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Entropy-Driven Genome Organization

Davide Marenduzzo ^*, Cristian Micheletti  and Peter R. Cook 

^* Mathematics Institute, University of Warwick, Coventry, United Kingdom; International School for Advanced Studies (SISSA) and Istituto Nazionale Fisica della Materia (INFM), Trieste, Italy; and Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom

Correspondence: Address reprint requests to P. R. Cook, Sir William Dunn School of Pathology, University of Oxford, South Parks Rd., Oxford, OX1 3RE, UK. Tel.: 44-0-1865-275528; Fax: 44-0-1865-275515; E-mail: peter.cook{at}path.ox.ac.uk.

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.

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