title: Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo.
abstract: Poly(dA.dT) sequences (T-tracts) are abundant genomic DNA elements with unusual properties in vitro and an established role in transcriptional regulation of yeast genes. In vitro T-tracts are rigid, contribute to DNA bending, affect assembly in nucleosomes and generate a characteristic pattern of CPDs (cyclobutane pyrimidine dimers) upon irradiation with UV light (UV photofootprint). In eukaryotic cells, where DNA is packaged in chromatin, the DNA structure of T-tracts is unknown. Here we have used in vivo UV photofootprinting and DNA repair by photolyase to investigate the structure and accessibility of T-tracts in yeast promoters (HIS3, URA3 and ILV1). The same characteristic photofootprints were obtained in yeast and in naked DNA, demonstrating that the unusual T-tract structure exists in living cells. Rapid repair of CPDs in the T-tracts demonstrates that these T-tracts were not folded in nucleosomes. Moreover, neither datin, a T-tract binding protein, nor Gcn5p, a histone acetyltransferase involved in nucleosome remodelling, showed an influence on the structure and accessibility of T-tracts. The data support a contribution of this unusual DNA structure to transcriptional regulation.
authors.affiliation: Institut für Zellbiologie, ETH-Zürich, Hönggerberg, CH-8093 Zürich, Switzerland.
authors.forename: B
authors.initials: B
authors.lastname: Suter
authors.forename: G
authors.initials: G
authors.lastname: Schnappauf
authors.forename: F
authors.initials: F
authors.lastname: Thoma
mesh_terms: D000123:Acetyltransferases / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D015825:Chromosomes, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism / Q000528:radiation effects; D004249:DNA Damage / Q000235:genetics / Q000528:radiation effects; D018983:DNA Footprinting; D004260:DNA Repair / Q000235:genetics; D004271:DNA, Fungal / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism / Q000528:radiation effects; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D004255:Deoxyribodipyrimidine Photo-Lyase / Q000378:metabolism; D050483:Dopamine Plasma Membrane Transport Proteins; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal / Q000235:genetics; D016681:Genome, Fungal; D051548:Histone Acetyltransferases; D006836:Hydro-Lyases / Q000235:genetics; D008562:Membrane Glycoproteins; D026901:Membrane Transport Proteins; D009419:Nerve Tissue Proteins; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000502:physiology*; D018583:Pliability; D011061:Poly A / Q000235:genetics*; D011071:Poly T / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011494:Protein Kinases / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins; D014466:Ultraviolet Rays; D015003:Yeasts / Q000201:enzymology / Q000235:genetics* / Q000528:radiation effects
chemical_list: C060858:DAT1 protein, S cerevisiae; D004271:DNA, Fungal; D004268:DNA-Binding Proteins; D050483:Dopamine Plasma Membrane Transport Proteins; D005656:Fungal Proteins; D008562:Membrane Glycoproteins; D026901:Membrane Transport Proteins; D009419:Nerve Tissue Proteins; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D011061:Poly A; D011071:Poly T; C008950:poly A-T; D000123:Acetyltransferases; D051548:Histone Acetyltransferases; D011494:Protein Kinases; D004255:Deoxyribodipyrimidine Photo-Lyase; D006836:Hydro-Lyases; C021434:imidazoleglycerolphosphate dehydratase