title: Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association.
abstract: We determined the distribution of repressor-activator protein 1 (Rap1) and the accessory silencing proteins Sir2, Sir3 and Sir4 in vivo on the entire yeast genome, at a resolution of 2 kb. Rap1 is central to the cellular economy during rapid growth, targeting 294 loci, about 5% of yeast genes, and participating in the activation of 37% of all RNA polymerase II initiation events in exponentially growing cells. Although the DNA sequence recognized by Rap1 is found in both coding and intergenic sequences, the binding of Rap1 to the genome was highly specific to intergenic regions with the potential to act as promoters. This global phenomenon, which may be a general characteristic of sequence-specific transcriptional factors, indicates the existence of a genome-wide molecular mechanism for marking promoter regions.
authors.affiliation: Department of Biochemistry, Stanford University, Stanford, California 94305-5428, USA.
authors.forename: J D
authors.initials: JD
authors.lastname: Lieb
authors.forename: X
authors.initials: X
authors.lastname: Liu
authors.forename: D
authors.initials: D
authors.lastname: Botstein
authors.forename: P O
authors.initials: PO
authors.lastname: Brown
mesh_terms: D001665:Binding Sites / Q000235:genetics; D004247:DNA / Q000378:metabolism*; D021901:DNA, Intergenic / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005656:Fungal Proteins / Q000378:metabolism; D005786:Gene Expression Regulation / Q000502:physiology; D005800:Genes, Fungal / Q000502:physiology; D016681:Genome, Fungal; D006019:Glycolysis / Q000235:genetics; D006655:Histone Deacetylases / Q000378:metabolism; D016366:Open Reading Frames / Q000502:physiology; D020161:Physical Chromosome Mapping / Q000379:methods*; D011401:Promoter Regions, Genetic / Q000502:physiology*; D011485:Protein Binding / Q000502:physiology; D012319:RNA Polymerase II / Q000378:metabolism; D012269:Ribosomal Proteins / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D038281:Silent Information Regulator Proteins, Saccharomyces cerevisiae; D056565:Sirtuin 2; D037761:Sirtuins; D016615:Telomere / Q000378:metabolism; D015534:Trans-Activators / Q000378:metabolism
chemical_list: D021901:DNA, Intergenic; D004268:DNA-Binding Proteins; D005656:Fungal Proteins; D012269:Ribosomal Proteins; C084122:SIR3 protein, S cerevisiae; C061573:SIR4 protein, S cerevisiae; D038281:Silent Information Regulator Proteins, Saccharomyces cerevisiae; D015534:Trans-Activators; D004247:DNA; D012319:RNA Polymerase II; C087778:SIR2 protein, S cerevisiae; D056565:Sirtuin 2; D037761:Sirtuins; D006655:Histone Deacetylases