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Mol Cell Biol. 1996 May; 16(5): 1978–1988.
doi: 10.1128/mcb.16.5.1978
PMCID: PMC231185
PMID: 8628264

Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation.

L Verdone, G Camilloni, E Di Mauro, and M Caserta
Author information Copyright and License information PMC Disclaimer

Abstract

We have analyzed at both low and high resolution the distribution of nucleosomes over the Saccharomyces cerevisiae ADH2 promoter region in its chromosomal location, both under repressing (high-glucose) conditions and during derepression. Enzymatic treatments (micrococcal nuclease and restriction endonucleases) were used to probe the in vivo chromatin structure during ADH2 gene activation. Under glucose-repressed conditions, the ADH2 promoter was bound by a precise array of nucleosomes, the principal ones positioned at the RNA initiation sites (nucleosome +1), at the TATA box (nucleosome -1), and upstream of the ADR1-binding site (UAS1) (nucleosome -2). The UAS1 sequence and the adjacent UAS2 sequence constituted a nucleosome-free region. Nucleosomes -1 and +1 were destabilized soon after depletion of glucose and had become so before the appearance of ADH2 mRNA. When the transcription rate was high, nucleosomes -2 and +2 also underwent rearrangement. When spheroplasts were prepared from cells grown in minimal medium, detection of this chromatin remodeling required the addition of a small amount of glucose. Cells lacking the ADR1 protein did not display any of these chromatin modifications upon glucose depletion. Since the UAS1 sequence to which Adr1p binds is located immediately upstream of nucleosome -1, Adr1p is presumably required for destabilization of this nucleosome and for aiding the TATA-box accessibility to the transcription machinery.

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Selected References

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  • Adams CC, Workman JL. Nucleosome displacement in transcription. Cell. 1993 Feb 12;72(3):305–308. [PubMed] [Google Scholar]
  • Adams CC, Workman JL. Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Mol Cell Biol. 1995 Mar;15(3):1405–1421. [PMC free article] [PubMed] [Google Scholar]
  • Almer A, Rudolph H, Hinnen A, Hörz W. Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J. 1986 Oct;5(10):2689–2696. [PMC free article] [PubMed] [Google Scholar]
  • Archer TK, Lefebvre P, Wolford RG, Hager GL. Transcription factor loading on the MMTV promoter: a bimodal mechanism for promoter activation. Science. 1992 Mar 20;255(5051):1573–1576. [PubMed] [Google Scholar]
  • Axelrod JD, Reagan MS, Majors J. GAL4 disrupts a repressing nucleosome during activation of GAL1 transcription in vivo. Genes Dev. 1993 May;7(5):857–869. [PubMed] [Google Scholar]
  • Beier DR, Sledziewski A, Young ET. Deletion analysis identifies a region, upstream of the ADH2 gene of Saccharomyces cerevisiae, which is required for ADR1-mediated derepression. Mol Cell Biol. 1985 Jul;5(7):1743–1749. [PMC free article] [PubMed] [Google Scholar]
  • Bresnick EH, Rories C, Hager GL. Evidence that nucleosomes on the mouse mammary tumor virus promoter adopt specific translational positions. Nucleic Acids Res. 1992 Feb 25;20(4):865–870. [PMC free article] [PubMed] [Google Scholar]
  • Buttinelli M, Di Mauro E, Negri R. Multiple nucleosome positioning with unique rotational setting for the Saccharomyces cerevisiae 5S rRNA gene in vitro and in vivo. Proc Natl Acad Sci U S A. 1993 Oct 15;90(20):9315–9319. [PMC free article] [PubMed] [Google Scholar]
  • Carlson M, Laurent BC. The SNF/SWI family of global transcriptional activators. Curr Opin Cell Biol. 1994 Jun;6(3):396–402. [PubMed] [Google Scholar]
  • Cavalli G, Thoma F. Chromatin transitions during activation and repression of galactose-regulated genes in yeast. EMBO J. 1993 Dec;12(12):4603–4613. [PMC free article] [PubMed] [Google Scholar]
  • Cheng C, Kacherovsky N, Dombek KM, Camier S, Thukral SK, Rhim E, Young ET. Identification of potential target genes for Adr1p through characterization of essential nucleotides in UAS1. Mol Cell Biol. 1994 Jun;14(6):3842–3852. [PMC free article] [PubMed] [Google Scholar]
