. Nucleic Acids Res. 18:3495–3502
   PubMedGoogle Scholar
• Mahadevan, S., and Struhl, K.. 1990. TC, an unusual promoter element required for constitutive transcription of the yeast his3 gene. Mol. Cell. Biol. 10:4447–4455
   PubMedGoogle Scholar
• Morse, R. H.. 1993. Nucleosome disruption by transcription factor binding in yeast. Science 262:1563–1566
   PubMedGoogle Scholar
• Mumberg, D., Muller, R., and Funk, M.. 1995. Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene 156:119–122
   PubMed Web of Science ®Google Scholar
• Natsoulis, G., Thomas, W., Roghmann, M. C., Winston, F., and Boeke, J. D.. 1989. Ty1 transposition in Saccharomyces cerevisiae is nonrandom. Genetics 123:269–279
   PubMedGoogle Scholar
• Oliphant, A. R., Brandl, C. J., and Struhl, K.. 1989. Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol. Cell. Biol. 9:2944–2949
   PubMed Web of Science ®Google Scholar
• Pavlović, B., and Hörz, W.. 1988. The chromatin structure at the promoter of a glyceraldehyde phosphate dehydrogenase gene from Saccharomyces cerevisiae reflects its functional state. Mol. Cell. Biol. 8:5513–5520
   PubMedGoogle Scholar
• Quinn, J., Fyrberg, A. M., Ganster, R. W., Schmidt, M. C., and Peterson, C. L.. 1996. DNA-binding properties of the yeast SWI/SNF complex. Nature 379:844–847
   PubMedGoogle Scholar
• Robzyk, K., Recht, L., and Osley, M. A.. 2000. Rad6-dependent ubiquitination of histone H2B in yeast. Science 287:501–504
   PubMed Web of Science ®Google Scholar
• Rundlett, S. E., Carmen, A. A., Suka, N., Turner, B. M., and Grunstein, M.. 1998. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature 392:831–835
   PubMed Web of Science ®Google Scholar
• Satchwell, S. C., Drew, H. R., and Travers, A. A.. 1986. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191:659–675
   PubMed Web of Science ®Google Scholar
• Struhl, K.. 1982. Promoter elements, regulatory elements, and chromatin structure of the yeast his3 gene. Cold Spring Harbor Symp. Quant. Biol. 47:901–910
   Google Scholar
• Struhl, K.. 1984. Genetic properties and chromatin structure of the yeast gal regulatory element: an enhancer-like sequence. Proc. Natl. Acad. Sci. USA 81:7865–7869
   PubMedGoogle Scholar
• 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
   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
• Struhl, K.. 1998. Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 12:599–606
   PubMed Web of Science ®Google Scholar
• Struhl, K.. 1999. Fundamentally different logic of gene expression in eukaryotes and prokaryotes. Cell 98:1–4
   PubMed Web of Science ®Google Scholar
• Struhl, K., and Hill, D. E.. 1987. Two related regulatory sequences are required for maximal induction of Saccharomyces cerevisiae his3 transcription. Mol. Cell. Biol. 7:104–110
   PubMedGoogle Scholar
• Suter, B., Livingstone-Zatchej, M., and Thoma, F.. 1997. Chromatin structure modulates DNA repair by photolyase in vivo. EMBO J. 16:2150–2160
   PubMed Web of Science ®Google Scholar
• Verdone, L., Camilloni, G., Di Mauro, E., and Caserta, M.. 1996. Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation. Mol. Cell. Biol. 16:1978–1988
   PubMedGoogle Scholar
• Wilke, C. M., Heidler, S. H., Brown, N., and Liebman, S. W.. 1989. Analysis of yeast retrotransposon Ty insertions at the CAN1 locus. Genetics 123:655–665
   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
• Workman, J. L., and Kingston, R. E.. 1998. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67:545–579
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar