Combined global localization analysis and transcriptome data identify genes that are directly coregulated by Adr1 and Cat8

Molecular and Cellular Biology

Volumn 25, Issue 6, 2005, Pages 2138-2146

  Tachibana, Christine ^a   Yoo, Jane Y ^b   Tagne, Jean Basco ^b   Kacherovsky, Nataly ^a   Lee, Tong I ^b   Young, Elton T ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN ADR 1; PROTEIN CAT 8; REGULATOR PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE;

CHROMATIN IMMUNOPRECIPITATION; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENOME, FUNGAL; GLUCOSE; PROMOTER REGIONS (GENETICS); SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

SACCHAROMYCES CEREVISIAE;

EID: 14844338858     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.25.6.2138-2146.2005     Document Type: Article

References (51)

1. Allocco, D. J., I. S. Kohane, and A. J. Butte. 2004. Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics 5:18.
2. Baur, M., R. K. Esch, and B. Errede. 1997. Cooperative binding interactions required for function of the Ty1 sterile responsive element. Mol. Cell. Biol. 17:4330-4337.
3. Blumberg, H., T. A. Hartshorne, and E. T. Young. 1988. Regulation of expression and activity of the yeast transcription factor ADR1. Mol. Cell. Biol. 8:1868-1876.
4. Bojunga, N., and K. D. Entian. 1999. Cat8p, the activator of gluconeogenic genes in Saccharomyces cerevisiae, regulates carbon source-dependent expression of NADP-dependent cytosolic isocitrate dehydrogenase (Idp2p) and lactate permease (Jen1p). Mol. Gen. Genet. 262:869-875.
5. Bojunga, N., P. Kotter, and K. D. Entian. 1998. The succinate/fumarate transporter Acr1p of Saccharomyces cerevisiae is part of the gluconeogenic pathway and its expression is regulated by Cat8p. Mol. Gen. Genet. 260: 453-461.
6. Brons, J. F., M. De Jong, M. Valens, L. A. Grivell, M. Bolotin-Fukuhara, and J. Blom. 2002. Dissection of the promoter of the HAP4 gene in S. cerevisiae unveils a complex regulatory framework of transcriptional regulation. Yeast 19:923-932.
7. Carey, M., Y. S. Lin, M. R. Green, and M. Ptashne. 1990. A mechanism for synergistic activation of a mammalian gene by GAL4 derivatives. Nature 345:361-364.
8. Carlson, M. 1999. Glucose repression in yeast. Curr. Opin. Microbiol. 2:202-207.
9. Caspary, F., A. Hartig, and H. J. Schuller. 1997. Constitutive and carbon source-responsive promoter elements are involved in the regulated expression of the Saccharomyces cerevisiae malate synthase gene MLS1. Mol. Gen. Genet. 255:619-627.
10. 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.
11. Charbon, G., K. D. Breunig, R. Wattiez, J. Vandenhaute, and I. Noel-Georis. 2004. Key role of Ser562/661 in Snf1-dependent regulation of Cat8p in Saccharomyces cerevisiae and Kluyveromyces lactis. Mol. Cell. Biol. 24:4083-4091.
12. 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.
13. De Vit, M. J., J. A. Waddle, and M. Johnston. 1997. Regulated nuclear translocation of the Mig1 glucose repressor. Mol. Biol. Cell 8:1603-1618.
14. Di Mauro, E., S. G. Kendrew, and M. Caserta. 2000. Two distinct nucleosome alterations characterize chromatin remodeling at the Saccharomyces cerevisiae ADH2 promoter. J. Biol. Chem. 275:7612-7618.
15. Di Mauro, E., L. Verdone, B. Chiappini, and M. Caserta. 2002. In vivo changes of nucleosome positioning in the pretranscription state. J. Biol. Chem. 277:7002-7009.
16. Dombek, K. M., and E. T. Young. 1997. Cyclic AMP-dependent protein kinase inhibits ADH2 expression in part by decreasing expression of the transcription factor gene ADR1. Mol. Cell. Biol. 17:1450-1458.
