title: The yeast PHO5 promoter: from single locus to systems biology of a paradigm for gene regulation through chromatin.
abstract: Chromatin dynamics crucially contributes to gene regulation. Studies of the yeast PHO5 promoter were key to establish this nowadays accepted view and continuously provide mechanistic insight in chromatin remodeling and promoter regulation, both on single locus as well as on systems level. The PHO5 promoter is a context independent chromatin switch module where in the repressed state positioned nucleosomes occlude transcription factor sites such that nucleosome remodeling is a prerequisite for and not consequence of induced gene transcription. This massive chromatin transition from positioned nucleosomes to an extensive hypersensitive site, together with respective transitions at the co-regulated PHO8 and PHO84 promoters, became a prime model for dissecting how remodelers, histone modifiers and chaperones co-operate in nucleosome remodeling upon gene induction. This revealed a surprisingly complex cofactor network at the PHO5 promoter, including five remodeler ATPases (SWI/SNF, RSC, INO80, Isw1, Chd1), and demonstrated for the first time histone eviction in trans as remodeling mode in vivo. Recently, the PHO5 promoter and the whole PHO regulon were harnessed for quantitative analyses and computational modeling of remodeling, transcription factor binding and promoter input-output relations such that this rewarding single-locus model becomes a paradigm also for theoretical and systems approaches to gene regulatory networks.
authors.affiliation: Adolf-Butenandt-Institute, Molecular Biology, University of Munich, Munich 80336, Germany pkorber@lmu.de.
authors.forename: Philipp
authors.initials: P
authors.lastname: Korber
authors.affiliation: Faculty of Food Technology and Biotechnology, Laboratory of Biochemistry, University of Zagreb, Zagreb 10000, Croatia pkorber@lmu.de.
authors.forename: Slobodan
authors.initials: S
authors.lastname: Barbaric
mesh_terms: D000135:Acid Phosphatase / Q000235:genetics*; D002843:Chromatin / Q000737:chemistry; D042002:Chromatin Assembly and Disassembly; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D018085:Regulon; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*
chemical_list: D002843:Chromatin; D029701:Saccharomyces cerevisiae Proteins; D000135:Acid Phosphatase; C488916:PHO5 protein, S cerevisiae