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Nucleosomal location of the STE6 TATA box and Mat alpha 2p-mediated repression.
Abstract
It has been proposed that yeast MATa cell-specific genes are repressed in MAT alpha cells by the Mat alpha 2p repressor-directed placement of a nucleosome in a position that incorporates the TATA box of the MATa-specific gene close to the nucleosomal pseudodyad. In this study, we address this proposal directly with a series of plasmids designed to place the MATa-specific STE6 TATA box at different locations in a nucleosome and in the internucleosomal linker. These plasmids contain different lengths of synthetic random DNA between the Mat alpha 2p operator and the TATA box of the STE6 promoter, which is located upstream of a lacZ reporter gene in a multicopy plasmid. We show that in MAT alpha cells, a nucleosome is retained in an identical translational frame relative to the Mat alpha 2p operator in all the constructs investigated, irrespective of the sequence of the DNA wrapped onto the histone octamer. This result shows that the nucleosomal organization of the STE6 promoter in MAT alpha cells is not conferred by the sequence of the promoter itself. No expression of the lacZ reporter gene was detectable in MAT alpha cells in any of the constructs, even with the TATA box located in a short internucleosomal linker. These data indicate that repression of MATa-specific genes in MAT alpha cells does not require the precise translational placement of the TATA box close to the nucleosomal pseudodyad; the gene remains repressed when the TATA box is located within the investigated 250-bp region in the organized chromatin domain abutting the Mat alpha 2p operator in MAT alpha cells and may remain repressed with the TATA box located anywhere within this organized repression domain.
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- Ammerer G. Identification, purification, and cloning of a polypeptide (PRTF/GRM) that binds to mating-specific promoter elements in yeast. Genes Dev. 1990 Feb;4(2):299–312. [PubMed] [Google Scholar]
- Brent R. Repression of transcription in yeast. Cell. 1985 Aug;42(1):3–4. [PubMed] [Google Scholar]
- Buratowski S, Hahn S, Guarente L, Sharp PA. Five intermediate complexes in transcription initiation by RNA polymerase II. Cell. 1989 Feb 24;56(4):549–561. [PubMed] [Google Scholar]
- Christianson TW, Sikorski RS, Dante M, Shero JH, Hieter P. Multifunctional yeast high-copy-number shuttle vectors. Gene. 1992 Jan 2;110(1):119–122. [PubMed] [Google Scholar]
- Dolan JW, Kirkman C, Fields S. The yeast STE12 protein binds to the DNA sequence mediating pheromone induction. Proc Natl Acad Sci U S A. 1989 Aug;86(15):5703–5707. [PMC free article] [PubMed] [Google Scholar]
- Drew HR, Travers AA. DNA bending and its relation to nucleosome positioning. J Mol Biol. 1985 Dec 20;186(4):773–790. [PubMed] [Google Scholar]
- Errede B, Ammerer G. STE12, a protein involved in cell-type-specific transcription and signal transduction in yeast, is part of protein-DNA complexes. Genes Dev. 1989 Sep;3(9):1349–1361. [PubMed] [Google Scholar]
- Flick JT, Eissenberg JC, Elgin SC. Micrococcal nuclease as a DNA structural probe: its recognition sequences, their genomic distribution and correlation with DNA structure determinants. J Mol Biol. 1986 Aug 20;190(4):619–633. [PubMed] [Google Scholar]
- Ghosh D. A relational database of transcription factors. Nucleic Acids Res. 1990 Apr 11;18(7):1749–1756. [PMC free article] [PubMed] [Google Scholar]
- Grunstein M. Histone function in transcription. Annu Rev Cell Biol. 1990;6:643–678. [PubMed] [Google Scholar]
- Han M, Kim UJ, Kayne P, Grunstein M. Depletion of histone H4 and nucleosomes activates the PHO5 gene in Saccharomyces cerevisiae. EMBO J. 1988 Jul;7(7):2221–2228. [PMC free article] [PubMed] [Google Scholar]
- Herschbach BM, Johnson AD. The yeast alpha 2 protein can repress transcription by RNA polymerases I and II but not III. Mol Cell Biol. 1993 Jul;13(7):4029–4038. [PMC free article] [PubMed] [Google Scholar]