17. Donoviel, M. S., N. Kacherorsky, and E. T. Young. 1995. Synergistic activation of ADH2 expression is sensitive to upstream activation sequence 2 (UAS2) orientation, copy number and UAS1-UAS2 helical phasing. Mol. Cell. Biol. 15:3442-3449.
18. Errede, B., and G. Ammerer. 1989. STE12, a protein involved in cell-type-specific transcription and signal transduction in yeast, is part of protein-DNA complexes. Genes Dev. 3:1349-1361.
19. Ferre, P., D. Azzout-Marniche, and F. Foufelle. 2003. AMP-activated protein kinase and hepatic genes involved in glucose metabolism. Biochem. Soc. Trans. 31:220-223.
20. Geisberg, J. V., and K. Struhl. 2004. Cellular stress alters the transcriptional properties of promoter-bound Mot1-TBP complexes. Mol. Cell 14:479-489.
21. Guarente, L. 1983. Yeast promoters and lacZ fusions designed to study expression of cloned genes in yeast. Methods Enzymol. 101:181-191.
22. Guldener, U., S. Heck, T. Fielder, J. Beinhauer, and J. H. Hegemann. 1996. A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res. 24:2519-2524.
23. Haurie, V., M. Perrot, T. Mini, P. Jeno, F. Sagliocco, and H. Boucherie. 2001. The transcriptional activator Cat8p provides a major contribution to the reprogramming of carbon metabolism during the diauxic shift in Saccharomyces cerevisiae. J. Biol. Chem. 276:76-85.
24. Hedges, D., M. Proft, and K. D. Entian. 1995. CAT8, a new zinc cluster-encoding gene necessary for derepression of gluconeogenic enzymes in the yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 15:1915-1922.
25. Hiesinger, M., S. Roth, E. Meissner, and H. J. Schuller. 2001. Contribution of Cat8 and Sip4 to the transcriptional activation of yeast gluconeogenic genes by carbon source-responsive elements. Curr. Genet. 39:68-76.
26. Knop, M., K. Siegers, G. Pereira, W. Zachariae, B. Winsor, K. Nasmyth, and E. Schiebel. 1999. Epitope tagging of yeast genes using a PCR-based strategy: more tags and improved practical routines. Yeast 15:963-972.
27. Kohler, T., S. Wesche, N. Taheri, G. H. Braus, and H. U. Mosch. 2002. Dual role of the Saccharomyces cerevisiae TEA/ATTS family transcription factor Tec1p in regulation of gene expression and cellular development. Eukaryot. Cell 1:673-686.
28. Kratzer, S., and H. J. Schuller. 1997. Transcriptional control of the yeast acetyl-CoA synthetase gene, ACS1, by the positive regulators CAT8 and ADR1 and the pleiotropic repressor UME6. Mol. Microbiol. 26:631-641.
29. Kurdistani, S. K., and M. Grunstein. 2003. In vivo protein-protein and protein-DNA crosslinking for genomewide binding microarray. Methods 31:90-95.
30. Laybourn, P. J., and J. T. Kadonaga. 1992. Threshold phenomena and long-distance activation of transcription by RNA polymerase II. Science 257:1682-1685.
31. Lee, T. I., N. J. Rinaldi, F. Robert, D. T. Odom, Z. Bar-Joseph, G. K. Gerber, N. M. Hannett, C. T. Harbison, C. M. Thompson, I. Simon, J. Zeitlinger, E. G. Jennings, H. L. Murray, D. B. Gordon, B. Ren, J. J. Wyrick, J. B. Tagne, T. L. Volkert, E. Fraenkel, D. K. Gifford, and R. A. Young. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804.
32. Lo, W. S., L. Duggan, N. C. Emre, R. Belotserkovskya, W. S. Lane, R. Shiekhattar, and S. L. Berger. 2001. Snf1 - a histone kinase that works in concert with the histone acetyltransferase Gcn5 to regulate transcription. Science 293:1142-1146.
33. Madhani, H. D., and G. R. Fink. 1997. Combinatorial control required for the specificity of yeast MAPK signaling. Science 275:1314-1317.
