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PMID: 1915278 Published · ppublish English Journal Article

Nucleosomes are positioned with base pair precision adjacent to the alpha 2 operator in Saccharomyces cerevisiae.

The EMBO journal ·Vol. 10 ·No. 10 ·1991-10-00 ·Pages 3033-41

Shimizu M, Roth SY, Szent-Gyorgyi C, Simpson RT

Abstract

Analysis of the chromatin structure of minichromosomes containing the binding site for the yeast alpha 2 repressor protein by indirect end-labeling has previously indicated that nucleosomes are stably positioned over sequences adjacent to the alpha 2 operator in the presence of the repressor. Development of a primer extension assay for nucleosome position now allows a more detailed examination of the location of these nucleosomes relative to the operator sequence, and indicates that nucleosomes are precisely and stably positioned both translationally and rotationally over sequences adjoining the operator. In addition, this assay enables analysis of the chromatin structure of single copy, genomic sequences. Chromatin structures determined for two genes regulated by alpha 2, STE6 and BAR1, are consistent with nucleosomes precisely positioned downstream of the operator sequence, incorporating promoter elements, in alpha cells but not in a-cells. The location of these nucleosomes relative to the operator sequence is highly analogous to that observed in the minichromosome. The stability of the nucleosomes adjacent to the operator together with the precision of their location suggests that they may play a role in repression of a specific gene expression by alpha 2. Further, the primer extension assay allows a comparison of the structure of these positioned nucleosomes formed in vivo to that previously described for core particles reconstituted in vitro.

