title: Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast.
abstract: Previous studies indicate that eukaryotic promoters display a stereotypical chromatin landscape characterized by a well-positioned +1 nucleosome near the transcription start site and an upstream -1 nucleosome that together demarcate a nucleosome-free (or -depleted) region. Here we present evidence that there are two distinct types of promoters distinguished by the resistance of the -1 nucleosome to micrococcal nuclease digestion. These different architectures are characterized by two sequence motifs that are broadly deployed at one set of promoters where a nuclease-sensitive ("fragile") nucleosome forms, but concentrated in a narrower, nucleosome-free region at all other promoters. The RSC nucleosome remodeler acts through the motifs to establish stable +1 and -1 nucleosome positions, while binding of a small set of general regulatory (pioneer) factors at fragile nucleosome promoters plays a key role in their destabilization. We propose that the fragile nucleosome promoter architecture is adapted for regulation of highly expressed, growth-related genes.
authors.affiliation: Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland.
authors.forename: Slawomir
authors.initials: S
authors.lastname: Kubik
authors.affiliation: Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland.
authors.forename: Maria Jessica
authors.initials: MJ
authors.lastname: Bruzzone
authors.affiliation: Swiss Institute of Bioinformatics (SIB) and Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Philippe
authors.initials: P
authors.lastname: Jacquet
authors.affiliation: Center for Advanced Modeling Sciences, Computer Science Department, University of Geneva, 7 route de Drize, 1227 Carouge, Switzerland.
authors.forename: Jean-Luc
authors.initials: JL
authors.lastname: Falcone
authors.affiliation: Swiss Institute of Bioinformatics (SIB) and Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
authors.forename: Jacques
authors.initials: J
authors.lastname: Rougemont
authors.affiliation: Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland. Electronic address: David.Shore@unige.ch.
authors.forename: David
authors.initials: D
authors.lastname: Shore
mesh_terms: D015966:Gene Expression Regulation, Fungal / Q000502:physiology*; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000502:physiology*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000096:biosynthesis* / Q000235:genetics
chemical_list: D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins