title: Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle.
abstract: Cells decide when, where, and to what level to express their genes by "computing" information from transcription factors (TFs) binding to regulatory DNA. How is the information contained in multiple TF-binding sites integrated to dictate the rate of transcription? The dominant conceptual and quantitative model is that TFs combinatorially recruit one another and RNA polymerase to the promoter by direct physical interactions. Here, we develop a quantitative framework to explore kinetic control, an alternative model in which combinatorial gene regulation can result from TFs working on different kinetic steps of the transcription cycle. Kinetic control can generate a wide range of analog and Boolean computations without requiring the input TFs to be simultaneously bound to regulatory DNA. We propose experiments that will illuminate the role of kinetic control in transcription and discuss implications for deciphering the cis-regulatory "code."
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Clarissa
authors.initials: C
authors.lastname: Scholes
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: angela_depace@hms.harvard.edu.
authors.forename: Angela H
authors.initials: AH
authors.lastname: DePace
authors.affiliation: The Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA. Electronic address: alvaro.sanchez@yale.edu.
authors.forename: Álvaro
authors.initials: Á
authors.lastname: Sánchez
mesh_terms: D000818:Animals; D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000378:metabolism; D005786:Gene Expression Regulation / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D007700:Kinetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors; D004247:DNA
keywords: Boolean computations; combinatorial control; frequency modulation; kinetics; quantitative modeling; transcription