title: RNA synthesis is associated with multiple TBP-chromatin binding events.
abstract: Competition ChIP is an experimental method that allows transcription factor (TF) chromatin turnover dynamics to be measured across a genome. We develop and apply a physical model of TF-chromatin competitive binding using chemical reaction rate theory and are able to derive the physical half-life or residence time for TATA-binding protein (TBP) across the yeast genome from competition ChIP data. Using our physical modeling approach where we explicitly include the induction profile of the competitor in the model, we are able to estimate yeast TBP-chromatin residence times as short as 1.3 minutes, demonstrating that competition ChIP is a relatively high temporal-resolution approach. Strikingly, we find a median value of ~5 TBP-chromatin binding events associated with the synthesis of one RNA molecule across Pol II genes, suggesting multiple rounds of pre-initiation complex assembly and disassembly before productive elongation of Pol II is achieved at most genes in the yeast genome.
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
authors.forename: Hussain A
authors.initials: HA
authors.lastname: Zaidi
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
authors.forename: David T
authors.initials: DT
authors.lastname: Auble
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
authors.forename: Stefan
authors.initials: S
authors.lastname: Bekiranov
mesh_terms: D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D005786:Gene Expression Regulation; D008954:Models, Biological; D008956:Models, Chemical; D011485:Protein Binding; D012313:RNA / Q000096:biosynthesis* / Q000235:genetics; D035181:TATA-Box Binding Protein / Q000235:genetics / Q000378:metabolism*; D015003:Yeasts / Q000235:genetics
chemical_list: D002843:Chromatin; D035181:TATA-Box Binding Protein; D012313:RNA