Abstract
The Saccharomyces cerevisiae alpha2 repressor controls two classes of cell-type-specific genes in yeast through association with different partners. alpha2-Mcm1 complexes repress a cell-specific gene expression in haploid alpha cells and diploid a/alpha cells, while a1-alpha2 complexes repress haploid-specific genes in diploid cells. In both cases, repression is mediated through Ssn6-Tu1 corepressor complexes that are recruited via direct interactions with alpha2. We have previously shown that nucleosomes are positioned adjacent to the alpha2-Mcm1 operator under conditions of repression and that Tupl interacts directly with histones H3 and H4. Here, we examine the role of chromatin in a1-alpha2 repression to determine if chromatin is a general feature of repression by Ssn6-Tup1. We find that mutations in the amino terminus of histone H4 cause a 4- to 11-fold derepression of a reporter gene under a1-alpha2 control, while truncation of the H3 amino terminus has a more modest (3-fold or less) effect. Strikingly, combination of the H3 truncation with an H4 mutation causes a 40-fold decrease in repression, clearly indicating a central role for these histones in a1-alpha2-mediated repression. However, in contrast to the ordered positioning of nucleosomes adjacent to the alpha2-Mcm1 operator, nucleosomes are not positioned adjacent to the a1-alpha2 operator in diploid cells. Our data indicate that chromatin is important to Ssn6-Tup1-mediated repression but that the degrees of chromatin organization directed by these proteins differ at different promoters.
Full Text
The Full Text of this article is available as a PDF (1.3 MB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Axelrod J. D., Majors J. An improved method for photofootprinting yeast genes in vivo using Taq polymerase. Nucleic Acids Res. 1989 Jan 11;17(1):171–183. doi: 10.1093/nar/17.1.171. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chen J., Ding M., Pederson D. S. Binding of TFIID to the CYC1 TATA boxes in yeast occurs independently of upstream activating sequences. Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):11909–11913. doi: 10.1073/pnas.91.25.11909. [DOI] [PMC free article] [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]
- Dranginis A. M. Binding of yeast a1 and alpha 2 as a heterodimer to the operator DNA of a haploid-specific gene. Nature. 1990 Oct 18;347(6294):682–685. doi: 10.1038/347682a0. [DOI] [PubMed] [Google Scholar]
- Dranginis A. M. Regulation of STA1 gene expression by MAT during the life cycle of Saccharomyces cerevisiae. Mol Cell Biol. 1989 Sep;9(9):3992–3998. doi: 10.1128/mcb.9.9.3992. [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]
- Goutte C., Johnson A. D. a1 protein alters the DNA binding specificity of alpha 2 repressor. Cell. 1988 Mar 25;52(6):875–882. doi: 10.1016/0092-8674(88)90429-1. [DOI] [PubMed] [Google Scholar]
- Grunstein M. Nucleosomes: regulators of transcription. Trends Genet. 1990 Dec;6(12):395–400. doi: 10.1016/0168-9525(90)90299-l. [DOI] [PubMed] [Google Scholar]
- Guarente L., Lalonde B., Gifford P., Alani E. Distinctly regulated tandem upstream activation sites mediate catabolite repression of the CYC1 gene of S. cerevisiae. Cell. 1984 Feb;36(2):503–511. doi: 10.1016/0092-8674(84)90243-5. [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]
- Herskowitz I. A regulatory hierarchy for cell specialization in yeast. Nature. 1989 Dec 14;342(6251):749–757. doi: 10.1038/342749a0. [DOI] [PubMed] [Google Scholar]
- Hill J., Donald K. A., Griffiths D. E., Donald G. DMSO-enhanced whole cell yeast transformation. Nucleic Acids Res. 1991 Oct 25;19(20):5791–5791. doi: 10.1093/nar/19.20.5791. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Johnson A. D., Herskowitz I. A repressor (MAT alpha 2 Product) and its operator control expression of a set of cell type specific genes in yeast. Cell. 1985 Aug;42(1):237–247. doi: 10.1016/s0092-8674(85)80119-7. [DOI] [PubMed] [Google Scholar]
