Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure.

Many yeast promoters contain homopolymeric dA:dT sequences that affect nucleosome formation in vitro and are required for wild‐type levels of transcription in vivo. Here, we show that poly(dA:dT) is a novel promoter element whose function depends on its intrinsic structure, not its interaction with sequence‐specific, DNA‐binding proteins. First, poly(dA:dT) stimulates Gcn4‐activated transcription in a manner that is length dependent and inversely related to intracellular Gcn4 levels. Second, Datin, the only known poly(dA:dT)‐binding protein, behaves as a repressor through poly(dA:dT) sequences. Third, poly(dG:dC), a structurally dissimilar homopolymer that also affects nucleosomes, has transcriptional properties virtually identical to those of poly(dA:dT). Three probes of chromatin structure including HinfI endonuclease cleavage in vivo indicate that poly(dA:dT) increases accessibility of the Gcn4 binding site and adjacent sequences in physiological chromatin. These observations suggest that, by virtue of its intrinsic structure, poly(dA:dT) locally affects nucleosomes and increases the accessibility of transcription factors bound to nearby sequences.

[1]  L. Bird,et al.  Chromatin analysis in yeast using NP-40 permeabilised sphaeroplasts. , 1993, Nucleic acids research.

[2]  G. Thireos,et al.  5' untranslated sequences are required for the translational control of a yeast regulatory gene. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[3]  K. Struhl.  Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[4]  L. Bracco,et al.  Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. , 1989, The EMBO journal.

[5]  M. Cerdán,et al.  A hypoxic consensus operator and a constitutive activation region regulate the ANB1 gene of Saccharomyces cerevisiae , 1990, Molecular and cellular biology.

[6]  R. Tjian,et al.  Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. , 1989, Science.

[7]  D. Thiele.  ACE1 regulates expression of the Saccharomyces cerevisiae metallothionein gene , 1988, Molecular and cellular biology.

[8]  Michael E. Smith,et al.  DNA sequences of two yeast promoter-up mutants , 1983, Nature.

[9]  P. Silver,et al.  Context affects nuclear protein localization in Saccharomyces cerevisiae , 1989, Molecular and cellular biology.

[10]  E. Winter,et al.  A DNA binding protein that recognizes oligo(dA).oligo(dT) tracts. , 1989, The EMBO journal.

[11]  S Karlin,et al.  Assessments of DNA inhomogeneities in yeast chromosome III. , 1993, Nucleic acids research.

[12]  K. Struhl,et al.  Saturation mutagenesis of the yeast his3 regulatory site: requirements for transcriptional induction and for binding by GCN4 activator protein. , 1986, Science.

[13]  A. Klar,et al.  Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast. , 1992, Genes & development.

[14]  L. J. Peck,et al.  Sequence dependence of the helical repeat of DNA in solution , 1981, Nature.

[15]  M. Ptashne,et al.  Activators and targets , 1990, Nature.

[16]  K. Struhl,et al.  Functional dissection of the yeast Cyc8–Tupl transcriptional co-repressor complex , 1994, Nature.

[17]  R. W. Davis,et al.  A physical, genetic and transcriptional map of the cloned his3 gene region of Saccharomyces cerevisiae. , 1980, Journal of molecular biology.

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

[19]  D. Reinberg,et al.  Initiation of transcription by RNA polymerase II: a multi-step process. , 1993, Progress in nucleic acid research and molecular biology.

[20]  K. Struhl,et al.  Distinguishing between mechanisms of eukaryotic transcriptional activation with bacteriophage T7 RNA polymerase , 1987, Cell.

[21]  A. Hinnebusch.  Mechanisms of gene regulation in the general control of amino acid biosynthesis in Saccharomyces cerevisiae. , 1988, Microbiological reviews.

[22]  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.

[23]  M. Wigler,et al.  Purification of a RAS-responsive adenylyl cyclase complex from Saccharomyces cerevisiae by use of an epitope addition method , 1988, Molecular and cellular biology.

[24]  K. Struhl.  Molecular mechanisms of transcriptional regulation in yeast. , 1990, Annual review of biochemistry.

[25]  E. Winter,et al.  A peptide motif that recognizes A.T tracts in DNA. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[26]  A. Lipanov,et al.  Poly(dA)\ṁpoly(dT) is a B-type double helix with a distinctively narrow minor groove , 1987, Nature.

[27]  D. Engelke,et al.  Direct sequence and footprint analysis of yeast DNA by primer extension. , 1991, Methods in enzymology.

[28]  K. Struhl,et al.  Increased recruitment of TATA-binding protein to the promoter by transcriptional activation domains in vivo. , 1994, Science.

[29]  A. Hinnebusch.  Evidence for translational regulation of the activator of general amino acid control in yeast. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[30]  R. D. Gietz,et al.  New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. , 1988, Gene.

[31]  S. Buratowski,et al.  The basics of basal transcription by RNA polymerase II , 1994, Cell.

[32]  A. Klug,et al.  The structure of an oligo(dA)·oligo(dT) tract and its biological implications , 1987, Nature.

[33]  R. Conaway,et al.  General initiation factors for RNA polymerase II. , 1993, Annual review of biochemistry.

[34]  M. Behe,et al.  Poly[d(A.T)] and other synthetic polydeoxynucleotides containing oligoadenosine tracts form nucleosomes easily. , 1991, Journal of molecular biology.

[35]  K. Struhl,et al.  The UV response involving the ras signaling pathway and AP-1 transcription factors is conserved between yeast and mammals , 1994, Cell.

[36]  K. Struhl,et al.  Saturation mutagenesis of a yeast his3 "TATA element": genetic evidence for a specific TATA-binding protein. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[37]  R. Simpson,et al.  Cromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence. , 1979, Nucleic acids research.

[38]  H. Drew,et al.  Sequence periodicities in chicken nucleosome core DNA. , 1986, Journal of molecular biology.

[39]  K. Struhl,et al.  Mutations in the bZIP domain of yeast GCN4 that alter DNA-binding specificity. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[40]  D. Hamer,et al.  Copper activates metallothionein gene transcription by altering the conformation of a specific DNA binding protein , 1988, Cell.

[41]  J. Greenblatt,et al.  Initiation of transcription by RNA polymerase II is limited by melting of the promoter DNA in the region immediately upstream of the initiation site. , 1994, The Journal of biological chemistry.

[42]  S. Jayasena,et al.  Competitive nucleosome reconstitution of polydeoxynucleotides containing oligoguanosine tracts. , 1989, Journal of molecular biology.

[43]  D. Rhodes,et al.  Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones. , 1979, Nucleic acids research.

[44]  K. Struhl.  Promoter elements, regulatory elements, and chromatin structure of the yeast his3 gene. , 1983, Cold Spring Harbor symposia on quantitative biology.

[45]  A. Klug,et al.  Sequence-dependent helical periodicity of DNA , 1981, Nature.

[46]  O Kennard,et al.  The crystal structure of d(G-G-G-G-C-C-C-C). A model for poly(dG).poly(dC). , 1985, Journal of molecular biology.

[47]  H. Smith,et al.  Cloning and sequencing the HinfI restriction and modification genes. , 1988, Gene.

[48]  D. Crothers,et al.  Synthetic DNA bending sequences increase the rate of in vitro transcription initiation at the Escherichia coli lac promoter. , 1991, Journal of molecular biology.