Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast.

Arrays of nucleosomes were positioned with respect to the GAL1-GAL10 intergenic region inserted into Saccharomyces cerevisiae minichromosomes. Deletions of DNA flanking the upstream activation sequence left the array unaltered, showing that nucleosome positioning was not a consequence of sequence-specific histone-DNA interactions but depended on proximity to the galactose-responsive upstream activation sequence (UASG). Replacement of the upstream activation sequence by synthetic oligonucleotides with different protein-binding properties identified a short sequence within this region that is responsible for the ordered array. This sequence overlaps a binding site for GAL4 protein, a positive regulator of transcription, but exerts its effect on chromatin structure independently of GAL4, probably through binding a novel factor that is not GAL-specific.

[1]  K. Murata,et al.  Transformation of intact yeast cells treated with alkali cations , 1983 .

[2]  D. Lohr,et al.  The relationship of regulatory proteins and DNase I hypersensitive sites in the yeast GAL1-10 genes. , 1985, Nucleic acids research.

[3]  D. Lohr.  The chromatin structure of an actively expressed, single copy yeast gene. , 1983, Nucleic acids research.

[4]  A. Hinnen,et al.  Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. , 1986, The EMBO journal.

[5]  H. Martinson,et al.  Nucleosomes will not form on double-stranded RNa or over poly(dA).poly(dT) tracts in recombinant DNA. , 1981, Nucleic acids research.

[6]  H R Drew,et al.  DNA bending and its relation to nucleosome positioning. , 1985, Journal of molecular biology.

[7]  M. Noll,et al.  Multiple phases of nucleosomes in the hsp 70 genes of Drosophila melanogaster. , 1980, Nucleic acids research.

[8]  A. Mirzabekov,et al.  Chromatin structure of hsp 70 genes, activated by heat shock: Selective removal of histones from the coding region and their absence from the 5′ region , 1984, Cell.

[9]  M. Ptashne,et al.  The carboxy-terminal 30 amino acids of GAL4 are recognized by GAL80 , 1987, Cell.

[10]  F. Thoma.  Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin. , 1986, Journal of molecular biology.

[11]  P. Chambon,et al.  Transcription by eukaryotic RNA polymerases A and B of chromatin assembled in vitro. , 1979, European journal of biochemistry.

[12]  D. Chasman,et al.  Interaction of GAL4 and GAL80 gene regulatory proteins in vitro , 1987, Molecular and cellular biology.

[13]  R. W. Davis,et al.  Sequences that regulate the divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae , 1984, Molecular and cellular biology.

[14]  L. Bergman,et al.  Nuclease digestion of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease-sensitive regions. , 1984, Journal of molecular biology.

[15]  H. Zentgraf,et al.  A transcription enhancer acts in vitro over distances of hundreds of base-pairs on both circular and linear templates but not on chromatin-reconstituted DNA. , 1984, Journal of molecular biology.

[16]  W Hörz,et al.  Nuclease hypersensitive regions with adjacent positioned nucleosomes mark the gene boundaries of the PHO5/PHO3 locus in yeast. , 1986, The EMBO journal.

[17]  C. Louis,et al.  Chromatin structure of the histone genes of D. melanogaster , 1981, Cell.

[18]  J. Proffitt.  DNase I-hypersensitive sites in the galactose gene cluster of Saccharomyces cerevisiae , 1985, Molecular and cellular biology.

[19]  M. Ptashne,et al.  Specific DNA binding of GAL4, a positive regulatory protein of yeast , 1985, Cell.

[20]  J. Hopper,et al.  Disruption of regulatory gene GAL80 in Saccharomyces cerevisiae: effects on carbon-controlled regulation of the galactose/melibiose pathway genes , 1984, Molecular and cellular biology.

[21]  V. Zakian,et al.  Construction, replication, and chromatin structure of TRP1 RI circle, a multiple-copy synthetic plasmid derived from Saccharomyces cerevisiae chromosomal DNA , 1982, Molecular and cellular biology.

[22]  A. Laughon,et al.  Identification of two proteins encoded by the Saccharomyces cerevisiae GAL4 gene , 1984, Molecular and cellular biology.

[23]  Sarah C. R. Elgin,et al.  DNAase I-hypersensitive sites of chromatin , 1981, Cell.

[24]  K. Matsumoto,et al.  Recessive mutations conferring resistance to carbon catabolite repression of galactokinase synthesis in Saccharomyces cerevisiae , 1983, Journal of bacteriology.

[25]  D. Botstein,et al.  Structure and function of the yeast URA3 gene. Differentially regulated expression of hybrid beta-galactosidase from overlapping coding sequences in yeast. , 1983, Journal of molecular biology.

[26]  S. Elgin,et al.  Nucleosomal instability and induction of new upstream protein-DNA associations accompany activation of four small heat shock protein genes in Drosophila melanogaster , 1986, Molecular and cellular biology.

[27]  G. Felsenfeld,et al.  A 145‐base pair DNA sequence that positions itself precisely and asymmetrically on the nucleosome core. , 1984, The EMBO journal.

