title: Models of transcription factor binding: sensitivity of activation functions to model assumptions.
abstract: We present three models of how transcription factors (TFs) bind to their specific binding sites on the DNA: a model based on statistical physics, a Markov-chain model and a computational simulation. Comparison of these models suggests that the effect of non-specific binding can be significant. We also investigate possible mechanisms for cooperativity. The simulation model suggests that direct interactions between TFs are unlikely to be the main source of cooperativity between specific binding sites, because such interactions tend to lead to the formation of clusters on the DNA with undesirable side-effects.
authors.affiliation: Computing Laboratory, University of Kent, CT2 7NF, Canterbury, UK. D.F.Chu@kent.ac.uk
authors.forename: Dominique
authors.initials: D
authors.lastname: Chu
authors.forename: Nicolae Radu
authors.initials: NR
authors.lastname: Zabet
authors.forename: Boris
authors.initials: B
authors.lastname: Mitavskiy
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000378:metabolism; D006801:Humans; D008390:Markov Chains; D008957:Models, Genetic; D015233:Models, Statistical; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA