EBP2 Is a Member of the Yeast RRB Regulon, a Transcriptionally Coregulated Set of Genes That Are Required for Ribosome and rRNA Biosynthesis

REFERENCES

• Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl. 1993. Current protocols in molecular biology. Wiley Interscience, New York, N.Y
   Google Scholar
• Bailey, T. L., and C. Elkan. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2:28–36.
   PubMedGoogle Scholar
• Basu, U., K. Si, J. R. Warner, and U. Maitra. 2001. The Saccharomyces cerevisiae TIF6 gene encoding translation initiation factor 6 is required for 60S ribosomal subunit biogenesis. Mol. Cell. Biol. 21:1453–1462.
   PubMed Web of Science ®Google Scholar
• Bustin, S. A.. 2000. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 25:169–193.
   PubMed Web of Science ®Google Scholar
• Causton, H. C., B. Ren, S. S. Koh, C. T. Harbison, E. Kanin, E. G. Jennings, T. I. Lee, H. L. True, E. S. Lander, and R. A. Young. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell 12:323–337.
   PubMed Web of Science ®Google Scholar
• Chang, Y. C., and W. E. Timberlake. 1993. Identification of Aspergillus brlA response elements (BREs) by genetic selection in yeast. Genetics 133:29–38.
   PubMed Web of Science ®Google Scholar
• Chu, S., J. DeRisi, M. Eisen, J. Mulholland, D. Botstein, P. O. Brown, and I. Herskowitz. 1998. The transcriptional program of sporulation in budding yeast. Science 282:699–705.
   PubMed Web of Science ®Google Scholar
• Dequard-Chablat, M., M. Riva, C. Carles, and A. Sentenac. 1991. RPC19, the gene for a subunit common to yeast RNA polymerases A (I) and C (III). J. Biol. Chem. 266:15300–15307.
   PubMedGoogle Scholar
• DeRisi, J. L., V. R. Iyer, and P. O. Brown. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680–686.
   PubMed Web of Science ®Google Scholar
• Futcher, B.. 2000. Microarrays and cell cycle transcription in yeast. Curr. Opin. Cell Biol. 12:710–715.
   PubMedGoogle Scholar
• Gasch, A. P., P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D. Botstein, and P. O. Brown. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11:4241–4257.
   PubMed Web of Science ®Google Scholar
• Guthrie, C., and G. R. Fink. 1991. Methods in enzymology 194:305 Guide to yeast genetics and molecular biology. Academic Press, Inc., San Diego, Calif.
   Google Scholar
• Huber, M. D., J. H. Dworet, K. Shire, L. Frappier, and M. A. McAlear. 2000. The budding yeast homolog of the human EBNA1-binding protein 2 (Ebp2p) is an essential nucleolar protein required for pre-rRNA processing. J. Biol. Chem. 275:28764–28773.
   PubMed Web of Science ®Google Scholar
• Hughes, J. D., P. W. Estep, S. Tavazoie, and G. M. Church. 2000. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296:1205–1214.
   PubMed Web of Science ®Google Scholar
• Kaufman, L., and P. J. Rousseauw. 1990. Finding groups in data: an introduction to cluster analysis. Wiley Interscience, New York, N.Y
   Google Scholar
• Kendall, A., M. W. Hull, E. Bertrand, P. D. Good, R. H. Singer, and D. R. Engelke. 2000. A CBF5 mutation that disrupts nucleolar localization of early tRNA biosynthesis in yeast also suppresses tRNA gene-mediated transcriptional silencing. Proc. Natl. Acad. Sci. USA 97:13108–13113.
   PubMed Web of Science ®Google Scholar
• Lascaris, R. F., W. H. Mager, and R. J. Planta. 1999. DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences. Bioinformatics 15:267–277.
   PubMed Web of Science ®Google Scholar
• Li, B., C. R. Nierras, and J. R. Warner. 1999. Transcriptional elements involved in the repression of ribosomal protein synthesis. Mol. Cell. Biol. 19:5393–5404.
   PubMed Web of Science ®Google Scholar
• Mizuta, K., and J. R. Warner. 1994. Continued functioning of the secretory pathway is essential for ribosome synthesis. Mol. Cell. Biol. 14:2493–2502.
   PubMed Web of Science ®Google Scholar
• Moehle, C. M., and A. G. Hinnebusch. 1991. Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:2723–2735.
   PubMed Web of Science ®Google Scholar
• Planta, R. J.. 1997. Regulation of ribosome synthesis in yeast. Yeast 13:1505–1518.
   PubMed Web of Science ®Google Scholar
• Ripley, B. D., and W. N. Venables. 1997. Applied statistics with S-Plus. Springer-Verlag, New York, N.Y
   Google Scholar
• Spellman, P. T., G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein, and B. Futcher. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9:3273–3297.
   PubMed Web of Science ®Google Scholar
• Tollervey, D.. 1996. trans-Acting factors in ribosome synthesis. Exp. Cell Res. 229:226–232.
   PubMedGoogle Scholar
• Tsuno, A., K. Miyoshi, R. Tsujii, T. Miyakawa, and K. Mizuta. 2000. RRS1, a conserved essential gene, encodes a novel regulatory protein required for ribosome biogenesis in Saccharomyces cerevisiae. Mol. Cell. Biol. 20:2066–2074.
   PubMed Web of Science ®Google Scholar
• Vai, M., L. Popolo, and L. Alberghina. 1987. Effect of tunicamycin on cell cycle progression in budding yeast. Exp. Cell Res. 171:448–459.
   PubMedGoogle Scholar
• Warner, J. R.. 1999. The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 24:437–440.
   PubMed Web of Science ®Google Scholar
• Wolfsberg, T. G., A. E. Gabrielian, M. J. Campbell, R. J. Cho, J. L. Spouge, and D. Landsman. 1999. Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae. Genome Res. 9:775–792.
   PubMedGoogle Scholar
• Zhang, M. Q.. 1999. Promoter analysis of coregulated genes in the yeast genome. Comput. Chem. 23:233–250.
   PubMedGoogle Scholar