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PMID: 19307305 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Differential cofactor requirements for histone eviction from two nucleosomes at the yeast PHO84 promoter are determined by intrinsic nucleosome stability.

Molecular and cellular biology ·Vol. 29 ·No. 11 ·2009-06-00 ·Pages 2960-81

Wippo CJ, Krstulovic BS, Ertel F, Musladin S, Blaschke D, Stürzl S, Yuan GC, Hörz W, Korber P, Barbaric S

Abstract

We showed previously that the strong PHO5 promoter is less dependent on chromatin cofactors than the weaker coregulated PHO8 promoter. In this study we asked if chromatin remodeling at the even stronger PHO84 promoter was correspondingly less cofactor dependent. The repressed PHO84 promoter showed a short hypersensitive region that was flanked upstream and downstream by a positioned nucleosome and contained two transactivator Pho4 sites. Promoter induction generated an extensive hypersensitive and histone-depleted region, yielding two more Pho4 sites accessible. This remodeling was strictly Pho4 dependent, strongly dependent on the remodelers Snf2 and Ino80 and on the histone acetyltransferase Gcn5, and more weakly on the acetyltransferase Rtt109. Importantly, remodeling of each of the two positioned nucleosomes required Snf2 and Ino80 to different degrees. Only remodeling of the upstream nucleosome was strictly dependent on Snf2. Further, remodeling of the upstream nucleosome was more dependent on Ino80 than remodeling of the downstream nucleosome. Both nucleosomes differed in their intrinsic stabilities as predicted in silico and measured in vitro. The causal relationship between the different nucleosome stabilities and the different cofactor requirements was shown by introducing destabilizing mutations in vivo. Therefore, chromatin cofactor requirements were determined by intrinsic nucleosome stabilities rather than correlated to promoter strength.

MeSH Terms
Base Sequence Binding Sites Chromatin Assembly and Disassembly Gene Expression Regulation, Fungal Histones/metabolism Kinetics Nucleic Acid Conformation Nucleosomes/chemistry,metabolism Promoter Regions, Genetic Proton-Phosphate Symporters/genetics Saccharomyces cerevisiae/genetics Saccharomyces cerevisiae Proteins/genetics,metabolism Sequence Deletion TATA Box/genetics Transcription, Genetic
Chemicals
Histones Nucleosomes PHO84 protein, S cerevisiae Proton-Phosphate Symporters Saccharomyces cerevisiae Proteins
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Wippo Christian J
Adolf-Butenandt-Institut, Universität München, Munich, Germany.
Krstulovic Bojana Silic
Ertel Franziska
Musladin Sanja
Blaschke Dorothea
Stürzl Sabrina
Yuan Guo-Cheng
Hörz Wolfram
Korber Philipp
Barbaric Slobodan
References (85)
85 references, click to expand
  1. Evidence for nucleosome depletion at active regulatory regions genome-wide.
    Nat Genet. 2004 Aug;36(8):900-5 PMID: 15247917
  2. A high-resolution atlas of nucleosome occupancy in yeast.
    Nat Genet. 2007 Oct;39(10):1235-44 PMID: 17873876
  3. ATP-dependent nucleosome remodelling: factors and functions.
    J Cell Sci. 2004 Aug 1;117(Pt 17):3707-11 PMID: 15286171
  4. Comprehensive profiling of histone modifications using a label-free approach and its applications in determining structure-function relationships.
    Anal Chem. 2008 Sep 1;80(17):6698-707 PMID: 18671409
  5. The "megaprimer" method of site-directed mutagenesis.
    Biotechniques. 1990 Apr;8(4):404-7 PMID: 2340178
  6. Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes.
    Mol Cell. 2004 Jun 4;14(5):657-66 PMID: 15175160
  7. The role of chromatin during transcription.
    Cell. 2007 Feb 23;128(4):707-19 PMID: 17320508
  8. Genomic sequence is highly predictive of local nucleosome depletion.
    PLoS Comput Biol. 2008 Jan;4(1):e13 PMID: 18225943
  9. Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex.
    Mol Cell. 2004 Nov 5;16(3):465-77 PMID: 15525518
  10. Essential functional interactions of SAGA, a Saccharomyces cerevisiae complex of Spt, Ada, and Gcn5 proteins, with the Snf/Swi and Srb/mediator complexes.