  • Ciriacy M, Freidel K, Löhning C. Characterization of trans-acting mutations affecting Ty and Ty-mediated transcription in Saccharomyces cerevisiae. Curr Genet. 1991 Dec;20(6):441–448. [PubMed] [Google Scholar]
  • Cook WJ, Chase D, Audino DC, Denis CL. Dissection of the ADR1 protein reveals multiple, functionally redundant activation domains interspersed with inhibitory regions: evidence for a repressor binding to the ADR1c region. Mol Cell Biol. 1994 Jan;14(1):629–640. [PMC free article] [PubMed] [Google Scholar]
  • Cook WJ, Mosley SP, Audino DC, Mullaney DL, Rovelli A, Stewart G, Denis CL. Mutations in the zinc-finger region of the yeast regulatory protein ADR1 affect both DNA binding and transcriptional activation. J Biol Chem. 1994 Mar 25;269(12):9374–9379. [PubMed] [Google Scholar]
  • Costanzo G, Di Mauro E, Negri R, Pereira G, Hollenberg C. Multiple overlapping positions of nucleosomes with single in vivo rotational setting in the Hansenula polymorpha RNA polymerase II MOX promoter. J Biol Chem. 1995 May 12;270(19):11091–11097. [PubMed] [Google Scholar]
  • Denis CL, Malvar T. The CCR4 gene from Saccharomyces cerevisiae is required for both nonfermentative and spt-mediated gene expression. Genetics. 1990 Feb;124(2):283–291. [PMC free article] [PubMed] [Google Scholar]
  • Denis CL, Young ET. Isolation and characterization of the positive regulatory gene ADR1 from Saccharomyces cerevisiae. Mol Cell Biol. 1983 Mar;3(3):360–370. [PMC free article] [PubMed] [Google Scholar]
  • Di Mauro E, Camilloni G, Verdone L, Caserta M. DNA topoisomerase I controls the kinetics of promoter activation and DNA topology in Saccharomyces cerevisiae. Mol Cell Biol. 1993 Nov;13(11):6702–6710. [PMC free article] [PubMed] [Google Scholar]
  • Draper MP, Liu HY, Nelsbach AH, Mosley SP, Denis CL. CCR4 is a glucose-regulated transcription factor whose leucine-rich repeat binds several proteins important for placing CCR4 in its proper promoter context. Mol Cell Biol. 1994 Jul;14(7):4522–4531. [PMC free article] [PubMed] [Google Scholar]
  • Eisen A, Taylor WE, Blumberg H, Young ET. The yeast regulatory protein ADR1 binds in a zinc-dependent manner to the upstream activating sequence of ADH2. Mol Cell Biol. 1988 Oct;8(10):4552–4556. [PMC free article] [PubMed] [Google Scholar]
  • Fascher KD, Schmitz J, Hörz W. Structural and functional requirements for the chromatin transition at the PHO5 promoter in Saccharomyces cerevisiae upon PHO5 activation. J Mol Biol. 1993 Jun 5;231(3):658–667. [PubMed] [Google Scholar]
  • Fedor MJ, Kornberg RD. Upstream activation sequence-dependent alteration of chromatin structure and transcription activation of the yeast GAL1-GAL10 genes. Mol Cell Biol. 1989 Apr;9(4):1721–1732. [PMC free article] [PubMed] [Google Scholar]
  • Fedor MJ, Lue NF, Kornberg RD. Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast. J Mol Biol. 1988 Nov 5;204(1):109–127. [PubMed] [Google Scholar]
  • Felsenfeld G. Chromatin as an essential part of the transcriptional mechanism. Nature. 1992 Jan 16;355(6357):219–224. [PubMed] [Google Scholar]
  • Fragoso G, John S, Roberts MS, Hager GL. Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames. Genes Dev. 1995 Aug 1;9(15):1933–1947. [PubMed] [Google Scholar]
  • Gancedo JM. Carbon catabolite repression in yeast. Eur J Biochem. 1992 Jun 1;206(2):297–313. [PubMed] [Google Scholar]
  • Georgel P, Dretzen G, Jagla K, Bellard F, Dubrovsky E, Calco V, Bellard M. GEBF-I activates the Drosophila Sgs3 gene enhancer by altering a positioned nucleosomal core particle. J Mol Biol. 1993 Nov 20;234(2):319–330. [PubMed] [Google Scholar]
  • Grunstein M. Histone function in transcription. Annu Rev Cell Biol. 1990;6:643–678. [PubMed] [Google Scholar]
  • Han M, Grunstein M. Nucleosome loss activates yeast downstream promoters in vivo. Cell. 1988 Dec 23;55(6):1137–1145. [PubMed] [Google Scholar]
  • Hayes JJ, Bashkin J, Tullius TD, Wolffe AP. The histone core exerts a dominant constraint on the structure of DNA in a nucleosome. Biochemistry. 1991 Aug 27;30(34):8434–8440. [PubMed] [Google Scholar]
  • Hecht A, Laroche T, Strahl-Bolsinger S, Gasser SM, Grunstein M. Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell. 1995 Feb 24;80(4):583–592. [PubMed] [Google Scholar]
