Promoter-dependent roles for the Srb10 cyclin-dependent kinase and the Hda1 deacetylase in Tup1-mediated repression in Saccharomyces cerevisiae

Molecular Biology of the Cell

Volumn 15, Issue 9, 2004, Pages 4191-4202

  Green, Sarah R ^a   Johnson, Alexander D ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE; HISTONE DEACETYLASE; HISTONE DEACETYLASE 1; HISTONE H3; LYSINE; PROTEIN SRB10; PROTEIN TUP1; REPRESSOR PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; DEACETYLATION; ENZYME ACTIVITY; ENZYME REPRESSION; GENE DELETION; GENE REPRESSION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; METAZOON; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; SACCHAROMYCES CEREVISIAE;

ACETYLATION; CYCLIN-DEPENDENT KINASES; DNA-BINDING PROTEINS; FUNGAL PROTEINS; GENE DELETION; GENE EXPRESSION PROFILING; GENES, FUNGAL; HISTONE DEACETYLASES; HISTONES; MODELS, BIOLOGICAL; NUCLEAR PROTEINS; PROMOTER REGIONS (GENETICS); REPRESSOR PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC;

EUKARYOTA; METAZOA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 4344672753     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.E04-05-0412     Document Type: Article

References (58)

1. Amillet, J.M., Buisson, N., and Labbe-Bois, R. (1995). Positive and negative elements involved in the differential regulation by heme and oxygen of the HEM13 gene (coproporphyrinogen oxidase) in Saccharomyces cerevisiae. Curr. Genet. 28, 503-511.
2. Ansari, A.Z., Koh, S.S., Zaman, Z., Bongards, C., Lehming, N., Young, R.A., and Ptashne, M. (2002). Transcriptional activating regions target a cyclin-dependent kinase. Proc. Natl. Acad. Sci. USA 99, 14706-14709.
3. Balasubramanian, B., Lowry, C.V., and Zitomer, R.S. (1993). The Rox1 repressor of the Saccharomyces cerevisiae hypoxic genes is a specific DNA-binding protein with a high-mobility-group motif. Mol. Cell. Biol. 13, 6071-6078.
4. Basehoar, A.D., Zanton, S.J., and Pugh, B.F. (2004). Identification and distinct regulation of yeast TATA box-containing genes. Cell 116, 699-709.
5. Becerra, M., Lombardia-Ferreira, L.J., Hauser, N.C., Hoheisel, J.D., Tizon, B., and Cerdan, M.E. (2002). The yeast transcriptome in aerobic and hypoxic conditions: effects of hap1, rox1, rox3 and srb10 deletions. Mol. Microbiol. 43, 545-555.
6. Bone, J.R., and Roth, S.Y. (2001). Recruitment of the yeast Tup1p-Ssn6p repressor is associated with localized decreases in histone acetylation. J. Biol. Chem. 276, 1808-1813.
7. Borggrefe, T., Davis, R., Erdjument-Bromage, H., Tempst, P., and Kornberg, R.D. (2002). A complex of the Srb8, -9, -10, and -11 transcriptional regulatory proteins from yeast. J. Biol. Chem. 277, 44202-44207.
8. Brachmann, C.B., Davies, A., Cost, G.J., Caputo, E., Li, J., Hieter, P., and Boeke, J.D. (1998). Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14, 115-132.
9. Carlson, M. (1997). Genetics of transcriptional regulation in yeast: connections to the RNA polymerase II CTD. Annu. Rev. Cell Dev. Biol. 13, 1-23.
10. Chi, Y., Huddleston, M.J., Zhang, X., Young, R.A., Annan, R.S., Carr, S.A., and Deshaies, R.J. (2001). Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev. 15, 1078-1092.
11. Davie, J.K., Trumbly, R.J., and Dent, S.Y. (2002). Histone-dependent association of Tup1-Ssn6 with repressed genes in vivo. Mol. Cell. Biol. 22, 693-703.
12. Deckert, J., Torres, A.M., Hwang, S.M., Kastaniotis, A.J., and Zitomer, R.S. (1998). The anatomy of a hypoxic operator in Saccharomyces cerevisiae. Genetics 150, 1429-1441.
13. DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997). Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686.
14. Edmondson, D.G., Smith, M.M., and Roth, S.Y. (1996). Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4. Genes Dev. 10, 1247-1259.
15. Erdman, S., Lin, L., Malczynski, M., and Snyder, M. (1998). Pheromone-regulated genes required for yeast mating differentiation. J. Cell Biol. 140, 461-483.
