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dc.contributor.authorTesoro, Salvatoreen
dc.contributor.authorAli, Ien
dc.contributor.authorMorozov, ANen
dc.contributor.authorSulaiman, Nen
dc.contributor.authorMarenduzzo, Den
dc.date.accessioned2016-01-26T16:58:45Z
dc.date.available2016-01-26T16:58:45Z
dc.date.issued2016-02-12en
dc.identifier.citationTesoro et al. Physical Biology (2016)en
dc.identifier.issn1478-3967
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/253492
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.
dc.description.sponsorshipA. M. acknowledges support form the UK Engineering and Physical Sciences Research Council (EP/I004262/1). S. T. acknowledges support form the UK Engineering and Physical Sciences Research Council (EP/L504920/1).
dc.languageEnglishen
dc.language.isoenen
dc.publisherIOP Science
dc.relation.ispartofhttp://dx.doi.org/10.7488/ds/1331
dc.rightsAttribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.source.urihttp://creativecommons.org/licenses/by/4.0/
dc.titleA 1-dimensional statistical mechanics model for nucleosome positioning on genomic DNAen
dc.typeArticle
dc.description.versionThis is the final version of the article. It first appeared from IOP Science via https://doi.org/10.1088/1478-3975/13/1/016004en
prism.number1-016004en
prism.publicationDate2016en
prism.publicationNamePhysical Biologyen
prism.volume13en
dc.rioxxterms.funderEPSRC
dc.rioxxterms.projectidEP/I004262/1
dc.rioxxterms.projectidEP/L504920/1
rioxxterms.versionofrecord10.1088/1478-3975/13/1/016004en
rioxxterms.versionVoR
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/en
rioxxterms.licenseref.startdate2016-02-12en
dc.contributor.orcidTesoro, Salvatore [0000-0003-4011-366X]
dc.identifier.eissn1478-3975
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idEPSRC (EP/L504920/1)
cam.orpheus.successThu Jan 30 12:55:21 GMT 2020 - The item has an open VoR version.*
rioxxterms.freetoread.startdate2100-01-01


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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International