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Depositordc.contributorMorozov, Alexander
Funderdc.contributor.otherEPSRC - Engineering and Physical Sciences Research Councilen_UK
Spatial Coveragedc.coverage.spatialUKen
Spatial Coveragedc.coverage.spatialUNITED KINGDOMen
Time Perioddc.coverage.temporalstart=2014-01; end=2015-10; scheme=W3C-DTFen
Data Creatordc.creatorTesoro, S
Data Creatordc.creatorAli, I
Data Creatordc.creatorMorozov, Alexander N
Data Creatordc.creatorSulaiman, N
Data Creatordc.creatorMarenduzzo, Davide
Citationdc.identifier.citationTesoro, S; Ali, I; Morozov, AN; Sulaiman, N; Marenduzzo, D. (2016). A 1-dimensional statistical mechanics model for nucleosome positioning on genomic DNA, 2014-2015 [dataset]. University of Edinburgh. School of Physics and Astronomy.
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Dataset Description (abstract)dc.description.abstractThe first level of folding of DNA in eukaryotes is provided by the so-called “10-nm chromatin fibre”, where DNA wraps around histone proteins (∼10 nm in size) to form nucleosomes, which go on to create a zig-zagging bead-on-a-string structure. In this work we present a 1-dimensional statistical mechanics model to study nucleosome positioning within one such 10 nm fibre. We focus on the case of genomic sheep DNA, and we start from effective potentials valid at infinite dilution and determined from high-resolution in vitro salt dialysis experiments. We study positioning within a polynucleosome chain, and compare the results for genomic DNA to that obtained in the simplest case of homogeneous DNA, where the problem can be mapped to a Tonks gas [1]. First, we consider the simple, analytically solvable, case where nucleosomes are assumed to be point-like. Then, we perform numerical simulations to gauge the effect of their finite size on the nucleosomal distribution probabilities. Finally we compare nucleosome distributions and simulated nuclease digestion patterns for the two cases (homogeneous and sheep DNA), thereby providing testable predictions of the effect of sequence on experimentally observable quantities in experiments on polynucleosome chromatin fibres reconstituted in vitro.en_UK
Publisherdc.publisherUniversity of Edinburgh. School of Physics and Astronomyen_UK
Relation (Is Referenced By)dc.relation.isreferencedby
Rightsdc.rightsCreative Commons Attribution 4.0 International Public Licenseen
Subjectdc.subjectnucleosome positioning
Subjectdc.subjectnuclease digestion
Subjectdc.subjectDNA biophysics
Subject Classificationdc.subject.classificationBiological Sciences::Molecular Biology Biophysics and Biochemistryen_UK
Titledc.titleA 1-dimensional statistical mechanics model for nucleosome positioning on genomic DNAen_UK

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