16. Fisher, A.L., and Caudy, M. (1998). Groucho proteins: transcriptional corepressors for specific subsets of DNA-binding transcription factors in vertebrates and invertebrates. Genes Dev. 12, 1931-1940.
17. Grbavec, D., Lo, R., Liu, Y., Greenfield, A., and Stifani, S. (1999). Groucho/transducin-like enhancer of split (TLE) family members interact with the yeast transcriptional co-repressor SSN6 and mammalian SSN6-related proteins: implications for evolutionary conservation of transcription repression mechanisms. Biochem. J. 337, 13-17.
18. Gromoller, A., and Lehming, N. (2000). Srb7p is a physical and physiological target of Tup1p. EMBO J. 19, 6845-6852.
19. Herschbach, B.M., Arnaud, M.B., and Johnson, A.D. (1994). Transcriptional repression directed by the yeast alpha 2 protein in vitro. Nature 370, 309-311.
20. Holstege, F.C., Jennings, E.G., Wyrick, J.J., Lee, T.I., Hengartner, C.J., Green, M.R., Golub, T.R., Lander, E.S., and Young, R.A. (1998). Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717-728.
21. Hughes, T.R., et al. (2000a). Functional discovery via a compendium of expression profiles. Cell 102, 109-126.
22. Hughes, T.R., et al. (2000b). Widespread aneuploidy revealed by DNA microarray expression profiling. Nat. Genet. 25, 333-337.
23. Huisinga, K.L., and Pugh, B.F. (2004). A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol. Cell 13, 573-585.
24. Johnston, M. (1999). Feasting, fasting and fermenting. Glucose sensing in yeast and other cells. Trends Genet. 15, 29-33.
25. Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. (2003). Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254.
26. Kuchin, S., and Carlson, M. (1998). Functional relationships of Srb10-Srb11 kinase, carboxy-terminal domain kinase CTDK-I, and transcriptional corepressor Ssn6-Tup1. Mol. Cell. Biol. 18, 1163-1171.
27. Kuchin, S., Yeghiayan, P., and Carlson, M. (1995). Cyclin-dependent protein kinase and cyclin homologs SSN3 and SSN8 contribute to transcriptional control in yeast. Proc. Natl. Acad. Sci. USA 92, 4006-4010.
28. Lee, M., Chatterjee, S., and Struhl, K. (2000). Genetic analysis of the role of Pol II holoenzyme components in repression by the Cyc8-Tup1 corepressor in yeast. Genetics 155, 1535-1542.
29. Lee, T.I., et al. (2002). Transcriptional regulatory networks in Saccharomyces cerevisiae Science 298, 799-804.
30. Levanon, D., Goldstein, R.E., Bernstein, Y., Tang, H., Goldenberg, D., Stifani, S., Paroush, Z., and Groner, Y. (1998). Transcriptional repression by AML1 and LEF-1 is mediated by the TLE/Groucho corepressors. Proc. Natl. Acad. Sci. USA 95, 11590-11595.
31. Liao, S.M., Zhang, J., Jeffery, D.A., Koleske, A.J., Thompson, C.M., Chao, D.M., Viljoen, M., van Vuuren, H.J., and Young, R.A. (1995). A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature 374, 193-196.
32. Lowry, C.V., Cerdan, M.E., and Zitomer, R.S. (1990). A hypoxic consensus operator and a constitutive activation region regulate the ANB1 gene of Saccharomyces cerevisiae. Mol. Cell. Biol. 10, 5921-5926.
33. Lutfiyya, L.L., Iyer, V.R., DeRisi, J., DeVit, M.J., Brown, P.O., and Johnston, M. (1998). Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae. Genetics 150, 1377-1391.
34. Mennella, T.A., Klinkenberg, L.G., and Zitomer, R.S. (2003). Recruitment of Tup1-Ssn6 by yeast hypoxic genes and chromatin-independent exclusion of TATA binding protein. Eukaryot. Cell 2, 1288-1303.
35. Myer, V.E., and Young, R.A. (1998). RNA polymerase II holoenzymes and subcomplexes. J. Biol. Chem. 273, 27757-27760.
36. Ozcan, S., and Johnston, M. (1996). Two different repressors collaborate to restrict expression of the yeast glucose transporter genes HXT2 and HXT4 to low levels of glucose. Mol. Cell. Biol. 16, 5536-5545.
37. Papamichos-Chronakis, M., Conlan, R.S., Gounalaki, N., Copf, T., and Tzamarias, D. (2000). Hrs1/Med3 is a Cyc8-Tup1 corepressor target in the RNA polymerase II holoenzyme. J. Biol. Chem. 275, 8397-8403.
