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Chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement

BACKGROUND: 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 o...

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Autores principales: Kinney, Nicholas Allen, Sharakhov, Igor V., Onufriev, Alexey V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5776839/
https://www.ncbi.nlm.nih.gov/pubmed/29357905
http://dx.doi.org/10.1186/s13072-018-0173-5
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author Kinney, Nicholas Allen
Sharakhov, Igor V.
Onufriev, Alexey V.
author_facet Kinney, Nicholas Allen
Sharakhov, Igor V.
Onufriev, Alexey V.
author_sort Kinney, Nicholas Allen
collection PubMed
description BACKGROUND: 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13072-018-0173-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-57768392018-01-31 Chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement Kinney, Nicholas Allen Sharakhov, Igor V. Onufriev, Alexey V. Epigenetics Chromatin Research BACKGROUND: 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13072-018-0173-5) contains supplementary material, which is available to authorized users. BioMed Central 2018-01-22 /pmc/articles/PMC5776839/ /pubmed/29357905 http://dx.doi.org/10.1186/s13072-018-0173-5 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Kinney, Nicholas Allen
Sharakhov, Igor V.
Onufriev, Alexey V.
Chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement
title Chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement
title_full Chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement
title_fullStr Chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement
title_full_unstemmed Chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement
title_short Chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement
title_sort chromosome–nuclear envelope attachments affect interphase chromosome territories and entanglement
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5776839/
https://www.ncbi.nlm.nih.gov/pubmed/29357905
http://dx.doi.org/10.1186/s13072-018-0173-5
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AT onufrievalexeyv chromosomenuclearenvelopeattachmentsaffectinterphasechromosometerritoriesandentanglement