  • Hirschhorn JN, Brown SA, Clark CD, Winston F. Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. Genes Dev. 1992 Dec;6(12A):2288–2298. [PubMed] [Google Scholar]
  • Lee MS, Garrard WT. Transcription-induced nucleosome 'splitting': an underlying structure for DNase I sensitive chromatin. EMBO J. 1991 Mar;10(3):607–615. [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, Omari S, Thoma F. Poly(dA).poly(dT) rich sequences are not sufficient to exclude nucleosome formation in a constitutive yeast promoter. Nucleic Acids Res. 1990 Jun 25;18(12):3495–3502. [PMC free article] [PubMed] [Google Scholar]
  • Lu Q, Wallrath LL, Elgin SC. Nucleosome positioning and gene regulation. J Cell Biochem. 1994 May;55(1):83–92. [PubMed] [Google Scholar]
  • Morse RH. Nucleosome disruption by transcription factor binding in yeast. Science. 1993 Dec 3;262(5139):1563–1566. [PubMed] [Google Scholar]
  • Paranjape SM, Kamakaka RT, Kadonaga JT. Role of chromatin structure in the regulation of transcription by RNA polymerase II. Annu Rev Biochem. 1994;63:265–297. [PubMed] [Google Scholar]
  • Pérez-Ortín JE, Estruch F, Matallana E, Franco L. Fine analysis of the chromatin structure of the yeast SUC2 gene and of its changes upon derepression. Comparison between the chromosomal and plasmid-inserted genes. Nucleic Acids Res. 1987 Sep 11;15(17):6937–6956. [PMC free article] [PubMed] [Google Scholar]
  • Peterson CL, Herskowitz I. Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription. Cell. 1992 Feb 7;68(3):573–583. [PubMed] [Google Scholar]
  • Peterson CL, Tamkun JW. The SWI-SNF complex: a chromatin remodeling machine? Trends Biochem Sci. 1995 Apr;20(4):143–146. [PubMed] [Google Scholar]
  • Piña B, Brüggemeier U, Beato M. Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter. Cell. 1990 Mar 9;60(5):719–731. [PubMed] [Google Scholar]
  • Puhl HL, Behe MJ. Poly(dA).poly(dT) forms very stable nucleosomes at higher temperatures. J Mol Biol. 1995 Feb 3;245(5):559–567. [PubMed] [Google Scholar]
  • Richard-Foy H, Hager GL. Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter. EMBO J. 1987 Aug;6(8):2321–2328. [PMC free article] [PubMed] [Google Scholar]
  • Ronne H. Glucose repression in fungi. Trends Genet. 1995 Jan;11(1):12–17. [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]
  • Russell DW, Smith M, Cox D, Williamson VM, Young ET. DNA sequences of two yeast promoter-up mutants. Nature. 1983 Aug 18;304(5927):652–654. [PubMed] [Google Scholar]
  • Russell DW, Smith M, Williamson VM, Young ET. Nucleotide sequence of the yeast alcohol dehydrogenase II gene. J Biol Chem. 1983 Feb 25;258(4):2674–2682. [PubMed] [Google Scholar]
  • Satchwell SC, Drew HR, Travers AA. Sequence periodicities in chicken nucleosome core DNA. J Mol Biol. 1986 Oct 20;191(4):659–675. [PubMed] [Google Scholar]
  • Satchwell SC, Travers AA. Asymmetry and polarity of nucleosomes in chicken erythrocyte chromatin. EMBO J. 1989 Jan;8(1):229–238. [PMC free article] [PubMed] [Google Scholar]
  • Schild C, Claret FX, Wahli W, Wolffe AP. A nucleosome-dependent static loop potentiates estrogen-regulated transcription from the Xenopus vitellogenin B1 promoter in vitro. EMBO J. 1993 Feb;12(2):423–433. [PMC free article] [PubMed] [Google Scholar]
  • Schmid A, Fascher KD, Hörz W. Nucleosome disruption at the yeast PHO5 promoter upon PHO5 induction occurs in the absence of DNA replication. Cell. 1992 Nov 27;71(5):853–864. [PubMed] [Google Scholar]
  • Schmitt ME, Brown TA, Trumpower BL. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 1990 May 25;18(10):3091–3092. [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]
  • Shuster J, Yu J, Cox D, Chan RV, Smith M, Young E. ADR1-mediated regulation of ADH2 requires an inverted repeat sequence. Mol Cell Biol. 1986 Jun;6(6):1894–1902. [PMC free article] [PubMed] [Google Scholar]
  • Simon M, Adam G, Rapatz W, Spevak W, Ruis H. The Saccharomyces cerevisiae ADR1 gene is a positive regulator of transcription of genes encoding peroxisomal proteins. Mol Cell Biol. 1991 Feb;11(2):699–704. [PMC free article] [PubMed] [Google Scholar]