Related Genes
BAR1 STE6
MeSH Terms
Base Composition Base Sequence Chromatin DNA, Fungal/genetics Genes, Fungal Molecular Sequence Data Nucleosomes Operator Regions, Genetic Plasmids Saccharomyces cerevisiae/genetics
Chemicals
Chromatin DNA, Fungal Nucleosomes
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Shimizu M
Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.
Roth S Y
Szent-Gyorgyi C
Simpson R T
References (44)
44 references, click to expand
  1. Nucleosome positioning: occurrence, mechanisms, and functional consequences.
    Prog Nucleic Acid Res Mol Biol. 1991;40:143-84 PMID: 2031082
  2. Yeast alpha 2 repressor positions nucleosomes in TRP1/ARS1 chromatin.
    Mol Cell Biol. 1990 May;10(5):2247-60 PMID: 2183026
  3. Histone function in transcription.
    Annu Rev Cell Biol. 1990;6:643-78 PMID: 2275823
  4. Nucleosomes are phased along the mouse beta-major globin gene in erythroid and nonerythroid cells.
    Cell. 1986 Mar 14;44(5):697-704 PMID: 3081263
  5. A regulatory hierarchy for cell specialization in yeast.
    Nature. 1989 Dec 14;342(6251):749-57 PMID: 2513489
  6. 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
  7. 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):2536-40 PMID: 3517872
  8. DNA bending and its relation to nucleosome positioning.
    J Mol Biol. 1985 Dec 20;186(4):773-90 PMID: 3912515
  9. 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):237-47 PMID: 3893743
  10. Local protein-DNA interactions may determine nucleosome positions on yeast plasmids.
    Nature. 1985 May 16-22;315(6016):250-2 PMID: 3889654
  11. New approaches to chromatin function.
    New Biol. 1990 Mar;2(3):211-8 PMID: 2279025
  12. The Saccharomyces cerevisiae BAR1 gene encodes an exported protein with homology to pepsin.
    Proc Natl Acad Sci U S A. 1988 Jan;85(1):55-9 PMID: 3124102
  13. DNA sequencing with Thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reaction-amplified DNA.
    Proc Natl Acad Sci U S A. 1988 Dec;85(24):9436-40 PMID: 3200828
  14. 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 PMID: 2159934
  15. Nucleosome positioning modulates accessibility of regulatory proteins to the mouse mammary tumor virus promoter.
    Cell. 1990 Mar 9;60(5):719-31 PMID: 2155706
  16. In vivo degradation of a transcriptional regulator: the yeast alpha 2 repressor.
    Cell. 1990 May 18;61(4):697-708 PMID: 2111732
  17. Transcriptional repression in eukaryotes.
    Trends Genet. 1990 Jun;6(6):192-7 PMID: 2196723
  18. Nucleosome positioning can affect the function of a cis-acting DNA element in vivo.
    Nature. 1990 Jan 25;343(6256):387-9 PMID: 2405281
  19. The organization of oligonucleosomes in yeast.
    Nucleic Acids Res. 1983 Jun 11;11(11):3717-36 PMID: 6344013
  20. Structural features of a phased nucleosome core particle.
    Proc Natl Acad Sci U S A. 1983 Jan;80(1):51-5 PMID: 6572008
  21. Mapping DNAase l-susceptible sites in nucleosomes labeled at the 5' ends.
    Cell. 1976 Oct;9(2):347-53 PMID: 975247
  22. Quantitative analysis of the digestion of yeast chromatin by staphylococcal nuclease.
    Biochemistry. 1977 Feb 8;16(3):463-71 PMID: 319824
  23. Kinetic analysis of deoxyribonuclease I cleavages in the nucleosome core: evidence for a DNA superhelix.
    J Mol Biol. 1978 Sep 15;124(2):391-420 PMID: 568667
  24. An improved method for photofootprinting yeast genes in vivo using Taq polymerase.
    Nucleic Acids Res. 1989 Jan 11;17(1):171-83 PMID: 2643080
  25. The yeast alpha-factor receptor: structural properties deduced from the sequence of the STE2 gene.
    Nucleic Acids Res. 1985 Dec 9;13(23):8463-75 PMID: 3001640
  26. 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):807-16 PMID: 3061876
  27. Chromatin folding modulates nucleosome positioning in yeast minichromosomes.
    Cell. 1988 Dec 23;55(6):945-53 PMID: 3060264
  28. Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast.
    J Mol Biol. 1988 Nov 5;204(1):109-27 PMID: 3063825
  29. Saccharomyces cerevisiae protein involved in plasmid maintenance is necessary for mating of MAT alpha cells.
    J Mol Biol. 1988 Dec 5;204(3):593-606 PMID: 3066908
  30. The yeast cell-type-specific repressor alpha 2 acts cooperatively with a non-cell-type-specific protein.
    Cell. 1988 Jun 17;53(6):927-36 PMID: 3289753
  31. Transcriptional repression of eukaryotic promoters.
    Cell. 1989 Nov 3;59(3):405-8 PMID: 2572326
  32. The yeast STE6 gene encodes a homologue of the mammalian multidrug resistance P-glycoprotein.
    Nature. 1989 Aug 3;340(6232):400-4 PMID: 2569166
  33. The yeast transcription activator PRTF, a homolog of the mammalian serum response factor, is encoded by the MCM1 gene.
    Genes Dev. 1989 Jul;3(7):936-45 PMID: 2550323
  34. Initiation of transcription on nucleosomal templates.
    Proc Natl Acad Sci U S A. 1989 Dec;86(24):9817-21 PMID: 2690074
  35. Yeast repressor alpha 2 binds to its operator cooperatively with yeast protein Mcm1.
    Mol Cell Biol. 1989 Nov;9(11):5228-30 PMID: 2689875
  36. Genomic footprinting of a yeast tRNA gene reveals stable complexes over the 5'-flanking region.
    Mol Cell Biol. 1989 Aug;9(8):3244-52 PMID: 2677668
  37. Stabilization of Z DNA in vivo by localized supercoiling.
    Science. 1989 Oct 20;246(4928):358-63 PMID: 2678475
  38. A protein involved in minichromosome maintenance in yeast binds a transcriptional enhancer conserved in eukaryotes.
    Genes Dev. 1989 Jul;3(7):921-35 PMID: 2673922
  39. Identification of a DNA segment that is necessary and sufficient for alpha-specific gene control in Saccharomyces cerevisiae: implications for regulation of alpha-specific and a-specific genes.
    Mol Cell Biol. 1988 Jan;8(1):309-20 PMID: 3275872
  40. Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism.
    Nucleic Acids Res. 1988 Jul 25;16(14A):6677-90 PMID: 3399412
  41. A 145-base pair DNA sequence that positions itself precisely and asymmetrically on the nucleosome core.
    EMBO J. 1984 Nov;3(11):2605-11 PMID: 6096135
  42. A yeast operator overlaps an upstream activation site.
    Cell. 1987 Jul 31;50(3):369-77 PMID: 3301002
  43. Sharp boundaries demarcate the chromatin structure of a yeast heat-shock gene.
    J Mol Biol. 1987 Jan 5;193(1):71-80 PMID: 3295258
  44. Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin.
    J Mol Biol. 1986 Jul 20;190(2):177-90 PMID: 3540310
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
0261-4189
Published
1991-10-00
Pages
3033-41
Language
English
Region
England
NLM ID
8208664
PMCID
PMC453018
Subset
IM
External Links
PubMed source PMC Full Text View journal details
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