TY - JOUR T1 - Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization A1 - Junier, Ivan A1 - Martin, Olivier A1 - Képès, François Y1 - 2010/02/12 N2 - Author Summary The good operation of cells relies on a coordination between chromosome structure and genetic regulation which is yet to be understood. This can be seen in particular from the transcription machinery: in some eukaryotes and bacteria, transcription of highly active genes occurs within discrete foci called transcription factories, where RNA polymerases, transcription factors and their target genes co-localize. The mechanisms underlying the formation of these foci and the resulting topological structure of the chromosome remain to be elucidated. Here, we propose a thermodynamic framework based on a polymer description of DNA in which genes effectively interact through attractive forces in physical space. The formation of transcription foci then corresponds to a self-organizing process whereby the interacting genes and the non-interacting DNA form two phases that tend to separate. Numerical simulations of the model unveil a rich zoology of the topological ordering of DNA around the foci and show that regularities in the positions of the interacting genes make the spatial co-localization of multiple families of genes particularly efficient. Experimental testing of the predictions of our model should shed new light on the relation between transcriptional regulation and cellular conformations of chromosomes. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 6 IS - 2 UR - https://doi.org/10.1371/journal.pcbi.1000678 SP - e1000678 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1000678 ER -