Regulation of rRNA Synthesis by TATA-Binding Protein-Associated Factor Mot1

REFERENCES

• Andrau, J.-C., C. J. C. Van Oevelen, H. A. A. M. Van Teeffelen, P. A. Weil, F. C. P. Holstege, and H. T. M. Timmers. 2002. Mot1p is essential for TBP recruitment to selected promoters during in vivo gene activation. EMBO J. 21:5173–5183.
   PubMed Web of Science ®Google Scholar
• Angermayr, M., U. Oechsner, and W. Bandlow. 2003. Reb1p-dependent DNA bending effects nucleosome positioning and constitutive transcription at the yeast profilin promoter. J. Biol. Chem. 278:17918–17926.
   PubMedGoogle Scholar
• Aprikian, P., B. Moorefield, and R. H. Reeder. 2001. New model for the yeast RNA polymerase I transcription cycle. Mol. Cell. Biol. 21:4847–4855.
   PubMedGoogle Scholar
• Auble, D. T., K. E. Hansen, C. G. F. Mueller, W. S. Lane, J. Thorner, and S. Hahn. 1994. Mot1, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism. Genes Dev. 8:1920–1934.
   PubMed Web of Science ®Google Scholar
• Auble, D. T., D. Wang, K. W. Post, and S. Hahn. 1997. Molecular analysis of the SNF2/SWI2 protein family member MOT1, an ATP-driven enzyme that dissociates TATA-binding protein from DNA. Mol. Cell. Biol. 17:4842–4851.
   PubMedGoogle Scholar
• Bernstein, K. A., J. E. G. Gallagher, B. M. Mitchell, S. Granneman, and S. J. Baserga. 2004. The small-subunit processome is a ribosome assembly intermediate. Eukaryot. Cell 3:1619–1626.
   PubMed Web of Science ®Google Scholar
• Bordi, L., F. Cioci, and G. Camilloni. 2001. In vivo binding and hierarchy of assembly of the yeast RNA polymerase I transcription factors. Mol. Biol. Cell 12:753–760.
   PubMedGoogle Scholar
• Buck, S. W., J. J. Sandmeier, and J. S. Smith. 2002. RNA polymerase I propagates unidirectional spreading of rDNA silent chromatin. Cell 111:1003–1014.
   PubMedGoogle Scholar
• Claypool, J. A., S. French, K. Johzuka, K. Eliason, L. Vu, J. A. Dodd, A. L. Beyer, and M. Nomura. 2004. Tor pathway regulates Rrn3p-dependent recruitment of yeast RNA polymerase I to the promoter but does not participate in alteration of the number of active genes. Mol. Biol. Cell 15:946–956.
   PubMed Web of Science ®Google 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
• Dammann, R., R. Lucchini, T. Koller, and J. M. Sogo. 1993. Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae. Nucleic Acids Res. 21:2331–2338.
   PubMed Web of Science ®Google Scholar
• Darst, R. P., A. Dasgupta, C. Zhu, J.-Y. Hsu, A. Vroom, T. A. Muldrow, and D. T. Auble. 2003. Mot1 regulates the DNA binding activity of free TATA-binding protein in an ATP-dependent manner. J. Biol. Chem. 278:13216–13226.
   PubMedGoogle Scholar
• Dasgupta, A., R. P. Darst, K. J. Martin, C. A. Afshari, and D. T. Auble. 2002. Mot1 activates and represses transcription by direct, ATPase-dependent mechanisms. Proc. Natl. Acad. Sci. USA 99:2666–2671.
   PubMedGoogle Scholar
• Dasgupta, A., S. A. Juedes, R. O. Sprouse, and D. T. Auble. 2005. Mot1-mediated control of transcription complex assembly and activity. EMBO J. 24:1717–1729.
   PubMedGoogle Scholar
• Davierwala, A. P., J. Haynes, Z. Li, R. L. Brost, M. D. Robinson, L. Yu, S. Mnaimneh, H. Ding, H. Zhu, X. Chen, G. W. Brown, C. Boone, B. J. Andrews, and T. R. Hughes. 2005. The synthetic genetic interaction spectrum of essential genes. Nat. Genet. 37:1147–1152.
   PubMed Web of Science ®Google Scholar
• Davis, J. L., R. Kunisawa, and J. Thorner. 1992. A presumptive helicase (MOT1 gene product) affects gene expression and is required for viability in the yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 12:1879–1892.
