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Article

Functions of Saccharomyces cerevisiae TFIIF during Transcription Start Site Utilization

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Pages 3757-3766 | Received 21 Dec 2007, Accepted 13 Mar 2008, Published online: 27 Mar 2023

REFERENCES

  • 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.
  • 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.
  • Cairns, B. R., N. L. Henry, and R. D. Kornberg. 1996. TFG/TAF30/ANC1, a component of the yeast SWI/SNF complex that is similar to the leukemogenic proteins ENL and AF-9. Mol. Cell. Biol. 16:3308–3316.
  • Chambers, R. S., B. Q. Wang, Z. F. Burton, and M. E. Dahmus. 1995. The activity of COOH-terminal domain phosphatase is regulated by a docking site on RNA polymerase II and by the general transcription factors IIF and IIB. J. Biol. Chem. 270:14962–14969.
  • Chen, H. T., L. Warfield, and S. Hahn. 2007. The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex. Nat. Struct. Mol. Biol. 14:696–703.
  • Chung, W. H., J. L. Craighead, W. H. Chang, C. Ezeokonkwo, A. Bareket-Samish, R. D. Kornberg, and F. J. Asturias. 2003. RNA polymerase II/TFIIF structure and conserved organization of the initiation complex. Mol. Cell 12:1003–1013.
  • Cramer, P., D. A. Bushnell, and R. D. Kornberg. 2001. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292:1863–1876.
  • Eberharter, A., S. John, P. A. Grant, R. T. Utley, and J. L. Workman. 1998. Identification and analysis of yeast nucleosomal histone acetyltransferase complexes. Methods 15:315–321.
  • Escobar-Henriques, M., B. Daignan-Fornier, and M. A. Collart. 2003. The critical cis-acting element required for IMD2 feedback regulation by GDP is a TATA box located 202 nucleotides upstream of the transcription start site. Mol. Cell. Biol. 23:6267–6278.
  • Faitar, S. L., S. A. Brodie, and A. S. Ponticelli. 2001. Promoter-specific shifts in transcription initiation conferred by yeast TFIIB mutations are determined by the sequence in the immediate vicinity of the start sites. Mol. Cell. Biol. 21:4427–4440.
  • Fish, R. N., M. L. Ammerman, J. K. Davie, B. F. Lu, C. Pham, L. Howe, A. S. Ponticelli, and C. M. Kane. 2006. Genetic interactions between TFIIF and TFIIS. Genetics 173:1871–1884.
  • Flores, O., H. Lu, M. Killeen, J. Greenblatt, Z. F. Burton, and D. Reinberg. 1991. The small subunit of transcription factor IIF recruits RNA polymerase II into the preinitiation complex. Proc. Natl. Acad. Sci. USA 88:9999–10003.
  • Freire-Picos, M. A., S. Krishnamurthy, Z. W. Sun, and M. Hampsey. 2005. Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complex. Nucleic Acids Res. 33:5045–5052.
  • Ghazy, M. A., S. A. Brodie, M. L. Ammerman, L. M. Ziegler, and A. S. Ponticelli. 2004. Amino acid substitutions in yeast TFIIF confer upstream shifts in transcription initiation and altered interaction with RNA polymerase II. Mol. Cell. Biol. 24:10975–10985.
  • Giardina, C., and J. T. Lis. 1993. DNA melting on yeast RNA polymerase II promoters. Science 261:759–762.
  • Grosveld, G. C., C. K. Shewmaker, P. Jat, and R. A. Flavell. 1981. Localization of DNA sequences necessary for transcription of the rabbit beta-globin gene in vitro. Cell 25:215–226.
  • Hahn, S. 2004. Structure and mechanism of the RNA polymerase II transcription machinery. Nat. Struct. Mol. Biol. 11:394–403.
  • Hampsey, M. 1998. Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Biol. Rev. 62:465–503.
  • Hawley, D. K., and W. R. McClure. 1983. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 11:2237–2255.
  • Henry, N. L., A. M. Campbell, W. J. Feaver, D. Poon, P. A. Weil, and R. D. Kornberg. 1994. TFIIF-TAF-RNA polymerase II connection. Genes Dev. 8:2868–2878.
  • 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.
  • Izban, M. G., and D. S. Luse. 1992. Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates. J. Biol. Chem. 267:13647–13655.
  • 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.
  • Kabani, M., K. Michot, C. Boschiero, and M. Werner. 2005. Anc1 interacts with the catalytic subunits of the general transcription factors TFIID and TFIIF, the chromatin remodeling complexes RSC and INO80, and the histone acetyltransferase complex NuA3. Biochem. Biophys. Res. Commun. 332:398–403.
  • Keene, R. G., and D. S. Luse. 1999. Initially transcribed sequences strongly affect the extent of abortive initiation by RNA polymerase II. J. Biol. Chem. 274:11526–11534.
  • Kim, B., A. I. Nesvizhskii, P. G. Rani, S. Hahn, R. Aebersold, and J. A. Ranish. 2007. The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. Proc. Natl. Acad. Sci. USA 104:16068–16073.
  • Kuehner, J. N., and D. A. Brow. 2006. Quantitative analysis of in vivo initiator selection by yeast RNA polymerase II supports a scanning model. J. Biol. Chem. 281:14119–14128.
  • Maicas, E., and J. D. Friesen. 1990. A sequence pattern that occurs at the transcription initiation region of yeast RNA polymerase II promoters. Nucleic Acids Res. 18:3387–3393.
  • Majovski, R. C., D. A. Khaperskyy, M. A. Ghazy, and A. S. Ponticelli. 2005. A functional role for the switch 2 region of yeast RNA polymerase II in transcription start site utilization and abortive initiation. J. Biol. Chem. 280:34917–34923.
  • Maxon, M. E., J. A. Goodrich, and R. Tjian. 1994. Transcription factor IIE binds preferentially to RNA polymerase IIa and recruits TFIIH: a model for promoter clearance. Genes Dev. 8:515–524.
  • Miller, G., and S. Hahn. 2006. A DNA-tethered cleavage probe reveals the path for promoter DNA in the yeast preinitiation complex. Nat. Struct. Mol. Biol. 13:603–610.
  • Orphanides, G., T. Lagrange, and D. Reinberg. 1996. The general transcription factors of RNA polymerase II. Genes Dev. 10:2657–2683.
  • 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.
  • Pardee, T. S., M. A. Ghazy, and A. S. Ponticelli. 2003. Yeast and human RNA polymerase II elongation complexes: evidence for functional differences and postinitiation recruitment of factors. Eukaryot. Cell 2:318–327.
  • 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.
  • 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.
  • 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.
  • Prather, D. M., E. Larschan, and F. Winston. 2005. Evidence that the elongation factor TFIIS plays a role in transcription initiation at GAL1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 25:2650–2659.
  • Robert, F., M. Douziech, D. Forget, J. M. Egly, J. Greenblatt, Z. F. Burton, and B. Coulombe. 1998. Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF. Mol. Cell 2:341–351.
  • Shen, X., G. Mizuguchi, A. Hamiche, and C. Wu. 2000. A chromatin remodelling complex involved in transcription and DNA processing. Nature 406:541–544.
  • Steger, D. J., A. Eberharter, S. John, P. A. Grant, and J. L. Workman. 1998. Purified histone acetyltransferase complexes stimulate HIV-1 transcription from preassembled nucleosomal arrays. Proc. Natl. Acad. Sci. USA 95:12924–12929.
  • Struhl, K. 1995. Yeast transcriptional regulatory mechanisms. Annu. Rev. Genet. 29:651–674.
  • 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.
  • Tan, S., T. Aso, R. C. Conaway, and J. W. Conaway. 1994. Roles for both the RAP30 and RAP74 subunits of transcription factor IIF in transcription initiation and elongation by RNA polymerase II. J. Biol. Chem. 269:25684–25691.
  • Treich, I., and M. Carlson. 1997. Interaction of a Swi3 homolog with Sth1 provides evidence for a Swi/Snf-related complex with an essential function in Saccharomyces cerevisiae. Mol. Cell. Biol. 17:1768–1775.
  • Westover, K. D., D. A. Bushnell, and R. D. Kornberg. 2004. Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science 303:1014–1016.
  • Yagil, G. 2004. The over-representation of binary DNA tracts in seven sequenced chromosomes. BMC Genomics 5:19.
  • Yan, Q., R. J. Moreland, J. W. Conaway, and R. C. Conaway. 1999. Dual roles for transcription factor IIF in promoter escape by RNA polymerase II. J. Biol. Chem. 274:35668–35675.
  • Zhang, C., and Z. F. Burton. 2004. Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism. J. Mol. Biol. 342:1085–1099.
  • Zhang, D. Y., D. J. Carson, and J. Ma. 2002. The role of TFIIB-RNA polymerase II interaction in start site selection in yeast cells. Nucleic Acids Res. 30:3078–3085.
  • Zhang, Z., and F. S. Dietrich. 2005. Mapping of transcription start sites in Saccharomyces cerevisiae using 5′ SAGE. Nucleic Acids Res. 33:2838–2851.
  • Ziegler, L. M., D. A. Khaperskyy, M. L. Ammerman, and A. S. Ponticelli. 2003. Yeast RNA polymerase II lacking the Rpb9 subunit is impaired for interaction with transcription factor IIF. J. Biol. Chem. 278:48950–48956.

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