Promoter-Specific Shifts in Transcription Initiation Conferred by Yeast TFIIB Mutations Are Determined by the Sequence in the Immediate Vicinity of the Start Sites

REFERENCES

• Aiyar, A., and J. Leis. 1993. Modification of the megaprimer method of PCR mutagenesis: improved amplification of the final product. BioTechniques 14:366–367.
   PubMedGoogle Scholar
• Bagby, S., S. Kim, E. Maldonado, K. I. Tong, D. Reinberg, and M. Ikura. 1995. Solution structure of the C-terminal core domain of human TFIIB: similarity to cyclin A and interaction with TATA-binding protein. Cell 82:857–867.
   PubMedGoogle Scholar
• Bangur, C. S., T. S. Pardee, and A. S. Ponticelli. 1997. Mutational analysis of the D1/E1 core helices and the conserved N-terminal region of yeast transcription factor IIB (TFIIB): identification of an N-terminal mutant that stabilizes TATA-binding protein-TFIIB-DNA complexes. Mol. Cell. Biol. 17:6784–6793.
   PubMedGoogle Scholar
• Barberis, A., C. W. Muller, S. C. Harrison, and M. Ptashne. 1993. Delineation of two functional regions of transcription factor TFIIB. Proc. Natl. Acad. Sci. USA 90:5628–5632.
   PubMedGoogle Scholar
• Berroteran, R. W., and M. Hampsey. 1991. Genetic analysis of yeast iso-1-cytochrome c structural requirements: suppression of Gly6 replacements by an Asn52 Ile replacement. Arch. Biochem. Biophys. 288:261–269.
   PubMedGoogle Scholar
• Berroteran, R. W., D. E. Ware, and M. Hampsey. 1994. The sua8 suppressors of Saccharomyces cerevisiae encode replacements of conserved residues within the largest subunit of RNA polymerase II and affect transcription start site selection similarly to sua7 (TFIIB) mutations. Mol. Cell. Biol. 14:226–237.
   PubMedGoogle Scholar
• Boeke, J. D., J. Trueheart, G. Natsoulis, and G. R. Fink. 1987. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol. 154:164–175.
   PubMed Web of Science ®Google Scholar
• Buratowski, S., and H. Zhou. 1993. Functional domains of transcription factor TFIIB. Proc. Natl. Acad. Sci. USA 90:5633–5637.
   PubMedGoogle Scholar
• Bushnell, D. A., C. Bamdad, and R. D. Kornberg. 1996. A minimal set of RNA polymerase II transcription protein interactions. J. Biol. Chem. 271:20170–20174.
   PubMed Web of Science ®Google Scholar
• Chiang, Y. C., P. Komarnitsky, D. Chase, and C. L. Denis. 1996. ADR1 activation domains contact the histone acetyltransferase GCN5 and the core transcriptional factor TFIIB. J. Biol. Chem. 271:32359–32365.
   PubMedGoogle Scholar
• Colgan, J., H. Ashali, and J. L. Manley. 1995. A direct interaction between a glutamine-rich activator and the N terminus of TFIIB can mediate transcriptional activation in vivo. Mol. Cell. Biol. 15:2311–2320.
   PubMedGoogle Scholar
• Fang, S. M., and Z. F. Burton. 1996. RNA polymerase II-associated protein (RAP) 74 binds transcription factor (TF) IIB and blocks TFIIB-RAP30 binding. J. Biol. Chem. 271:11703–11709.
   PubMedGoogle Scholar
• Franklin, C. C., A. V. McCulloch, and A. S. Kraft. 1995. In vitro association between the Jun protein family and the general transcription factors, TBP and TFIIB. Biochem. J. 305:967–974.
   PubMedGoogle Scholar
• Furter-Graves, E. M., and B. D. Hall. 1990. DNA sequence elements required for transcription initiation of the Schizosaccharomyces pombe ADH gene in Saccharomyces cerevisiae. Mol. Gen. Genet. 223:407–416.
   PubMedGoogle Scholar
• Giardina, C., and J. T. Lis. 1993. DNA melting on yeast RNA polymerase II promoters. Science 261:759–762.
   PubMedGoogle Scholar
• Goodrich, J. A., T. Hoey, C. J. Thut, A. Admon, and R. Tjian. 1993. Drosophila TAFII40 interacts with both a VP16 activation domain and the basal transcription factor TFIIB. Cell 75:519–530.
   PubMedGoogle Scholar
• Guarente, L.. 1987. Regulatory proteins in yeast. Annu. Rev. Genet. 21:425–452.
   PubMedGoogle Scholar
• Ha, I., S. Roberts, E. Maldonado, X. Sun, L. U. Kim, M. Green, and D. Reinberg. 1993. Multiple functional domains of human transcription factor IIB: distinct interactions with two general transcription factors and RNA polymerase II. Genes Dev. 7:1021–1032.
   PubMedGoogle Scholar
• Hadzic, E., V. Desai-Yajnik, E. Helmer, S. Guo, S. Wu, N. Koudinova, J. Casanova, B. M. Raaka, and H. H. Samuels. 1995. A 10-amino-acid sequence in the N-terminal A/B domain of thyroid hormone receptor alpha is essential for transcriptional activation and interaction with the general transcription factor TFIIB. Mol. Cell. Biol. 15:4507–4517.
   PubMedGoogle Scholar
• Hahn, S., E. T. Hoar, and L. Guarente. 1985. Each of three “TATA elements” specifies a subset of transcription initiation sites at the CYC1 promoter of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 82:8562–8566.
   PubMedGoogle Scholar
• Hampsey, M., J. G. Na, I. Pinto, D. E. Ware, and R. W. Berroteran. 1991. Extragenic suppressors of a translational initiation defect in the cyc1 gene of Saccharomyces cerevisiae. Biochimie 73:1445–1455.
   PubMedGoogle Scholar
• Healy, A. M., T. L. Helser, and R. S. Zitomer. 1987. Sequences required for transcriptional initiation of the Saccharomyces cerevisiae CYC7 gene. Mol. Cell. Biol. 7:3785–3791.
   PubMedGoogle Scholar
• Hull, M. W., K. McKune, and N. A. Woychik. 1995. RNA polymerase II subunit RPB9 is required for accurate start site selection. Genes Dev. 9:481–490.
   PubMed Web of Science ®Google Scholar
• Iyer, V., and K. Struhl. 1995. Mechanism of differential utilization of the HIS3 TR and TC TATA elements. Mol. Cell. Biol. 15:7059–7066.
   PubMedGoogle Scholar
• Lagrange, T., A. N. Kapanidis, H. Tang, D. Reinberg, and R. H. Ebright. 1998. New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Dev. 12:34–44.
   PubMed Web of Science ®Google Scholar
• Lee, S., and S. Hahn. 1995. Model for binding of transcription factor TFIIB to the TBP-DNA complex. Nature 376:609–612.
   PubMed Web of Science ®Google Scholar
• Li, Y., P. M. Flanagan, H. Tschochner, and R. D. Kornberg. 1994. RNA polymerase II initiation factor interactions and transcription start site selection. Science 263:805–807.
   PubMedGoogle Scholar
• Lin, Y. S., I. Ha, E. Maldonado, D. Reinberg, and M. R. Green. 1991. Binding of general transcription factor TFIIB to an acidic activating region. Nature 353:569–571.
   PubMed Web of Science ®Google Scholar
• MacDonald, P. N., D. R. Sherman, D. R. Dowd, S. C. Jefcoat Jr., and R. K. DeLisle. 1995. The vitamin D receptor interacts with general transcription factor IIB. J. Biol. Chem. 270:4748–4752.
   PubMed Web of Science ®Google Scholar
• Maldonado, E., I. Ha, P. Cortes, L. Weis, and D. Reinberg. 1990. Factors involved in specific transcription by mammalian RNA polymerase II: role of transcription factors IIA, IID, and IIB during formation of a transcription-competent complex. Mol. Cell. Biol. 10:6335–6347.
   PubMedGoogle Scholar
• Malik, S., D. K. Lee, and R. G. Roeder. 1993. Potential RNA polymerase II-induced interactions of transcription factor TFIIB. Mol. Cell. Biol. 13:6253–6259.
