title: Analysis of chromatin binding dynamics using the crosslinking kinetics (CLK) method.
abstract: Transcription factor binding sites in chromatin are routinely inventoried by the chromatin immunoprecipitation assay, and these binding patterns can provide precise and detailed information about cell state. However, some fundamental molecular questions regarding transcription factor function require an understanding of in vivo binding dynamics as well as location information. Here we describe the crosslinking kinetics (CLK) assay, in which the time-dependence of formaldehyde crosslinking is used to extract on- and off-rates for chromatin binding in vivo.
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, United States.
authors.forename: Ramya
authors.initials: R
authors.lastname: Viswanathan
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, United States.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Hoffman
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, United States.
authors.forename: Savera J
authors.initials: SJ
authors.lastname: Shetty
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, United States.
authors.forename: Stefan
authors.initials: S
authors.lastname: Bekiranov
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, United States. Electronic address: auble@virginia.edu.
authors.forename: David T
authors.initials: DT
authors.lastname: Auble
mesh_terms: D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000379:methods; D005557:Formaldehyde / Q000737:chemistry; D005821:Genetic Techniques; D007700:Kinetics; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism; D015003:Yeasts / Q000235:genetics
chemical_list: D002843:Chromatin; D014157:Transcription Factors; D005557:Formaldehyde
keywords: Chromatin immunoprecipitation; Dynamics; Formaldehyde; Kinetic; Method