38. Papamichos-Chronakis, M., Petrakis, T., Ktistaki, E., Topalidou, I., and Tzamarias, D. (2002). Cti6, a PHD domain protein, bridges the Cyc8-Tup1 corepressor and the SAGA coactivator to overcome repression at GAL1. Mol. Cell 9, 1297-1305.
39. Pflugrad, A., Meir, J.Y., Barnes, T.M., and Miller, D.M., 3rd. (1997). The Groucho-like transcription factor UNC-37 functions with the neural specificity gene unc-4 to govern motor neuron identity in C. elegans. Development 124, 1699-1709.
40. Proft, M., and Struhl, K. (2002). Hog1 kinase converts the Sko1-Cyc8-Tup1 repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress. Mol. Cell 9, 1307-1317.
41. Redd, M.J., Arnaud, M.B., and Johnson, A.D. (1997). A complex composed of tup1 and ssn6 represses transcription in vitro. J. Biol. Chem. 272, 11193-11197.
42. Robyr, D., Suka, Y., Xènarios, I., Kurdistani, S.K., Wang, A., Suka, N., and Grunstein, M. (2002). Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109, 437-446.
43. Ruiz, C., Escribano, V., Morgado, E., Molina, M., and Mazon, M.J. (2003). Cell-type-dependent repression of yeast a-specific genes requires Itc1p, a subunit of the Isw2p-Itc1p chromatin remodelling complex. Microbiology 149, 341-351.
44. Sabet, N., Tong, F., Madigan, J.P., Volo, S., Smith, M.M., and Morse, R.H. (2003). Global and specific transcriptional repression by the histone H3 amino terminus in yeast. Proc. Natl. Acad. Sci. USA 100, 4084-4089.
45. Sakai, A., Shimizu, Y., Kondou, S., Chibazakura, T., and Hishinuma, F. (1990). Structure and molecular analysis of RGR1, a gene required for glucose repression of Saccharomyces cerevisiae. Mol. Cell. Biol. 10, 4130-4138.
46. Schreiber, S.L., and Bernstein, B.E. (2002). Signaling network model of chromatin. Cell 111, 771-778.
47. Smith, R.L., and Johnson, A.D. (2000). Turning genes off by Ssn6-Tup 1, a conserved system of transcriptional repression in eukaryotes. Trends Biochem. Sci. 25, 325-330.
48. Song, W., and Carlson, M. (1998). Srb/mediator proteins interact functionally and physically with transcriptional repressor Sfl1. EMBO J. 17, 5757-5765.
49. Song, W., Treich, I., Qian, N., Kuchin, S., and Carlson, M. (1996). SSN genes that affect transcriptional repression in Saccharomyces cerevisiae encode SIN4, ROX3, and SRB proteins associated with RNA polymerase II. Mol. Cell. Biol. 16, 115-120.
50. Strahl-Bolsinger, S., Hecht, A., Luo, K., and Grunstein, M. (1997). SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 11, 83-93.
51. Treitel, M.A., and Carlson, M. (1995). Repression by SSN6-TUP1 is directed by MIG1, a repressor/activator protein. Proc. Natl. Acad. Sci. USA 92, 3132-3136.
52. Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98, 5116-5121.
53. Varanasi, U.S., Klis, M., Mikesell, P.B., and Trumbly, R.J. (1996). The Cyc8 (Ssn6)-Tup1 corepressor complex is composed of one Cyc8 and four Tup1 subunits. Mol. Cell. Biol. 16, 6707-6714.
54. Wahi, M., and Johnson, A.D. (1995). Identification of genes required for alpha 2 repression in Saccharomyces cerevisiae. Genetics 140, 79-90.
55. Wu, J., Suka, N., Carlson, M., and Grunstein, M. (2001). TUP1 utilizes histone H3/H2B-specific HDA1 deacetylase to repress gene activity in yeast. Mol. Cell 7, 117-126.
56. Zaman, Z., Ansari, A.Z., Koh, S.S., Young, R., and Ptashne, M. (2001). Interaction of a transcriptional repressor with the RNA polymerase II holoenzyme plays a crucial role in repression. Proc. Natl. Acad. Sci. USA 98, 2550-2554.
57. Zhang, Z., Varanasi, U., and Trumbly, R.J. (2002). Functional dissection of the global repressor Tup1 in yeast: dominant role of the C-terminal repression domain. Genetics 161, 957-969.
58. Zitomer, R.S., and Lowry, C.V. (1992). Regulation of gene expression by oxygen in Saccharomyces cerevisiae. Microbiol. Rev. 56, 1-11.