title: Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins.
abstract: Genome structure and gene expression depend on a multitude of chromatin-binding proteins. The binding properties of these proteins to native chromatin in intact cells are largely unknown. Here, we describe an approach based on combined in vivo photobleaching microscopy and kinetic modeling to analyze globally the dynamics of binding of chromatin-associated proteins in living cells. We have quantitatively determined basic biophysical properties, such as off rate constants, residence time, and bound fraction, of a wide range of chromatin proteins of diverse functions in vivo. We demonstrate that most chromatin proteins have a high turnover on chromatin with a residence time on the order of seconds, that the major fraction of each protein is bound to chromatin at steady state, and that transient binding is a common property of chromatin-associated proteins. Our results indicate that chromatin-binding proteins find their binding sites by three-dimensional scanning of the genome space and our data are consistent with a model in which chromatin-associated proteins form dynamic interaction networks in vivo. We suggest that these properties are crucial for generating high plasticity in genome expression.
authors.affiliation: BioInformatics Services, Rockville, MD 20854, USA.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Phair
authors.forename: Paola
authors.initials: P
authors.lastname: Scaffidi
authors.forename: Cem
authors.initials: C
authors.lastname: Elbi
authors.forename: Jaromíra
authors.initials: J
authors.lastname: Vecerová
authors.forename: Anup
authors.initials: A
authors.lastname: Dey
authors.forename: Keiko
authors.initials: K
authors.lastname: Ozato
authors.forename: David T
authors.initials: DT
authors.lastname: Brown
authors.forename: Gordon
authors.initials: G
authors.lastname: Hager
authors.forename: Michael
authors.initials: M
authors.lastname: Bustin
authors.forename: Tom
authors.initials: T
authors.lastname: Misteli
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D036681:Fluorescence Recovery After Photobleaching; D016678:Genome; D006801:Humans; D008954:Models, Biological; D011485:Protein Binding; D011993:Recombinant Fusion Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D011993:Recombinant Fusion Proteins