- Herskowitz I. A regulatory hierarchy for cell specialization in yeast. Nature. 1989 Dec 14;342(6251):749–757. [PubMed] [Google Scholar]
- Higuchi R, Krummel B, Saiki RK. A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions. Nucleic Acids Res. 1988 Aug 11;16(15):7351–7367. [PMC free article] [PubMed] [Google Scholar]
- Hill J, Donald KA, Griffiths DE, Donald G. DMSO-enhanced whole cell yeast transformation. Nucleic Acids Res. 1991 Oct 25;19(20):5791–5791. [PMC free article] [PubMed] [Google Scholar]
- Hwang-Shum JJ, Hagen DC, Jarvis EE, Westby CA, Sprague GF., Jr Relative contributions of MCM1 and STE12 to transcriptional activation of a- and alpha-specific genes from Saccharomyces cerevisiae. Mol Gen Genet. 1991 Jun;227(2):197–204. [PubMed] [Google Scholar]
- Jerome JF, Jaehning JA. mRNA transcription in nuclei isolated from Saccharomyces cerevisiae. Mol Cell Biol. 1986 May;6(5):1633–1639. [PMC free article] [PubMed] [Google Scholar]
- Johnson AD, 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. [PubMed] [Google Scholar]
- Kalnins A, Otto K, Rüther U, Müller-Hill B. Sequence of the lacZ gene of Escherichia coli. EMBO J. 1983;2(4):593–597. [PMC free article] [PubMed] [Google Scholar]
- Keleher CA, Goutte C, Johnson AD. 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. [PubMed] [Google Scholar]
- Keleher CA, Redd MJ, Schultz J, Carlson M, Johnson AD. Ssn6-Tup1 is a general repressor of transcription in yeast. Cell. 1992 Feb 21;68(4):709–719. [PubMed] [Google Scholar]
- Kim JL, Nikolov DB, Burley SK. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 1993 Oct 7;365(6446):520–527. [PubMed] [Google Scholar]
- Kim Y, Geiger JH, Hahn S, Sigler PB. Crystal structure of a yeast TBP/TATA-box complex. Nature. 1993 Oct 7;365(6446):512–520. [PubMed] [Google Scholar]
- Kladde MP, Simpson RT. Positioned nucleosomes inhibit Dam methylation in vivo. Proc Natl Acad Sci U S A. 1994 Feb 15;91(4):1361–1365. [PMC free article] [PubMed] [Google Scholar]
- Knezetic JA, Luse DS. The presence of nucleosomes on a DNA template prevents initiation by RNA polymerase II in vitro. Cell. 1986 Apr 11;45(1):95–104. [PubMed] [Google Scholar]
- Kornberg RD. Structure of chromatin. Annu Rev Biochem. 1977;46:931–954. [PubMed] [Google Scholar]
- Kronstad JW, Holly JA, MacKay VL. A yeast operator overlaps an upstream activation site. Cell. 1987 Jul 31;50(3):369–377. [PubMed] [Google Scholar]
- Lee DK, Horikoshi M, Roeder RG. Interaction of TFIID in the minor groove of the TATA element. Cell. 1991 Dec 20;67(6):1241–1250. [PubMed] [Google Scholar]
- Lemontt JF, Fugit DR, Mackay VL. Pleiotropic Mutations at the TUP1 Locus That Affect the Expression of Mating-Type-Dependent Functions in SACCHAROMYCES CEREVISIAE. Genetics. 1980 Apr;94(4):899–920. [PMC free article] [PubMed] [Google Scholar]
- Lorch Y, LaPointe JW, Kornberg RD. Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell. 1987 Apr 24;49(2):203–210. [PubMed] [Google Scholar]
- Losa R, Brown DD. A bacteriophage RNA polymerase transcribes in vitro through a nucleosome core without displacing it. Cell. 1987 Aug 28;50(5):801–808. [PubMed] [Google Scholar]
- Matsui T. Transcription of adenovirus 2 major late and peptide IX genes under conditions of in vitro nucleosome assembly. Mol Cell Biol. 1987 Apr;7(4):1401–1408. [PMC free article] [PubMed] [Google Scholar]
- McGhee JD, Felsenfeld G. Nucleosome structure. Annu Rev Biochem. 1980;49:1115–1156. [PubMed] [Google Scholar]
- McGrath JP, Varshavsky A. The yeast STE6 gene encodes a homologue of the mammalian multidrug resistance P-glycoprotein. Nature. 1989 Aug 3;340(6232):400–404. [PubMed] [Google Scholar]
- Miller AM, MacKay VL, Nasmyth KA. Identification and comparison of two sequence elements that confer cell-type specific transcription in yeast. Nature. 1985 Apr 18;314(6012):598–603. [PubMed] [Google Scholar]
