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ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin

ChromoShake is a three-dimensional simulator designed to find the thermodynamically favored states for given chromosome geometries. The simulator has been applied to a geometric model based on experimentally determined positions and fluctuations of DNA and the distribution of cohesin and condensin i...

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Autores principales: Lawrimore, Josh, Aicher, Joseph K., Hahn, Patrick, Fulp, Alyona, Kompa, Ben, Vicci, Leandra, Falvo, Michael, Taylor, Russell M., Bloom, Kerry
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The American Society for Cell Biology 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4694754/
https://www.ncbi.nlm.nih.gov/pubmed/26538024
http://dx.doi.org/10.1091/mbc.E15-08-0575
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author Lawrimore, Josh
Aicher, Joseph K.
Hahn, Patrick
Fulp, Alyona
Kompa, Ben
Vicci, Leandra
Falvo, Michael
Taylor, Russell M.
Bloom, Kerry
author_facet Lawrimore, Josh
Aicher, Joseph K.
Hahn, Patrick
Fulp, Alyona
Kompa, Ben
Vicci, Leandra
Falvo, Michael
Taylor, Russell M.
Bloom, Kerry
author_sort Lawrimore, Josh
collection PubMed
description ChromoShake is a three-dimensional simulator designed to find the thermodynamically favored states for given chromosome geometries. The simulator has been applied to a geometric model based on experimentally determined positions and fluctuations of DNA and the distribution of cohesin and condensin in the budding yeast centromere. Simulations of chromatin in differing initial configurations reveal novel principles for understanding the structure and function of a eukaryotic centromere. The entropic position of DNA loops mirrors their experimental position, consistent with their radial displacement from the spindle axis. The barrel-like distribution of cohesin complexes surrounding the central spindle in metaphase is a consequence of the size of the DNA loops within the pericentromere to which cohesin is bound. Linkage between DNA loops of different centromeres is requisite to recapitulate experimentally determined correlations in DNA motion. The consequences of radial loops and cohesin and condensin binding are to stiffen the DNA along the spindle axis, imparting an active function to the centromere in mitosis.
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spelling pubmed-46947542016-03-16 ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin Lawrimore, Josh Aicher, Joseph K. Hahn, Patrick Fulp, Alyona Kompa, Ben Vicci, Leandra Falvo, Michael Taylor, Russell M. Bloom, Kerry Mol Biol Cell Articles ChromoShake is a three-dimensional simulator designed to find the thermodynamically favored states for given chromosome geometries. The simulator has been applied to a geometric model based on experimentally determined positions and fluctuations of DNA and the distribution of cohesin and condensin in the budding yeast centromere. Simulations of chromatin in differing initial configurations reveal novel principles for understanding the structure and function of a eukaryotic centromere. The entropic position of DNA loops mirrors their experimental position, consistent with their radial displacement from the spindle axis. The barrel-like distribution of cohesin complexes surrounding the central spindle in metaphase is a consequence of the size of the DNA loops within the pericentromere to which cohesin is bound. Linkage between DNA loops of different centromeres is requisite to recapitulate experimentally determined correlations in DNA motion. The consequences of radial loops and cohesin and condensin binding are to stiffen the DNA along the spindle axis, imparting an active function to the centromere in mitosis. The American Society for Cell Biology 2016-01-01 /pmc/articles/PMC4694754/ /pubmed/26538024 http://dx.doi.org/10.1091/mbc.E15-08-0575 Text en © 2016 Lawrimore et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0). “ASCB®,” “The American Society for Cell Biology®,” and “Molecular Biology of the Cell®” are registered trademarks of The American Society for Cell Biology.
spellingShingle Articles
Lawrimore, Josh
Aicher, Joseph K.
Hahn, Patrick
Fulp, Alyona
Kompa, Ben
Vicci, Leandra
Falvo, Michael
Taylor, Russell M.
Bloom, Kerry
ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin
title ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin
title_full ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin
title_fullStr ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin
title_full_unstemmed ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin
title_short ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin
title_sort chromoshake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4694754/
https://www.ncbi.nlm.nih.gov/pubmed/26538024
http://dx.doi.org/10.1091/mbc.E15-08-0575
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