  • Sledziewski A, Young ET. Chromatin conformational changes accompany transcriptional activation of a glucose-repressed gene in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1982 Jan;79(2):253–256. [PMC free article] [PubMed] [Google Scholar]
  • Straka C, Hörz W. A functional role for nucleosomes in the repression of a yeast promoter. EMBO J. 1991 Feb;10(2):361–368. [PMC free article] [PubMed] [Google Scholar]
  • Svaren J, Hörz W. Histones, nucleosomes and transcription. Curr Opin Genet Dev. 1993 Apr;3(2):219–225. [PubMed] [Google Scholar]
  • Taylor IC, Workman JL, Schuetz TJ, Kingston RE. Facilitated binding of GAL4 and heat shock factor to nucleosomal templates: differential function of DNA-binding domains. Genes Dev. 1991 Jul;5(7):1285–1298. [PubMed] [Google Scholar]
  • Thoma F. Nucleosome positioning. Biochim Biophys Acta. 1992 Feb 28;1130(1):1–19. [PubMed] [Google Scholar]
  • Thomas GH, Elgin SC. Protein/DNA architecture of the DNase I hypersensitive region of the Drosophila hsp26 promoter. EMBO J. 1988 Jul;7(7):2191–2201. [PMC free article] [PubMed] [Google Scholar]
  • Travers AA. The reprogramming of transcriptional competence. Cell. 1992 May 15;69(4):573–575. [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]
  • Truss M, Bartsch J, Schelbert A, Haché RJ, Beato M. Hormone induces binding of receptors and transcription factors to a rearranged nucleosome on the MMTV promoter in vivo. EMBO J. 1995 Apr 18;14(8):1737–1751. [PMC free article] [PubMed] [Google Scholar]
  • Tsukiyama T, Becker PB, Wu C. ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor. Nature. 1994 Feb 10;367(6463):525–532. [PubMed] [Google Scholar]
  • van Holde KE, Lohr DE, Robert C. What happens to nucleosomes during transcription? J Biol Chem. 1992 Feb 15;267(5):2837–2840. [PubMed] [Google Scholar]
  • Varga-Weisz PD, Blank TA, Becker PB. Energy-dependent chromatin accessibility and nucleosome mobility in a cell-free system. EMBO J. 1995 May 15;14(10):2209–2216. [PMC free article] [PubMed] [Google Scholar]
  • Venditti P, Costanzo G, Negri R, Camilloni G. ABFI contributes to the chromatin organization of Saccharomyces cerevisiae ARS1 B-domain. Biochim Biophys Acta. 1994 Nov 22;1219(3):677–689. [PubMed] [Google Scholar]
  • Venditti S, Camilloni G. In vivo analysis of chromatin following nystatin-mediated import of active enzymes into Saccharomyces cerevisiae. Mol Gen Genet. 1994 Jan;242(1):100–104. [PubMed] [Google Scholar]
  • Venter U, Svaren J, Schmitz J, Schmid A, Hörz W. A nucleosome precludes binding of the transcription factor Pho4 in vivo to a critical target site in the PHO5 promoter. EMBO J. 1994 Oct 17;13(20):4848–4855. [PMC free article] [PubMed] [Google Scholar]
  • Iyer V, Struhl K. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 1995 Jun 1;14(11):2570–2579. [PMC free article] [PubMed] [Google Scholar]
  • Wall G, Varga-Weisz PD, Sandaltzopoulos R, Becker PB. Chromatin remodeling by GAGA factor and heat shock factor at the hypersensitive Drosophila hsp26 promoter in vitro. EMBO J. 1995 Apr 18;14(8):1727–1736. [PMC free article] [PubMed] [Google Scholar]
  • Williamson VM, Young ET, Ciriacy M. Transposable elements associated with constitutive expression of yeast alcohol dehydrogenase II. Cell. 1981 Feb;23(2):605–614. [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]
  • Wu C. The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature. 1980 Aug 28;286(5776):854–860. [PubMed] [Google Scholar]
  • Yenidunya A, Davey C, Clark D, Felsenfeld G, Allan J. Nucleosome positioning on chicken and human globin gene promoters in vitro. Novel mapping techniques. J Mol Biol. 1994 Apr 8;237(4):401–414. [PubMed] [Google Scholar]
  • Young T, Williamson V, Taguchi A, Smith M, Sledziewski A, Russell D, Osterman J, Denis C, Cox D, Beier D. The alcohol dehydrogenase genes of the yeast, Saccharomyces cerevisiae: isolation, structure, and regulation. Basic Life Sci. 1982;19:335–361. [PubMed] [Google Scholar]
  • Yu J, Donoviel MS, Young ET. Adjacent upstream activation sequence elements synergistically regulate transcription of ADH2 in Saccharomyces cerevisiae. Mol Cell Biol. 1989 Jan;9(1):34–42. [PMC free article] [PubMed] [Google Scholar]
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