    Genetics. 1997 Oct;147(2):451-65 PMID: 9335585
  11. Chromatin modifications and their function.
    Cell. 2007 Feb 23;128(4):693-705 PMID: 17320507
  12. Promoter occupancy is a major determinant of chromatin remodeling enzyme requirements.
    Mol Cell Biol. 2005 Apr;25(7):2698-707 PMID: 15767675
  13. The histone chaperone Asf1 increases the rate of histone eviction at the yeast PHO5 and PHO8 promoters.
    J Biol Chem. 2006 Mar 3;281(9):5539-45 PMID: 16407267
  14. An intracellular phosphate buffer filters transient fluctuations in extracellular phosphate levels.
    Proc Natl Acad Sci U S A. 2005 Jul 5;102(27):9565-70 PMID: 15972809
  15. Structure and distribution of specific cis-elements for transcriptional regulation of PHO84 in Saccharomyces cerevisiae.
    Mol Gen Genet. 1995 Dec 10;249(4):406-16 PMID: 8552045
  16. 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):658-67 PMID: 8515443
  17. The phosphatase system in Saccharomyces cerevisiae.
    Genes Genet Syst. 1997 Dec;72(6):323-34 PMID: 9544531
  18. Polyphosphate loss promotes SNF/SWI- and Gcn5-dependent mitotic induction of PHO5.
    Mol Cell Biol. 2003 Jun;23(11):3788-97 PMID: 12748282
  19. A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.
    Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17846-51 PMID: 17101987
  20. Transcription factors vs nucleosomes: regulation of the PHO5 promoter in yeast.
    Trends Biochem Sci. 1997 Mar;22(3):93-7 PMID: 9066259
  21. Restriction nucleases as probes for chromatin structure.
    Methods Mol Biol. 1999;119:417-25 PMID: 10804529
  22. Dynamics of replication-independent histone turnover in budding yeast.
    Science. 2007 Mar 9;315(5817):1405-8 PMID: 17347438
  23. Functional analysis of the DNA-stimulated ATPase domain of yeast SWI2/SNF2.
    Nucleic Acids Res. 1996 Oct 1;24(19):3685-92 PMID: 8871545
  24. 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):4848-55 PMID: 7957054
  25. Nucleosome reconstitution on plasmid-inserted poly(dA) . poly(dT).
    EMBO J. 1982;1(2):173-9 PMID: 6325153
  26. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.
    Genome Res. 2006 Dec;16(12):1517-28 PMID: 17053089
  27. Chromatin remodelling at the PHO8 promoter requires SWI-SNF and SAGA at a step subsequent to activator binding.
    EMBO J. 1999 Nov 15;18(22):6407-14 PMID: 10562552
  28. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome.
    Nature. 2007 Mar 29;446(7135):572-6 PMID: 17392789
  29. Phosphorylation of the transcription factor PHO4 by a cyclin-CDK complex, PHO80-PHO85.
    Science. 1994 Feb 25;263(5150):1153-6 PMID: 8108735
  30. Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication.
    Science. 2007 Feb 2;315(5812):653-5 PMID: 17272723
  31. Analysis of a mutant histone H3 that perturbs the association of Swi/Snf with chromatin.
    Mol Cell Biol. 2004 Jan;24(2):561-72 PMID: 14701730
  32. Effects of Sin- versions of histone H4 on yeast chromatin structure and function.
    EMBO J. 1997 Apr 15;16(8):2086-95 PMID: 9155034
  33. Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1.
    Mol Cell. 2007 Aug 3;27(3):393-405 PMID: 17679090
  34. The transactivation domain of Pho4 is required for nucleosome disruption at the PHO5 promoter.
    EMBO J. 1994 Oct 17;13(20):4856-62 PMID: 7957055
  35. Transcriptional regulation of the yeast PHO8 promoter in comparison to the coregulated PHO5 promoter.
    J Biol Chem. 2000 Jul 28;275(30):22678-85 PMID: 10801809
  36. Acetylation in the globular core of histone H3 on lysine-56 promotes chromatin disassembly during transcriptional activation.
    Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):9000-5 PMID: 18577595
  37. Cooperative Pho2-Pho4 interactions at the PHO5 promoter are critical for binding of Pho4 to UASp1 and for efficient transactivation by Pho4 at UASp2.
    Mol Cell Biol. 1998 May;18(5):2629-39 PMID: 9566882
  38. Nucleosome stability at the yeast PHO5 and PHO8 promoters correlates with differential cofactor requirements for chromatin opening.
    Mol Cell Biol. 2005 Dec;25(24):10755-67 PMID: 16314501
  39. Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites.
    Mol Cell Biol. 2001 Jun;21(11):3830-9 PMID: 11340174
  40. Chromatin decouples promoter threshold from dynamic range.
    Nature. 2008 May 8;453(7192):246-50 PMID: 18418379
  41. Multi-site phosphorylation of Pho4 by the cyclin-CDK Pho80-Pho85 is semi-processive with site preference.
    J Mol Biol. 2001 Mar 9;306(5):997-1010 PMID: 11237614
  42. Identification and distinct regulation of yeast TATA box-containing genes.
    Cell. 2004 Mar 5;116(5):699-709 PMID: 15006352
  43. Exposing the core promoter is sufficient to activate transcription and alter coactivator requirement at RNR3.
    Proc Natl Acad Sci U S A. 2007 May 22;104(21):8833-8 PMID: 17502614
  44. Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements.
    EMBO J. 1986 Oct;5(10):2689-96 PMID: 3536481
  45. Genome-scale identification of nucleosome positions in S. cerevisiae.
    Science. 2005 Jul 22;309(5734):626-30 PMID: 15961632
  46. Global nucleosome occupancy in yeast.
    Genome Biol. 2004;5(9):R62 PMID: 15345046
  47. Continuous histone H2B and transcription-dependent histone H3 exchange in yeast cells outside of replication.
    Mol Cell. 2007 Feb 9;25(3):345-55 PMID: 17289583
  48. SWI/SNF displaces SAGA-acetylated nucleosomes.
    Eukaryot Cell. 2006 Oct;5(10):1738-47 PMID: 17030999
  49. Effectors of lysine 4 methylation of histone H3 in Saccharomyces cerevisiae are negative regulators of PHO5 and GAL1-10.
    J Biol Chem. 2004 Aug 6;279(32):33057-62 PMID: 15180994
  50. A deletion that includes the signal peptidase cleavage site impairs processing, glycosylation, and secretion of cell surface yeast acid phosphatase.
    Mol Cell Biol. 1984 Dec;4(12):2668-75 PMID: 6098819
  51. Activation of the weakly regulated PHO8 promoter in S. cerevisiae: chromatin transition and binding sites for the positive regulatory protein PHO4.
    Nucleic Acids Res. 1992 Mar 11;20(5):1031-8 PMID: 1567507
  52. Redundancy of chromatin remodeling pathways for the induction of the yeast PHO5 promoter in vivo.
    J Biol Chem. 2007 Sep 21;282(38):27610-21 PMID: 17631505
  53. Redundant roles for the TFIID and SAGA complexes in global transcription.
    Nature. 2000 Jun 8;405(6787):701-4 PMID: 10864329
  54. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer.
    Cell. 1999 Jun 25;97(7):843-52 PMID: 10399913
  55. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast.
    Genes Dev. 1997 Jan 1;11(1):83-93 PMID: 9000052
  56. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure.
    EMBO J. 1995 Jun 1;14(11):2570-9 PMID: 7781610
  57. Chromatin remodelling at promoters suppresses antisense transcription.
    Nature. 2007 Dec 13;450(7172):1031-5 PMID: 18075583
  58. Partially phosphorylated Pho4 activates transcription of a subset of phosphate-responsive genes.
    PLoS Biol. 2003 Nov;1(2):E28 PMID: 14624238
  59. Increasing the rate of chromatin remodeling and gene activation--a novel role for the histone acetyltransferase Gcn5.
    EMBO J. 2001 Sep 3;20(17):4944-51 PMID: 11532958
  60. The in vivo functions of ATP-dependent chromatin-remodelling factors.
    Nat Rev Mol Cell Biol. 2002 Jun;3(6):422-9 PMID: 12042764
  61. Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56.
