Modelling of crowded polymers elucidate effects of double-strand breaks in topological domains of bacterial chromosomes.
Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015-Lausanne, Switzerland and Vital-IT, Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland.
Using numerical simulations of pairs of long polymeric chains confined in microscopic cylinders, we investigate consequences of double-strand DNA breaks occurring in independent topological domains, such as these constituting bacterial chromosomes. Our simulations show a transition between segregated and mixed state upon linearization of one of the modelled topological domains. Our results explain how chromosomal organization into topological domains can fulfil two opposite conditions: (i) effectively repulse various loops from each other thus promoting chromosome separation and (ii) permit local DNA intermingling when one or more loops are broken and need to be repaired in a process that requires homology search between broken ends and their homologous sequences in closely positioned sister chromatid.
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