   PubMed Web of Science ®Google Scholar
• Dragon, F., J. E. G. Gallagher, P. A. Compagnone-Post, B. M. Mitchell, K. A. Porwancher, K. A. Wehner, S. Wormsley, R. E. Settlage, J. Shabanowitz, Y. N. Osheim, A. L. Beyer, D. F. Hunt, and S. J. Baserga. 2002. A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature 417:967–970.
   PubMed Web of Science ®Google Scholar
• Elemento, O., and S. Tavazole. 2005. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol. 6:R18.
   PubMed Web of Science ®Google Scholar
• French, S., Y. N. Osheim, F. Cioci, M. Nomura, and A. L. Beyer. 2003. In exponentially growing Saccharomyces cerevisiae cells, ribosomal RNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes. Mol. Cell. Biol. 23:1558–1568.
   PubMed Web of Science ®Google Scholar
• Gallagher, J. E. G., D. A. Dunbar, S. Granneman, B. M. Mitchell, Y. N. Osheim, A. L. Beyer, and S. J. Baserga. 2004. RNA polymerase I transcription and pre-rRNA processing are linked by specific SSU processome components. Genes Dev. 18:2506–2517.
   PubMed Web of Science ®Google Scholar
• Gavin, A.-C., et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141–147.
   PubMed Web of Science ®Google Scholar
• Gavin, A.-C., P. Aloy, P. Grandi, R. Krause, M. Boesche, M. Marzioch, C. Rau, L. J. Jensen, S. Bastuck, B. Dumpelfeld, A. Edelmann, M.-A. Heurtier, V. Hoffman, C. Hoefert, K. Klein, M. Hudak, A.-M. Michon, M. Schelder, M. Schirle, M. Remor, T. Rudi, S. Hooper, A. Bauer, T. Bouwmeester, G. Casari, G. Drewes, G. Neubauer, J. M. Rick, B. Kuster, P. Bork, R. B. Russell, and G. Superti-Furga. 2006. Proteome survey reveals modularity of the yeast cell machinery. Nature 440:631–636.
   PubMed Web of Science ®Google Scholar
• Geisberg, J. V., Z. Moqtaderi, L. Kuras, and K. Struhl. 2002. Mot1 associates with transcriptionally active promoters and inhibits association of NC2 in Saccharomyces cerevisiae. Mol. Cell. Biol. 22:8122–8134.
   PubMed Web of Science ®Google Scholar
• Hahn, S. 1998. The role of TAFs in RNA polymerase II transcription. Cell 95:579–582.
   PubMedGoogle Scholar
• Ju, Q. D., B. E. Morrow, and J. R. Warner. 1990. REB1, a yeast DNA-binding protein with many targets, is essential for growth and bears some resemblance to the oncogene myb. Mol. Cell. Biol. 10:5226–5234.
   PubMedGoogle Scholar
• Keener, J., J. A. Dodd, D. Lalo, and M. Nomura. 1997. Histones H3 and H4 are components of upstream activation factor required for the high-level transcription of yeast rDNA by RNA polymerase I. Proc. Natl. Acad. Sci. USA 94:13458–13462.
   PubMed Web of Science ®Google Scholar
• Keener, J., C. A. Josaitis, J. A. Dodd, and M. Nomura. 1998. Reconstitution of yeast RNA polymerase I transcription in vitro from purified components. TATA-binding protein is not required for basal transcription. J. Biol. Chem. 273:33795–33802.
   PubMed Web of Science ®Google Scholar
• Keys, D. A., B. S. Lee, J. A. Dodd, T. T. Nguyen, L. Vu, E. Fantino, L. M. Burson, Y. Nogi, and M. Nomura. 1996. Multiprotein transcription factor UAF interacts with the upstream element of the yeast RNA polymerase I promoter and forms stable preinitiation complex. Genes Dev. 10:887–903.
   PubMed Web of Science ®Google Scholar
• Lee, T. I., and R. A. Young. 1998. Regulation of gene expression by TBP-associated proteins. Genes Dev. 12:1398–1408.
   PubMedGoogle Scholar
• Longtine, M. S., A. McKenzie III, D. J. Demarini, N. G. Shah, A. Wach, A. Brachat, P. Philippsen, and J. R. Pringle. 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 F. Winston. 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
• Mayer, C., H. Bierhoff, and I. Grummt. 2005. The nucleolus as a stress sensor: JNK2 inactivates the transcription factor TIF-1A and down-regulates rRNA synthesis. Genes Dev. 19:933–941.
