title: Stochastic Model of Supercoiling-Dependent Transcription.
abstract: We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix and that these enzymes bind more favorably to regions where the genome is unwound. Within this model, we show that when the transcriptionally induced flux of supercoiling increases, there is a sharp crossover from a regime where torsional stresses relax quickly and gene transcription is random, to one where gene expression is highly correlated and tightly regulated by supercoiling. In the latter regime, the model displays transcriptional bursts, waves of supercoiling, and up regulation of divergent or bidirectional genes. It also predicts that topological enzymes which relax twist and writhe should provide a pathway to down regulate transcription.
authors.affiliation: SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom.
authors.forename: C A
authors.initials: CA
authors.lastname: Brackley
authors.affiliation: SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom.
authors.forename: J
authors.initials: J
authors.lastname: Johnson
authors.affiliation: Dipartimento di Fisica, Università di Bari and INFN, Sezione di Bari, 70126 Bari, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Bentivoglio
authors.affiliation: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.
authors.forename: S
authors.initials: S
authors.lastname: Corless
authors.affiliation: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.
authors.forename: N
authors.initials: N
authors.lastname: Gilbert
authors.affiliation: Dipartimento di Fisica, Università di Bari and INFN, Sezione di Bari, 70126 Bari, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Gonnella
authors.affiliation: SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom.
authors.forename: D
authors.initials: D
authors.lastname: Marenduzzo
mesh_terms: D004278:DNA, Superhelical; D011401:Promoter Regions, Genetic; D014158:Transcription, Genetic; D015533:Transcriptional Activation
chemical_list: D004278:DNA, Superhelical