- Morse RH, Pederson DS, Dean A, Simpson RT. Yeast nucleosomes allow thermal untwisting of DNA. Nucleic Acids Res. 1987 Dec 23;15(24):10311–10330. [PMC free article] [PubMed] [Google Scholar]
- Mukai Y, Harashima S, Oshima Y. AAR1/TUP1 protein, with a structure similar to that of the beta subunit of G proteins, is required for a1-alpha 2 and alpha 2 repression in cell type control of Saccharomyces cerevisiae. Mol Cell Biol. 1991 Jul;11(7):3773–3779. [PMC free article] [PubMed] [Google Scholar]
- Murphy MR, Shimizu M, Roth SY, Dranginis AM, Simpson RT. DNA-protein interactions at the S.cerevisiae alpha 2 operator in vivo. Nucleic Acids Res. 1993 Jul 11;21(14):3295–3300. [PMC free article] [PubMed] [Google Scholar]
- Nikolov DB, Hu SH, Lin J, Gasch A, Hoffmann A, Horikoshi M, Chua NH, Roeder RG, Burley SK. Crystal structure of TFIID TATA-box binding protein. Nature. 1992 Nov 5;360(6399):40–46. [PubMed] [Google Scholar]
- Roth SY, Dean A, Simpson RT. Yeast alpha 2 repressor positions nucleosomes in TRP1/ARS1 chromatin. Mol Cell Biol. 1990 May;10(5):2247–2260. [PMC free article] [PubMed] [Google Scholar]
- Roth SY, Shimizu M, Johnson L, Grunstein M, Simpson RT. 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. [PubMed] [Google Scholar]
- Sauer RT, Smith DL, Johnson AD. Flexibility of the yeast alpha 2 repressor enables it to occupy the ends of its operator, leaving the center free. Genes Dev. 1988 Jul;2(7):807–816. [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. [PMC free article] [PubMed] [Google Scholar]
- Shimizu M, Roth SY, Szent-Gyorgyi C, Simpson RT. Nucleosomes are positioned with base pair precision adjacent to the alpha 2 operator in Saccharomyces cerevisiae. EMBO J. 1991 Oct;10(10):3033–3041. [PMC free article] [PubMed] [Google Scholar]
- Simpson RT. Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature. 1990 Jan 25;343(6256):387–389. [PubMed] [Google Scholar]
- Simpson RT. Nucleosome positioning: occurrence, mechanisms, and functional consequences. Prog Nucleic Acid Res Mol Biol. 1991;40:143–184. [PubMed] [Google Scholar]
- Smith DL, Johnson AD. 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. [PubMed] [Google Scholar]
- Travers AA, Klug A. The bending of DNA in nucleosomes and its wider implications. Philos Trans R Soc Lond B Biol Sci. 1987 Dec 15;317(1187):537–561. [PubMed] [Google Scholar]
- Tschumper G, Carbon J. Sequence of a yeast DNA fragment containing a chromosomal replicator and the TRP1 gene. Gene. 1980 Jul;10(2):157–166. [PubMed] [Google Scholar]
- Vershon AK, Johnson AD. A short, disordered protein region mediates interactions between the homeodomain of the yeast alpha 2 protein and the MCM1 protein. Cell. 1993 Jan 15;72(1):105–112. [PubMed] [Google Scholar]
- Williams FE, Varanasi U, Trumbly RJ. The CYC8 and TUP1 proteins involved in glucose repression in Saccharomyces cerevisiae are associated in a protein complex. Mol Cell Biol. 1991 Jun;11(6):3307–3316. [PMC free article] [PubMed] [Google Scholar]
- Wilson KL, Herskowitz I. Negative regulation of STE6 gene expression by the alpha 2 product of Saccharomyces cerevisiae. Mol Cell Biol. 1984 Nov;4(11):2420–2427. [PMC free article] [PubMed] [Google Scholar]
- Wilson KL, Herskowitz I. Sequences upstream of the STE6 gene required for its expression and regulation by the mating type locus in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1986 Apr;83(8):2536–2540. [PMC free article] [PubMed] [Google Scholar]
- Winston F, Carlson M. Yeast SNF/SWI transcriptional activators and the SPT/SIN chromatin connection. Trends Genet. 1992 Nov;8(11):387–391. [PubMed] [Google Scholar]
- Wolffe AP, Drew HR. Initiation of transcription on nucleosomal templates. Proc Natl Acad Sci U S A. 1989 Dec;86(24):9817–9821. [PMC free article] [PubMed] [Google Scholar]
- Workman JL, Roeder RG. Binding of transcription factor TFIID to the major late promoter during in vitro nucleosome assembly potentiates subsequent initiation by RNA polymerase II. Cell. 1987 Nov 20;51(4):613–622. [PubMed] [Google Scholar]