   PubMed Web of Science ®Google Scholar
• Mayer, C., J. Zhao, X. Yuan, and I. Grummt. 2004. mTOR-dependent activation of the transcription factor TIF-IA links rRNA synthesis to nutrient availability. Genes Dev. 18:423–434.
   PubMed Web of Science ®Google Scholar
• Meier, A., and F. Thoma. 2005. RNA polymerase I transcription factors in active yeast rRNA gene promoters enhance UV damage formation and inhibit repair. Mol. Cell. Biol. 25:1586–1595.
   PubMedGoogle Scholar
• Milkereit, P., and H. Tschochner. 1998. A specialized form of RNA polymerase I, essential for initiation and growth-dependent regulation of rRNA synthesis, is disrupted during transcription. EMBO J. 17:3692–3703.
   PubMed Web of Science ®Google Scholar
• Moss, T. 2004. At the crossroads of growth control; making ribosomal RNA. Curr. Opin. Genet. Dev. 14:210–217.
   PubMed Web of Science ®Google Scholar
• Muldrow, T. A., A. M. Campbell, P. A. Weil, and D. T. Auble. 1999. MOT1 can activate basal transcription in vitro by regulating the distribution of TATA binding protein between promoter and nonpromoter sites. Mol. Cell. Biol. 19:2835–2845.
   PubMedGoogle Scholar
• Myers, C. L., D. Robson, A. Wible, M. A. Hibbs, C. Chiriac, C. L. Theesfeld, K. Dolinski, and O. G. Troyanskaya. 2005. Discovery of biological networks from diverse functional genomic data. Genome Biol. 6:R114.
   PubMedGoogle Scholar
• Nogi, Y., R. Yano, and M. Nomura. 1991. Synthesis of large rRNAs by RNA polymerase II in mutants of Saccharomyces cerevisiae defective in RNA polymerase I. Proc. Natl. Acad. Sci. USA 88:3962–3966.
   PubMed Web of Science ®Google Scholar
• Nomura, M. 1999. Regulation of ribosome biosynthesis in Escherichia coli and Saccharomyces cerevisiae: diversity and common principles. J. Bacteriol. 181:6857–6864.
   PubMed Web of Science ®Google Scholar
• Nomura, M. 2001. Ribosomal RNA genes, RNA polymerases, nucleolar structures, and synthesis of rRNA in the yeast Saccharomyces cerevisiae. Cold Spring Harbor Symp. Quant. Biol. 66:555–565.
   PubMedGoogle Scholar
• Osheim, Y. N., and A. L. Beyer. 1989. Electron microscopy of RNP complexes on nascent RNA using Miller chromatin spreading method. Methods Enzymol. 180:481–509.
   PubMedGoogle Scholar
• Osheim, Y. N., S. L. French, K. M. Keck, E. A. Champion, K. Spasov, F. Dragon, S. J. Baserga, and A. L. Beyer. 2004. Pre-18S ribosomal RNA is structurally compacted into the SSU processome prior to being cleaved from nascent transcripts in Saccharomyces cerevisiae. Mol. Cell 16:943–954.
   PubMed Web of Science ®Google Scholar
• Pereira, L. A., M. P. Klejman, and H. T. M. Timmers. 2003. Roles for BTAF1 and Mot1p in dynamics of TATA-binding protein and regulation of RNA polymerase II transcription. Gene 315:1–13.
   PubMedGoogle Scholar
• Poon, D., A. M. Campbell, Y. Bai, and P. A. Weil. 1994. Yeast Taf170 is encoded by MOT1 and exists in a TBP-TAF complex distinct from TFIID. J. Biol. Chem. 269:23135–23140.
   PubMedGoogle Scholar
• Raisner, R. M., P. D. Hartley, M. D. Meneghini, M. Z. Bao, C. L. Liu, S. L. Schreiber, O. J. Rando, and H. D. Madhani. 2005. Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell 123:233–248.
   PubMed Web of Science ®Google Scholar
• Reeder, R. H. 1999. Regulation of RNA polymerase I transcription in yeast and vertebrates. Prog. Nucleic Acid Res. Mol. Biol. 62:293–327.