   PubMedGoogle Scholar
• Nakajima, N., M. Horikoshi, and R. G. Roeder. 1988. Factors involved in specific transcription by mammalian RNA polymerase II: purification, genetic specificity, and TATA box-promoter interactions of TFIID. Mol. Cell. Biol. 8:4028–4040.
   PubMed Web of Science ®Google Scholar
• Nikolov, D. B., H. Chen, E. D. Halay, A. A. Usheva, K. Hisatake, D. K. Lee, R. G. Roeder, and S. K. Burley. 1995. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature 377:119–128.
   PubMed Web of Science ®Google Scholar
• Orphanides, G., T. Lagrange, and D. Reinberg. 1996. The general transcription factors of RNA polymerase II. Genes Dev. 10:2657–2683.
   PubMed Web of Science ®Google Scholar
• Pardee, T. S., C. S. Bangur, and A. S. Ponticelli. 1998. The N-terminal region of yeast TFIIB contains two adjacent functional domains involved in stable RNA polymerase II binding and transcription start site selection. J. Biol. Chem. 273:17859–17864.
   PubMedGoogle Scholar
• Parker, C. S., and J. Topol. 1984. A Drosophila RNA polymerase II transcription factor contains a promoter-region specific DNA-binding activity. Cell 36:357–369.
   PubMed Web of Science ®Google Scholar
• Pinto, I., D. E. Ware, and M. Hampsey. 1992. The yeast SUA7 gene encodes a homolog of human transcription factor TFIIB and is required for normal start site selection in vivo. Cell 68:977–988.
   PubMedGoogle Scholar
• Pinto, I., W. H. Wu, J. G. Na, and M. Hampsey. 1994. Characterization of sua7 mutations defines a domain of TFIIB involved in transcription start site selection in yeast. J. Biol. Chem. 269:30569–30573.
   PubMedGoogle Scholar
• Ponticelli, A. S., and K. Struhl. 1990. Analysis of Saccharomyces cerevisiae his3 transcription in vitro: biochemical support for multiple mechanisms of transcription. Mol. Cell. Biol. 10:2832–2839.
   PubMedGoogle Scholar
• Roberts, S. G., I. Ha, E. Maldonado, D. Reinberg, and M. R. Green. 1993. Interaction between an acidic activator and transcription factor TFIIB is required for transcriptional activation. Nature 363:741–744.
   PubMedGoogle Scholar
• Sauer, F., J. D. Fondell, Y. Ohkuma, R. G. Roeder, and H. Jackle. 1995. Control of transcription by Kruppel through interactions with TFIIB and TFIIE beta. Nature 375:162–164.
   PubMedGoogle Scholar
• Shaw, S. P., D. J. Carson, M. J. Dorsey, and J. Ma. 1997. Mutational studies of yeast transcription factor IIB in vivo reveal a functional surface important for gene activation. Proc. Natl. Acad. Sci. USA 94:2427–2432.
   PubMedGoogle Scholar
• Shaw, S. P., J. Wingfield, M. J. Dorsey, and J. Ma. 1996. Identifying a species-specific region of yeast TFIIB in vivo. Mol. Cell. Biol. 16:3651–3657.
   PubMedGoogle Scholar
• Sherman, F.. 1991. Getting started with yeast. Guide to yeast genetics and molecular biology. C. Guthrie, and G. R. Fink. 194:3–20. Academic Press, Inc., San Diego, Calif
   Google Scholar
• Struhl, K.. 1987. Promoters, activator proteins, and the mechanism of transcriptional initiation in yeast. Cell 49:295–297.
   PubMed Web of Science ®Google Scholar
• Sun, Z. W., A. Tessmer, and M. Hampsey. 1996. Functional interaction between TFIIB and the Rpb9 (Ssu73) subunit of RNA polymerase II in Saccharomyces cerevisiae. Nucleic Acids Res. 24:2560–2566.
   PubMedGoogle Scholar
• Wu, W. H., and M. Hamsey. 1999. An activation-specific role for transcription factor TFIIB in vivo. Proc. Natl. Acad. Sci. USA 96:2764–2769.
   PubMedGoogle Scholar
• Xing, L., V. K. Gopal, and P. G. Quinn. 1995. cAMP response element-binding protein (CREB) interacts with transcription factors IIB and IID. J. Biol. Chem. 270:17488–17493.
   PubMedGoogle Scholar