Finite-Size Conformational Transitions: A Unifying Concept Underlying Chromosome Dynamics

Bertrand R. Caré, Pascal Carrivain, Thierry Forné, Jean-Marc Victor, Annick Lesne
2014 Communications in Theoretical Physics  
Investigating average thermodynamic quantities is not sufficient to understand conformational transitions of a finite-size polymer. We propose that such transitions are better described in terms of the probability distribution of some finite-size order parameter, and the evolution of this distribution as a control parameter varies. We demonstrate this claim for the coil-globule transition of a linear polymer and its mapping onto a two-state model. In a biological context, polymer models
more » ... e the physical constraints experienced by the genome at different levels of organization, from DNA to chromatin to chromosome. We apply our finite-size approach to the formation of plectonemes in a DNA segment submitted to an applied torque and the ensuing helix-coil transition that can be numerically observed, with a coexistence of the helix and coil states in a range of parameters. Polymer models are also essential to analyze recent in vivo experiments providing the frequency of pairwise contacts between genomic loci. The probability distribution of these contacts yields quantitative information on the conformational fluctuations of chromosome regions. The changes observed in the shape of the distribution when the cell type or the physiological conditions vary may reveal an epigenetic modulation of the conformational constraints experienced by the chromosomes. PACS numbers:, 87.15.hp
doi:10.1088/0253-6102/62/4/18 fatcat:mgqr37rcojcqhaid2gdybjiiay