   PubMed Web of Science ®Google Scholar
• Sandmeier, J. J., S. French, Y. N. Osheim, W. L. Cheung, A. L. Beyer, and J. S. Smith. 2002. RPD3 is required for the inactivation of yeast ribosomal DNA genes in stationary phase. EMBO J. 21:4959–4968.
   PubMed Web of Science ®Google Scholar
• Schmitt, M. E., T. A. Brown, and B. L. Trumpower. 1990. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 18:3091–3092.
   PubMed Web of Science ®Google Scholar
• Schramm, L., and N. Hernandez. 2002. Recruitment of RNA polymerase III to its target promoters. Genes Dev. 16:2593–2620.
   PubMed Web of Science ®Google Scholar
• Schultz, M. C., R. H. Reeder, and S. Hahn. 1992. Variants of the TATA-binding protein can distinguish subsets of RNA polymerase I, II and III promoters. Cell 69:697–702.
   PubMedGoogle Scholar
• Shou, W., K. M. Sakamoto, J. Keener, K. W. Morimoto, E. E. Traverso, R. Azzam, G. J. Hoppe, R. M. Feldman, J. DeModena, D. Moazed, H. Charbonneau, M. Nomura, and R. J. Deshaies. 2001. Net1 stimulates RNA polymerase I transcription and regulates nucleolar structure independently of controlling mitotic exit. Mol. Cell 8:45–55.
   PubMed Web of Science ®Google Scholar
• Smith, J. S., and J. D. Boeke. 1997. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11:241–254.
   PubMed Web of Science ®Google Scholar
• Sprouse, R. O., M. Brenowitz, and D. T. Auble. 2006. Snf2/Swi2-related ATPase Mot1 drives displacement of TATA-binding protein by gripping DNA. EMBO J. 25:1492–1504.
   PubMedGoogle Scholar
• Stefanovsky, V., F. Langlois, T. Gagnon-Kugler, L. I. Rothblum, and T. Moss. 2006. Growth factor signaling regulates elongation of RNA polymerase I transcription in mammals via UBF phosphorylation and r-chromatin remodeling. Mol. Cell 21:629–639.
   PubMed Web of Science ®Google Scholar
• Steffan, J. S., D. A. Keys, J. A. Dodd, and M. Nomura. 1996. The role of TBP in rDNA transcription by RNA polymerase I in Saccharomyces cerevisiae: TBP is required for upstream activation factor-dependent recruitment of core factor. Genes Dev. 10:2551–2563.
   PubMed Web of Science ®Google Scholar
• Straight, A. F., W. Shou, G. J. Dowd, C. W. Turck, R. J. Deshaies, A. D. Johnson, and D. Moazed. 1999. Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity. Cell 97:245–256.
   PubMed Web of Science ®Google Scholar
• Thompson, N. E., T. H. Steinberg, D. B. Aronson, and R. R. Burgess. 1989. Inhibition of in vivo and in vitro transcription by monoclonal antibodies prepared against wheat germ RNA polymerase II that react with the heptapeptide repeat of eukaryotic RNA polymerase II. J. Biol. Chem. 264:11511–11520.
   PubMedGoogle Scholar
• Tongaonkar, P., S. L. French, M. Oakes, L. Vu, D. A. Schneider, A. L. Beyer, and M. Nomura. 2005. Histones are required for transcription of yeast rRNA genes by RNA polymerase I. Proc. Natl. Acad. Sci. USA 102:10129–10134.
   PubMedGoogle Scholar
• Veinot-Drebot, L. M., R. Singer, and G. C. Johnston. 1988. Rapid initial cleavage of nascent pre-rRNA transcripts in yeast. J. Mol. Biol. 199:107–113.
   PubMed Web of Science ®Google Scholar
• Vogelauer, M., F. Cioci, and G. Camilloni. 1998. DNA protein-interactions at the Saccharomyces cerevisiae 35S rRNA promoter and in its surrounding region. J. Mol. Biol. 275:197–209.
   PubMedGoogle Scholar
• Warner, J. R. 1999. The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 24:437–439.
   PubMed Web of Science ®Google Scholar
• Zanton, S. J., and B. F. Pugh. 2004. Changes in genomewide occupancy of core transcriptional regulators during heat stress. Proc. Natl. Acad. Sci. USA 101:16843–16848.
   PubMedGoogle Scholar