title: Establishing nucleosome architecture and stability at promoters: Roles of pioneer transcription factors and the RSC chromatin remodeler.
abstract: Improvements in deep sequencing, together with methods to rapidly deplete essential transcription factors (TFs) and chromatin remodelers, have recently led to a more detailed picture of promoter nucleosome architecture in yeast and its relationship to transcriptional regulation. These studies revealed that ∼40% of all budding yeast protein-coding genes possess a unique promoter structure, where we propose that an unusually unstable nucleosome forms immediately upstream of the transcription start site (TSS). This "fragile" nucleosome (FN) promoter architecture relies on the combined action of the essential RSC (Remodels Structure of Chromatin) nucleosome remodeler and pioneer transcription factors (PTFs). FNs are associated with genes whose expression is high, coupled to cell growth, and characterized by low cell-to-cell variability (noise), suggesting that they may promote these features. Recent studies in metazoans suggest that the presence of dynamic nucleosomes upstream of the TSS at highly expressed genes may be conserved throughout evolution.
authors.affiliation: Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, 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), University of Geneva, Geneva, Switzerland.
authors.forename: Maria Jessica
authors.initials: MJ
authors.lastname: Bruzzone
authors.affiliation: Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.
authors.forename: David
authors.initials: D
authors.lastname: Shore
mesh_terms: D000818:Animals; D042002:Chromatin Assembly and Disassembly / Q000235:genetics; D002873:Chromosome Fragility / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D005800:Genes, Fungal; D006801:Humans; D008957:Models, Genetic; D009707:Nucleosomes / Q000235:genetics*; D010944:Plants / Q000235:genetics; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D012568:Schizosaccharomyces / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D009707:Nucleosomes; C103337:RSC complex, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors
keywords: MNase digestion; chromatin; chromatin remodeler; fragile nucleosome; nucleosome; pioneer transcription factor; transcription