title: Entropy-driven genome organization.
abstract: DNA and RNA polymerases active on bacterial and human genomes in the crowded environment of a cell are modeled as beads spaced along a string. Aggregation of the large polymerizing complexes increases the entropy of the system through an increase in entropy of the many small crowding molecules; this occurs despite the entropic costs of looping the intervening DNA. Results of a quantitative cost/benefit analysis are consistent with observations that active polymerases cluster into replication and transcription "factories" in both pro- and eukaryotes. We conclude that the second law of thermodynamics acts through nonspecific entropic forces between engaged polymerases to drive the self-organization of genomes into loops containing several thousands (and sometimes millions) of basepairs.
authors.affiliation: Mathematics Institute, University of Warwick, Coventry, United Kingdom.
authors.forename: Davide
authors.initials: D
authors.lastname: Marenduzzo
authors.forename: Cristian
authors.initials: C
authors.lastname: Micheletti
authors.forename: Peter R
authors.initials: PR
authors.lastname: Cook
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry*; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry*; D019277:Entropy; D016678:Genome; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA; D012321:DNA-Directed RNA Polymerases; D004259:DNA-Directed DNA Polymerase