Abstract
The Cyc8-Tup1 corepressor complex is targeted to promoters by pathway-specific DNA-binding repressors, thereby inhibiting the transcription of specific classes of genes. Genetic screens have identified mutations in a variety of Pol II holoenzyme components (Srb8, Srb9, Srb10, Srb11, Sin4, Rgr1, Rox3, and Hrs1) and in the N-terminal tails of histones H3 and H4 that weaken repression by Cyc8-Tup1. Here, we analyze the effect of individual and multiple mutations in many of these components on transcriptional repression of natural promoters that are regulated by Cyc8-Tup1. In all cases tested, individual mutations have a very modest effect on SUC2 RNA levels and no detectable effect on levels of ANB1, MFA2, and RNR2. Furthermore, multiple mutations within the Srb components, between Srbs and Sin4, and between Srbs and histone tails affect Cyc8-Tup1 repression to the same modest extent as the individual mutations. These results argue that the weak effects of the various mutations on repression by Cyc8-Tup1 are not due to redundancy among components of the Pol II machinery, and they argue against a simple redundancy between the holoenzyme and chromatin pathways. In addition, phenotypic analysis indicates that, although Srbs8-11 are indistinguishable with respect to Cyc8-Tup1 repression, the individual Srbs are functionally distinct in other respects. Genetic interactions among srb mutations imply that a balance between the activities of Srb8 + Srb10 and Srb11 is important for normal cell growth.
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- Alani E., Cao L., Kleckner N. A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains. Genetics. 1987 Aug;116(4):541–545. doi: 10.1534/genetics.112.541.test. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Balciunas D., Ronne H. Three subunits of the RNA polymerase II mediator complex are involved in glucose repression. Nucleic Acids Res. 1995 Nov 11;23(21):4421–4425. doi: 10.1093/nar/23.21.4421. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brent R., Ptashne M. A bacterial repressor protein or a yeast transcriptional terminator can block upstream activation of a yeast gene. Nature. 1984 Dec 13;312(5995):612–615. doi: 10.1038/312612a0. [DOI] [PubMed] [Google Scholar]
- Chen S., West R. W., Jr, Johnson S. L., Gans H., Kruger B., Ma J. TSF3, a global regulatory protein that silences transcription of yeast GAL genes, also mediates repression by alpha 2 repressor and is identical to SIN4. Mol Cell Biol. 1993 Feb;13(2):831–840. doi: 10.1128/mcb.13.2.831. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Conlan R. S., Gounalaki N., Hatzis P., Tzamarias D. The Tup1-Cyc8 protein complex can shift from a transcriptional co-repressor to a transcriptional co-activator. J Biol Chem. 1999 Jan 1;274(1):205–210. doi: 10.1074/jbc.274.1.205. [DOI] [PubMed] [Google Scholar]
- Cooper J. P., Roth S. Y., Simpson R. T. The global transcriptional regulators, SSN6 and TUP1, play distinct roles in the establishment of a repressive chromatin structure. Genes Dev. 1994 Jun 15;8(12):1400–1410. doi: 10.1101/gad.8.12.1400. [DOI] [PubMed] [Google Scholar]
- DeRisi J. L., Iyer V. R., Brown P. O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 1997 Oct 24;278(5338):680–686. doi: 10.1126/science.278.5338.680. [DOI] [PubMed] [Google Scholar]
- Deckert J., Rodriguez Torres A. M., Simon J. T., Zitomer R. S. Mutational analysis of Rox1, a DNA-bending repressor of hypoxic genes in Saccharomyces cerevisiae. Mol Cell Biol. 1995 Nov;15(11):6109–6117. doi: 10.1128/mcb.15.11.6109. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Edmondson D. G., Smith M. M., Roth S. Y. Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4. Genes Dev. 1996 May 15;10(10):1247–1259. doi: 10.1101/gad.10.10.1247. [DOI] [PubMed] [Google Scholar]
- Edmondson D. G., Zhang W., Watson A., Xu W., Bone J. R., Yu Y., Stillman D., Roth S. Y. In vivo functions of histone acetylation/deacetylation in Tup1p repression and Gcn5p activation. Cold Spring Harb Symp Quant Biol. 1998;63:459–468. doi: 10.1101/sqb.1998.63.459. [DOI] [PubMed] [Google Scholar]
- Gavin I. M., Simpson R. T. Interplay of yeast global transcriptional regulators Ssn6p-Tup1p and Swi-Snf and their effect on chromatin structure. EMBO J. 1997 Oct 15;16(20):6263–6271. doi: 10.1093/emboj/16.20.6263. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gu W., Malik S., Ito M., Yuan C. X., Fondell J. D., Zhang X., Martinez E., Qin J., Roeder R. G. A novel human SRB/MED-containing cofactor complex, SMCC, involved in transcription regulation. Mol Cell. 1999 Jan;3(1):97–108. doi: 10.1016/s1097-2765(00)80178-1. [DOI] [PubMed] [Google Scholar]
- Hampsey M., Reinberg D. RNA polymerase II as a control panel for multiple coactivator complexes. Curr Opin Genet Dev. 1999 Apr;9(2):132–139. doi: 10.1016/S0959-437X(99)80020-3. [DOI] [PubMed] [Google Scholar]
- Hengartner C. J., Myer V. E., Liao S. M., Wilson C. J., Koh S. S., Young R. A. Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases. Mol Cell. 1998 Jul;2(1):43–53. doi: 10.1016/s1097-2765(00)80112-4. [DOI] [PubMed] [Google Scholar]
- Herschbach B. M., Arnaud M. B., Johnson A. D. Transcriptional repression directed by the yeast alpha 2 protein in vitro. Nature. 1994 Jul 28;370(6487):309–311. doi: 10.1038/370309a0. [DOI] [PubMed] [Google Scholar]
- Hirst M., Kobor M. S., Kuriakose N., Greenblatt J., Sadowski I. GAL4 is regulated by the RNA polymerase II holoenzyme-associated cyclin-dependent protein kinase SRB10/CDK8. Mol Cell. 1999 May;3(5):673–678. doi: 10.1016/s1097-2765(00)80360-3. [DOI] [PubMed] [Google Scholar]
- Huang L., Zhang W., Roth S. Y. Amino termini of histones H3 and H4 are required for a1-alpha2 repression in yeast. Mol Cell Biol. 1997 Nov;17(11):6555–6562. doi: 10.1128/mcb.17.11.6555. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Huang M., Zhou Z., Elledge S. J. The DNA replication and damage checkpoint pathways induce transcription by inhibition of the Crt1 repressor. Cell. 1998 Sep 4;94(5):595–605. doi: 10.1016/s0092-8674(00)81601-3. [DOI] [PubMed] [Google Scholar]
- Kadosh D., Struhl K. Histone deacetylase activity of Rpd3 is important for transcriptional repression in vivo. Genes Dev. 1998 Mar 15;12(6):797–805. doi: 10.1101/gad.12.6.797. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kadosh D., Struhl K. Repression by Ume6 involves recruitment of a complex containing Sin3 corepressor and Rpd3 histone deacetylase to target promoters. Cell. 1997 May 2;89(3):365–371. doi: 10.1016/s0092-8674(00)80217-2. [DOI] [PubMed] [Google Scholar]
- Kayne P. S., Kim U. J., Han M., Mullen J. R., Yoshizaki F., Grunstein M. Extremely conserved histone H4 N terminus is dispensable for growth but essential for repressing the silent mating loci in yeast. Cell. 1988 Oct 7;55(1):27–39. doi: 10.1016/0092-8674(88)90006-2. [DOI] [PubMed] [Google Scholar]
- Keleher C. A., Redd M. J., Schultz J., Carlson M., Johnson A. D. Ssn6-Tup1 is a general repressor of transcription in yeast. Cell. 1992 Feb 21;68(4):709–719. doi: 10.1016/0092-8674(92)90146-4. [DOI] [PubMed] [Google Scholar]
- Koleske A. J., Young R. A. An RNA polymerase II holoenzyme responsive to activators. Nature. 1994 Mar 31;368(6470):466–469. doi: 10.1038/368466a0. [DOI] [PubMed] [Google Scholar]
- Komachi K., Redd M. J., Johnson A. D. The WD repeats of Tup1 interact with the homeo domain protein alpha 2. Genes Dev. 1994 Dec 1;8(23):2857–2867. doi: 10.1101/gad.8.23.2857. [DOI] [PubMed] [Google Scholar]
- Kuchin S., Yeghiayan P., Carlson M. Cyclin-dependent protein kinase and cyclin homologs SSN3 and SSN8 contribute to transcriptional control in yeast. Proc Natl Acad Sci U S A. 1995 Apr 25;92(9):4006–4010. doi: 10.1073/pnas.92.9.4006. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lee Y. C., Park J. M., Min S., Han S. J., Kim Y. J. An activator binding module of yeast RNA polymerase II holoenzyme. Mol Cell Biol. 1999 Apr;19(4):2967–2976. doi: 10.1128/mcb.19.4.2967. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Liao S. M., Zhang J., Jeffery D. A., Koleske A. J., Thompson C. M., Chao D. M., Viljoen M., van Vuuren H. J., Young R. A. A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature. 1995 Mar 9;374(6518):193–196. doi: 10.1038/374193a0. [DOI] [PubMed] [Google Scholar]
- Matallana E., Franco L., Pérez-Ortín J. E. Chromatin structure of the yeast SUC2 promoter in regulatory mutants. Mol Gen Genet. 1992 Feb;231(3):395–400. doi: 10.1007/BF00292708. [DOI] [PubMed] [Google Scholar]
