title: ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin.
abstract: 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.
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280.
authors.forename: Josh
authors.initials: J
authors.lastname: Lawrimore
authors.affiliation: Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280.
authors.forename: Joseph K
authors.initials: JK
authors.lastname: Aicher
authors.affiliation: Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280.
authors.forename: Patrick
authors.initials: P
authors.lastname: Hahn
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280.
authors.forename: Alyona
authors.initials: A
authors.lastname: Fulp
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280.
authors.forename: Ben
authors.initials: B
authors.lastname: Kompa
authors.affiliation: Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280.
authors.forename: Leandra
authors.initials: L
authors.lastname: Vicci
authors.affiliation: Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280.
authors.forename: Michael
authors.initials: M
authors.lastname: Falvo
authors.affiliation: Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280.
authors.forename: Russell M
authors.initials: RM
authors.lastname: Taylor
authors.affiliation: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280 kerry_bloom@unc.edu.
authors.forename: Kerry
authors.initials: K
authors.lastname: Bloom
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018797:Cell Cycle Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D002503:Centromere / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018386:Kinetochores / Q000737:chemistry / Q000378:metabolism; D008870:Microtubules / Q000378:metabolism; D008957:Models, Genetic; D056004:Molecular Dynamics Simulation; D046912:Multiprotein Complexes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004718:Saccharomycetales / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008941:Spindle Apparatus / Q000378:metabolism; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D000097722:Cohesins
chemical_list: D000251:Adenosine Triphosphatases; D018797:Cell Cycle Proteins; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D004247:DNA; D004268:DNA-Binding Proteins; D046912:Multiprotein Complexes; D000097722:Cohesins; C108312:condensin complexes