[28]  P. Chomczyński,et al.  Alkaline transfer of DNA to plastic membrane. , 1984, Biochemical and biophysical research communications.

[29]  J. D. Engel,et al.  A 200 base pair region at the 5′ end of the chicken adult β-globin gene is accessible to nuclease digestion , 1981, Cell.

[30]  C. Cantor,et al.  Nucleosomes are phased along the mouse β-major globin gene in erythroid and nonerythroid cells , 1986, Cell.

[31]  E. Blackburn,et al.  Chromatin structure of the telomeric region and 3'-nontranscribed spacer of Tetrahymena ribosomal RNA genes. , 1986, The Journal of biological chemistry.

[32]  R. Firtel,et al.  Site-specific phasing in the chromatin of the rDNA in Dictyostelium discoideum. , 1984, Journal of molecular biology.

[33]  K. Bloom,et al.  Yeast centromere DNA is in a unique and highly ordered structure in chromosomes and small circular minichromosomes , 1982, Cell.

[34]  D. Finkelstein,et al.  Sharp boundaries demarcate the chromatin structure of a yeast heat-shock gene. , 1987, Journal of molecular biology.

[35]  R. Kornberg,et al.  Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones , 1987, Cell.

[36]  T. Matsui.  Transcription of adenovirus 2 major late and peptide IX genes under conditions of in vitro nucleosome assembly , 1987, Molecular and cellular biology.

[37]  J. Gottesfeld,et al.  Assembly of transcriptionally active 5S RNA gene chromatin in vitro , 1982, Cell.

[38]  R. W. Davis,et al.  Rapid DNA isolations for enzymatic and hybridization analysis. , 1980, Methods in enzymology.

[39]  F. Thoma,et al.  Core particle, fiber, and transcriptionally active chromatin structure. , 1986, Annual review of cell biology.

[40]  A. Udvardy,et al.  Chromatin organization of the 87A7 heat shock locus of Drosophila melanogaster. , 1984, Journal of molecular biology.

[41]  F. Thoma,et al.  Local protein–DNA interactions may determine nucleosome positions on yeast plasmids , 1985, Nature.

[42]  S. Johnston,et al.  Interaction of positive and negative regulatory proteins in the galactose regulon of yeast , 1987, Cell.

[43]  A. Feinberg,et al.  A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. , 1983, Analytical biochemistry.

[44]  Carl Wu.  The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I , 1980, Nature.

[45]  S. Nedospasov,et al.  Non-random cleavage of SV40 DNA in the compact minichromosome and free in solution by micrococcal nuclease. , 1980, Biochemical and biophysical research communications.

[46]  L. Lutter.  Kinetic analysis of deoxyribonuclease I cleavages in the nucleosome core: evidence for a DNA superhelix. , 1978, Journal of molecular biology.

[47]  K. Struhl.  Negative control at a distance mediates catabolite repression in yeast , 1985, Nature.

[48]  D. Lohr.  Organization of the GAL1-GAL10 intergenic control region chromatin. , 1984, Nucleic acids research.

[49]  J. Carbon,et al.  Sequence of a yeast DNA fragment containing a chromosomal replicator and the TRP1 gene. , 1980, Gene.

[50]  J. Gralla,et al.  DNA sequence directs placement of histone cores on restriction fragments during nucleosome formation. , 1979, Biochemistry.

[51]  R. W. Davis,et al.  Deletion analysis of the Saccharomyces GAL gene cluster. Transcription from three promoters. , 1981, Journal of molecular biology.

[52]  L. Bergman.  A DNA fragment containing the upstream activator sequence determines nucleosome positioning of the transcriptionally repressed PHO5 gene of Saccharomyces cerevisiae , 1986, Molecular and cellular biology.

[53]  R. Kornberg.  The location of nucleosomes in chromatin: specific or statistical? , 1981, Nature.

[54]  M. Ptashne,et al.  Saccharomyces cerevisiae GAL1-GAL10 divergent promoter region: location and function of the upstream activating sequence UASG , 1984, Molecular and cellular biology.

[55]  H. Richard-Foy,et al.  Sequence‐specific positioning of nucleosomes over the steroid‐inducible MMTV promoter. , 1987, The EMBO journal.

[56]  M. Ptashne,et al.  Use of lacZ fusions to delimit regulatory elements of the inducible divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae , 1984, Molecular and cellular biology.

[57]  T. Cech,et al.  Chromatin structure at the replication origins and transcription-initiation regions of the ribosomal RNA genes of tetrahymena , 1984, Cell.

[58]  G. H. Thomas,et al.  Selected topics in chromatin structure. , 1985, Annual review of genetics.

[59]  T. Cech,et al.  Chromatin structure of the molecular ends of oxytricha macronuclear DNA: phased nucleosomes and a telomeric complex , 1984, Cell.

[60]  J. Knezetic,et al.  The presence of nucleosomes on a DNA template prevents initiation by RNA polymerase II in vitro , 1986, Cell.

[61]  S. Selleck,et al.  In vivo DNA-binding properties of a yeast transcription activator protein , 1987, Molecular and cellular biology.