- Myers L. C., Gustafsson C. M., Bushnell D. A., Lui M., Erdjument-Bromage H., Tempst P., Kornberg R. D. The Med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain. Genes Dev. 1998 Jan 1;12(1):45–54. doi: 10.1101/gad.12.1.45. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Papamichos-Chronakis M., Conlan R. S., Gounalaki N., Copf T., Tzamarias D. Hrs1/Med3 is a Cyc8-Tup1 corepressor target in the RNA polymerase II holoenzyme. J Biol Chem. 2000 Mar 24;275(12):8397–8403. doi: 10.1074/jbc.275.12.8397. [DOI] [PubMed] [Google Scholar]
- Park S. H., Koh S. S., Chun J. H., Hwang H. J., Kang H. S. Nrg1 is a transcriptional repressor for glucose repression of STA1 gene expression in Saccharomyces cerevisiae. Mol Cell Biol. 1999 Mar;19(3):2044–2050. doi: 10.1128/mcb.19.3.2044. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Proft M., Serrano R. Repressors and upstream repressing sequences of the stress-regulated ENA1 gene in Saccharomyces cerevisiae: bZIP protein Sko1p confers HOG-dependent osmotic regulation. Mol Cell Biol. 1999 Jan;19(1):537–546. doi: 10.1128/mcb.19.1.537. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Redd M. J., Arnaud M. B., Johnson A. D. A complex composed of tup1 and ssn6 represses transcription in vitro. J Biol Chem. 1997 Apr 25;272(17):11193–11197. doi: 10.1074/jbc.272.17.11193. [DOI] [PubMed] [Google Scholar]
- Roth S. Y., Dean A., Simpson R. T. Yeast alpha 2 repressor positions nucleosomes in TRP1/ARS1 chromatin. Mol Cell Biol. 1990 May;10(5):2247–2260. doi: 10.1128/mcb.10.5.2247. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Roth S. Y., Shimizu M., Johnson L., Grunstein M., Simpson R. T. Stable nucleosome positioning and complete repression by the yeast alpha 2 repressor are disrupted by amino-terminal mutations in histone H4. Genes Dev. 1992 Mar;6(3):411–425. doi: 10.1101/gad.6.3.411. [DOI] [PubMed] [Google Scholar]
- Rundlett S. E., Carmen A. A., Kobayashi R., Bavykin S., Turner B. M., Grunstein M. HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14503–14508. doi: 10.1073/pnas.93.25.14503. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Singer V. L., Wobbe C. R., Struhl K. A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation. Genes Dev. 1990 Apr;4(4):636–645. doi: 10.1101/gad.4.4.636. [DOI] [PubMed] [Google Scholar]
- Song W., Carlson M. Srb/mediator proteins interact functionally and physically with transcriptional repressor Sfl1. EMBO J. 1998 Oct 1;17(19):5757–5765. doi: 10.1093/emboj/17.19.5757. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Song W., Treich I., Qian N., Kuchin S., Carlson M. SSN genes that affect transcriptional repression in Saccharomyces cerevisiae encode SIN4, ROX3, and SRB proteins associated with RNA polymerase II. Mol Cell Biol. 1996 Jan;16(1):115–120. doi: 10.1128/mcb.16.1.115. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sun X., Zhang Y., Cho H., Rickert P., Lees E., Lane W., Reinberg D. NAT, a human complex containing Srb polypeptides that functions as a negative regulator of activated transcription. Mol Cell. 1998 Aug;2(2):213–222. doi: 10.1016/s1097-2765(00)80131-8. [DOI] [PubMed] [Google Scholar]
- Tzamarias D., Struhl K. Distinct TPR motifs of Cyc8 are involved in recruiting the Cyc8-Tup1 corepressor complex to differentially regulated promoters. Genes Dev. 1995 Apr 1;9(7):821–831. doi: 10.1101/gad.9.7.821. [DOI] [PubMed] [Google Scholar]
- Tzamarias D., Struhl K. Functional dissection of the yeast Cyc8-Tup1 transcriptional co-repressor complex. Nature. 1994 Jun 30;369(6483):758–761. doi: 10.1038/369758a0. [DOI] [PubMed] [Google Scholar]
- Varanasi U. S., Klis M., Mikesell P. B., Trumbly R. J. The Cyc8 (Ssn6)-Tup1 corepressor complex is composed of one Cyc8 and four Tup1 subunits. Mol Cell Biol. 1996 Dec;16(12):6707–6714. doi: 10.1128/mcb.16.12.6707. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wahi M., Johnson A. D. Identification of genes required for alpha 2 repression in Saccharomyces cerevisiae. Genetics. 1995 May;140(1):79–90. doi: 10.1093/genetics/140.1.79. [DOI] [PMC free article] [PubMed] [Google Scholar]