34. Martone, R., G. Euskirchen, P. Bertone, S. Hartman, T. E. Royce, N. M. Luscombe, J. L. Rinn, F. K. Nelson, P. Miller, M. Gerstein, S. Weissman, and M. Snyder. 2003. Distribution of NF-κB-binding sites across human chromosome 22. Proc. Natl. Acad. Sci. USA 100:12247-12252.
35. Rahner, A., M. Hiesinger, and H. J. Scbuller. 1999. Deregulation of gluconeogenic structural genes by variants of the transcriptional activator Cat8p of the yeast Saccharomyces cerevisiae. Mol. Microbiol. 34:146-156.
36. Randez-Gil, F., N. Bojunga, M. Proft, and K. D. Entian. 1997. Glucose derepression of gluconeogenic enzymes in Saccharomyces cerevisiae correlates with phosphorylation of the gene activator Cat8p. Mol. Cell. Biol. 17:2502-2510.
37. Ren, B., F. Robert, J. J. Wyrick, O. Aparicio, E. G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E. Kanin, T. L. Volkert, C. J. Wilson, S. P. Bell, and R. A. Young. 2000. Genome-wide location and function of DNA binding proteins. Science 290:2306-2309.
38. Roth, S., J. Kumme, and H. J. Schuller. 2004. Transcriptional activators Cat8 and Sip4 discriminate between sequence variants of the carbon source-responsive promoter element in the yeast Saccharomyces cerevisiae. Curr. Genet. 45:121-128.
39. Roth, S., and H. J. Schuller. 2001. Cat8 and Sip4 mediate regulated transcriptional activation of the yeast malate dehydrogenase gene MDH2 by three carbon source-responsive promoter elements. Yeast 18:151-162.
40. Rundlett, S. E., A. A. Carmen, N. Suka, B. M. Turner, and M. Grunstein. 1998. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature 392:831-835.
41. Schuller, H. J. 2003. Transcriptional control of nonfermentative metabolism in the yeast Saccharomyces cerevisiae. Curr. Genet. 43:139-160.
42. Sikorski, R. S., and P. Hieter. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122:19-27.
43. Sloan, J. S., K. M. Dombek, and E. T. Young. 1999. Post-translational regulation of Adr1 activity is mediated by its DNA binding domain. J. Biol. Chem. 274:37575-37582.
44. Taylor, W. E., and E. T. Young. 1990. cAMP-dependent phosphorylation and inactivation of yeast transcription factor ADR1 does not affect DNA binding. Proc. Natl. Acad. Sci. USA 87:4098-4102.
45. Verdone, L., J. Wu, K. van Riper, N. Kacherovsky, M. Vogelauer, E. T. Young, M. Grunstein, E. Di Mauro, and M. Caserta. 2002. Hyperacetylation of chromatin at the ADH2 promoter allows Adr1 to bind in repressed conditions. EMBO J. 21:1101-1111.
46. Vincent, O., and J. M. Gancedo. 1995. Analysis of positive elements sensitive to glucose in the promoter of the FBP1 gene from yeast. J. Biol. Chem. 270:12832-12838.
47. Walther, K., and H. J. Schuller. 2001. Adr1 and Cat8 synergistically activate the glucose-regulated alcohol dehydrogenase gene ADH2 of the yeast Saccharomyces cerevisiae. Microbiology 147:2037-2044.
48. Williamson, V. M., J. Bennetzen, E. T. Young, K. Nasmyth, and B. D. Hall. 1980. Isolation of the structural gene for alcohol dehydrogenase by genetic complementation in yeast. Nature 283:214-216.
49. Young, E. T., K. M. Dombek, C. Tachibana, and T. Ideker. 2003. Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8. J. Biol. Chem. 278:26146-26158.
50. Young, E. T., N. Kacherovsky, and K. Van Riper. 2002. Snf1 protein kinase regulates Adr1 binding to chromatin but not transcription activation. J. Biol. Chem. 277:38095-38103.
51. Zaragoza, O., O. Vincent, and J. M. Gancedo. 2001. Regulatory elements in the FBP1 promoter respond differently to glucose-dependent signals in Saccharomyces cerevisiae. Biochem. J. 359:193-201.