    Science. 2007 Feb 2;315(5812):649-52 PMID: 17272722
  62. Nucleosomes unfold completely at a transcriptionally active promoter.
    Mol Cell. 2003 Jun;11(6):1587-98 PMID: 12820971
  63. Transcription factor access to promoter elements.
    J Cell Biochem. 2007 Oct 15;102(3):560-70 PMID: 17668451
  64. SAGA-associated Sgf73p facilitates formation of the preinitiation complex assembly at the promoters either in a HAT-dependent or independent manner in vivo.
    Nucleic Acids Res. 2006;34(21):6225-32 PMID: 17090597
  65. ATP-dependent nucleosome remodeling.
    Annu Rev Biochem. 2002;71:247-73 PMID: 12045097
  66. Nucleosome positions predicted through comparative genomics.
    Nat Genet. 2006 Oct;38(10):1210-5 PMID: 16964265
  67. Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.
    PLoS Biol. 2008 Mar 18;6(3):e65 PMID: 18351804
  68. A chromatin remodelling complex involved in transcription and DNA processing.
    Nature. 2000 Aug 3;406(6795):541-4 PMID: 10952318
  69. In vitro assembly of the characteristic chromatin organization at the yeast PHO5 promoter by a replication-independent extract system.
    J Biol Chem. 2004 Aug 13;279(33):35113-20 PMID: 15192097
  70. A new procedure for purifying histone pairs H2A + H2B and H3 + H4 from chromatin using hydroxylapatite.
    Nucleic Acids Res. 1979 Feb;6(2):689-96 PMID: 424310
  71. Crystal structure of the nucleosome core particle at 2.8 A resolution.
    Nature. 1997 Sep 18;389(6648):251-60 PMID: 9305837
  72. Regulation of chromatin remodeling by inositol polyphosphates.
    Science. 2003 Jan 3;299(5603):114-6 PMID: 12434012
  73. Rtt109 is required for proper H3K56 acetylation: a chromatin mark associated with the elongating RNA polymerase II.
    J Biol Chem. 2006 Dec 8;281(49):37270-4 PMID: 17046836
  74. The complex language of chromatin regulation during transcription.
    Nature. 2007 May 24;447(7143):407-12 PMID: 17522673
  75. Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes.
    Mol Cell. 2007 Mar 9;25(5):703-12 PMID: 17320445
  76. Role of trans-activating proteins in the generation of active chromatin at the PHO5 promoter in S. cerevisiae.
    EMBO J. 1990 Aug;9(8):2523-8 PMID: 2196175
  77. Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75.
    Nat Struct Mol Biol. 2008 Sep;15(9):948-56 PMID: 19172748
  78. Histone chaperones in nucleosome eviction and histone exchange.
    Curr Opin Struct Biol. 2008 Jun;18(3):282-9 PMID: 18534842
  79. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.
    Genome Res. 2008 Jul;18(7):1073-83 PMID: 18550805
  80. Anatomy of a hypersensitive site.
    Biochim Biophys Acta. 2004 Mar 15;1677(1-3):24-9 PMID: 15020042
  81. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter.
    Mol Cell. 2003 Jun;11(6):1599-607 PMID: 12820972
  82. A genomic code for nucleosome positioning.
    Nature. 2006 Aug 17;442(7104):772-8 PMID: 16862119
  83. Ubp8p, a histone deubiquitinase whose association with SAGA is mediated by Sgf11p, differentially regulates lysine 4 methylation of histone H3 in vivo.
    Mol Cell Biol. 2006 May;26(9):3339-52 PMID: 16611979
  84. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.
    Nature. 2007 Apr 12;446(7137):806-10 PMID: 17314980
  85. The PHO84 gene of Saccharomyces cerevisiae encodes an inorganic phosphate transporter.
    Mol Cell Biol. 1991 Jun;11(6):3229-38 PMID: 2038328
Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
1098-5549
DOI
10.1128/MCB.01054-08
Published
2009-06-00
Epub
2009-00-23
Pages
2960-81
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC2682004
Subset
IM
External Links
PubMed source DOI: 10.1128/MCB.01054-08 PMC Full Text View journal details
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