- Johnson L. M., Kayne P. S., Kahn E. S., Grunstein M. Genetic evidence for an interaction between SIR3 and histone H4 in the repression of the silent mating loci in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1990 Aug;87(16):6286–6290. doi: 10.1073/pnas.87.16.6286. [DOI] [PMC free article] [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., Goutte C., Johnson A. D. The yeast cell-type-specific repressor alpha 2 acts cooperatively with a non-cell-type-specific protein. Cell. 1988 Jun 17;53(6):927–936. doi: 10.1016/s0092-8674(88)90449-7. [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]
- 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]
- Megee P. C., Morgan B. A., Smith M. M. Histone H4 and the maintenance of genome integrity. Genes Dev. 1995 Jul 15;9(14):1716–1727. doi: 10.1101/gad.9.14.1716. [DOI] [PubMed] [Google Scholar]
- Morgan B. A., Mittman B. A., Smith M. M. The highly conserved N-terminal domains of histones H3 and H4 are required for normal cell cycle progression. Mol Cell Biol. 1991 Aug;11(8):4111–4120. doi: 10.1128/mcb.11.8.4111. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Murphy M. R., Shimizu M., Roth S. Y., Dranginis A. M., Simpson R. T. DNA-protein interactions at the S.cerevisiae alpha 2 operator in vivo. Nucleic Acids Res. 1993 Jul 11;21(14):3295–3300. doi: 10.1093/nar/21.14.3295. [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]
- Redd M. J., Stark M. R., Johnson A. D. Accessibility of alpha 2-repressed promoters to the activator Gal4. Mol Cell Biol. 1996 Jun;16(6):2865–2869. doi: 10.1128/mcb.16.6.2865. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Roth S. Y. Chromatin-mediated transcriptional repression in yeast. Curr Opin Genet Dev. 1995 Apr;5(2):168–173. doi: 10.1016/0959-437x(95)80004-2. [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]
- Schultz J., Carlson M. Molecular analysis of SSN6, a gene functionally related to the SNF1 protein kinase of Saccharomyces cerevisiae. Mol Cell Biol. 1987 Oct;7(10):3637–3645. doi: 10.1128/mcb.7.10.3637. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schultz J., Marshall-Carlson L., Carlson M. The N-terminal TPR region is the functional domain of SSN6, a nuclear phosphoprotein of Saccharomyces cerevisiae. Mol Cell Biol. 1990 Sep;10(9):4744–4756. doi: 10.1128/mcb.10.9.4744. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shimizu M., Li W., Shindo H., Mitchell A. P. Transcriptional repression at a distance through exclusion of activator binding in vivo. Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):790–795. doi: 10.1073/pnas.94.3.790. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shimizu M., Roth S. Y., Szent-Gyorgyi C., Simpson R. T. Nucleosomes are positioned with base pair precision adjacent to the alpha 2 operator in Saccharomyces cerevisiae. EMBO J. 1991 Oct;10(10):3033–3041. doi: 10.1002/j.1460-2075.1991.tb07854.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Smith D. L., Desai A. B., Johnson A. D. DNA bending by the a1 and alpha 2 homeodomain proteins from yeast. Nucleic Acids Res. 1995 Apr 11;23(7):1239–1243. doi: 10.1093/nar/23.7.1239. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Smith D. L., Johnson A. D. A molecular mechanism for combinatorial control in yeast: MCM1 protein sets the spacing and orientation of the homeodomains of an alpha 2 dimer. Cell. 1992 Jan 10;68(1):133–142. doi: 10.1016/0092-8674(92)90212-u. [DOI] [PubMed] [Google Scholar]
- Trumbly R. J. Isolation of Saccharomyces cerevisiae mutants constitutive for invertase synthesis. J Bacteriol. 1986 Jun;166(3):1123–1127. doi: 10.1128/jb.166.3.1123-1127.1986. [DOI] [PMC free article] [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]
- 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]
- Zhang L., Guarente L. Evidence that TUP1/SSN6 has a positive effect on the activity of the yeast activator HAP1. Genetics. 1994 Mar;136(3):813–817. doi: 10.1093/genetics/136.3.813. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zhou Z., Elledge S. J. Isolation of crt mutants constitutive for transcription of the DNA damage inducible gene RNR3 in Saccharomyces cerevisiae. Genetics. 1992 Aug;131(4):851–866. doi: 10.1093/genetics/131.4.851. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zitomer R. S., Lowry C. V. Regulation of gene expression by oxygen in Saccharomyces cerevisiae. Microbiol Rev. 1992 Mar;56(1):1–11. doi: 10.1128/mr.56.1.1-11.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]