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Topology, structures, and energy landscapes of human chromosomes.

Chromosome conformation capture experiments provide a rich set of data concerning the spatial organization of the genome. We use these data along with a maximum entropy approach to derive a least-biased effective energy landscape for the chromosome. Simulations of the ensemble of chromosome conforma... Full description

Journal Title: Proceedings of the National Academy of Sciences of the United States of America May 12, 2015, Vol.112(19), pp.6062-6067
Main Author: Zhang, Bin
Other Authors: Wolynes, Peter G
Format: Electronic Article Electronic Article
Language: English
Subjects:
DNA
ID: E-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1506257112
Link: http://search.proquest.com/docview/1680956680/?pq-origsite=primo
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title: Topology, structures, and energy landscapes of human chromosomes.
format: Article
creator:
  • Zhang, Bin
  • Wolynes, Peter G
subjects:
  • Cell Differentiation–Chemistry
  • Chromatin–Chemistry
  • Chromosomes–Chemistry
  • Chromosomes, Human–Chemistry
  • DNA–Genetics
  • Gene Expression Regulation–Genetics
  • Genome, Human–Genetics
  • Humans–Genetics
  • Interphase–Genetics
  • Models, Molecular–Genetics
  • Molecular Conformation–Genetics
  • Probability–Genetics
  • Thermodynamics–Genetics
  • Chromatin
  • DNA
  • Chromosome Conformation Capture
  • Liquid Crystal
  • Maximum Entropy
  • Topologically Associating Domains
ispartof: Proceedings of the National Academy of Sciences of the United States of America, May 12, 2015, Vol.112(19), pp.6062-6067
description: Chromosome conformation capture experiments provide a rich set of data concerning the spatial organization of the genome. We use these data along with a maximum entropy approach to derive a least-biased effective energy landscape for the chromosome. Simulations of the ensemble of chromosome conformations based on the resulting information theoretic landscape not only accurately reproduce experimental contact probabilities, but also provide a picture of chromosome dynamics and topology. The topology of the simulated chromosomes is probed by computing the distribution of their knot invariants. The simulated chromosome structures are largely free of knots. Topologically associating domains are shown to be crucial for establishing these knotless structures. The simulated chromosome conformations exhibit a tendency to form fibril-like structures like those observed via light microscopy. The topologically associating domains of the interphase chromosome exhibit multistability with varying liquid crystalline ordering that may allow discrete unfolding events and the landscape is locally funneled toward "ideal" chromosome structures that represent hierarchical fibrils of fibrils. chromosome conformation capture | maximum entropy | topologically associating domains | liquid crystal
language: eng
source:
identifier: E-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1506257112
fulltext: fulltext
issn:
  • 10916490
  • 1091-6490
url: Link


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titleTopology, structures, and energy landscapes of human chromosomes.
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ispartofProceedings of the National Academy of Sciences of the United States of America, May 12, 2015, Vol.112(19), pp.6062-6067
identifierE-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1506257112
subjectCell Differentiation–Chemistry ; Chromatin–Chemistry ; Chromosomes–Chemistry ; Chromosomes, Human–Chemistry ; DNA–Genetics ; Gene Expression Regulation–Genetics ; Genome, Human–Genetics ; Humans–Genetics ; Interphase–Genetics ; Models, Molecular–Genetics ; Molecular Conformation–Genetics ; Probability–Genetics ; Thermodynamics–Genetics ; Chromatin ; DNA ; Chromosome Conformation Capture ; Liquid Crystal ; Maximum Entropy ; Topologically Associating Domains
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descriptionChromosome conformation capture experiments provide a rich set of data concerning the spatial organization of the genome. We use these data along with a maximum entropy approach to derive a least-biased effective energy landscape for the chromosome. Simulations of the ensemble of chromosome conformations based on the resulting information theoretic landscape not only accurately reproduce experimental contact probabilities, but also provide a picture of chromosome dynamics and topology. The topology of the simulated chromosomes is probed by computing the distribution of their knot invariants. The simulated chromosome structures are largely free of knots. Topologically associating domains are shown to be crucial for establishing these knotless structures. The simulated chromosome conformations exhibit a tendency to form fibril-like structures like those observed via light microscopy. The topologically associating domains of the interphase chromosome exhibit multistability with varying liquid crystalline ordering that may allow discrete unfolding events and the landscape is locally funneled toward "ideal" chromosome structures that represent hierarchical fibrils of fibrils. chromosome conformation capture | maximum entropy | topologically associating domains | liquid crystal
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