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dc.contributor.authorKinney, Nicholas A.en
dc.contributor.authorSharakhov, Igor V.en
dc.contributor.authorOnufriev, Alexey V.en
dc.date.accessioned2018-01-29T13:07:31Zen
dc.date.available2018-01-29T13:07:31Zen
dc.date.issued2018-01-22en
dc.identifier.citationEpigenetics & Chromatin. 2018 Jan 22;11(1):3en
dc.identifier.urihttp://hdl.handle.net/10919/81951en
dc.description.abstractBackground It is well recognized that the interphase chromatin of higher eukaryotes folds into non-random configurations forming territories within the nucleus. Chromosome territories have biologically significant properties, and understanding how these properties change with time during lifetime of the cell is important. Chromosome–nuclear envelope (Chr–NE) interactions play a role in epigenetic regulation of DNA replication, repair, and transcription. However, their role in maintaining chromosome territories remains unclear. Results We use coarse-grained molecular dynamics simulations to study the effects of Chr–NE interactions on the dynamics of chromosomes within a model of the Drosophila melanogaster regular (non-polytene) interphase nucleus, on timescales comparable to the duration of interphase. The model simulates the dynamics of chromosomes bounded by the NE. Initially, the chromosomes in the model are prearranged in fractal-like configurations with physical parameters such as nucleus size and chromosome persistence length taken directly from experiment. Time evolution of several key observables that characterize the chromosomes is quantified during each simulation: chromosome territories, chromosome entanglement, compactness, and presence of the Rabl (polarized) chromosome arrangement. We find that Chr–NE interactions help maintain chromosome territories by slowing down and limiting, but not eliminating, chromosome entanglement on biologically relevant timescales. At the same time, Chr–NE interactions have little effect on the Rabl chromosome arrangement as well as on how chromosome compactness changes with time. These results are rationalized by simple dimensionality arguments, robust to model details. All results are robust to the simulated activity of topoisomerase, which may be present in the interphase cell nucleus. Conclusions Our study demonstrates that Chr–NE attachments may help maintain chromosome territories, while slowing down and limiting chromosome entanglement on biologically relevant timescales. However, Chr–NE attachments have little effect on chromosome compactness or the Rabl chromosome arrangement.en
dc.format.mimetypeapplication/pdfen
dc.language.isoen_USen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleChromosome–nuclear envelope attachments affect interphase chromosome territories and entanglementen
dc.typeArticle - Refereeden
dc.date.updated2018-01-28T09:46:21Zen
dc.description.versionPeer Revieweden
dc.rights.holderThe Author(s)en
dc.contributor.departmentCenter for Soft Matter and Biological Physicsen
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentEntomologyen
dc.contributor.departmentPhysicsen
dc.title.serialEpigenetics & Chromatinen
dc.identifier.doihttps://doi.org/10.1186/s13072-018-0173-5en
dc.type.dcmitypeTexten


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Creative Commons Attribution 4.0 International
License: Creative Commons Attribution 4.0 International