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Depositordc.contributorBrackley, Chris
Funderdc.contributor.otherERC - European Research Councilen_UK
Data Creatordc.creatorWiese, Oliver
Data Creatordc.creatorMarenduzzo, Davide
Data Creatordc.creatorBrackley, Chris
Date Accessioneddc.date.accessioned2019-08-21T10:26:14Z
Date Availabledc.date.available2019-08-21T10:26:14Z
Citationdc.identifier.citationWiese, Oliver; Marenduzzo, Davide; Brackley, Chris. (2019). Nucleosome positions alone can be used to predict domains in yeast chromosomes, [dataset]. University of Edinburgh. School of Physics and Astronomy. https://doi.org/10.7488/ds/2610.en
Persistent Identifierdc.identifier.urihttp://hdl.handle.net/10283/3401
Persistent Identifierdc.identifier.urihttps://doi.org/10.7488/ds/2610
Dataset Description (abstract)dc.description.abstractSimulation data related to the project "Nucleosome positions alone can be used to predict domains in yeast chromosomes". DNA is packaged into chromosomes, which are further organized into domains: Regions of the genome which are more likely to self-interact. Domains have been observed in species ranging from bacteria to humans and are thought to play an important role in gene regulation. Yet the mechanisms of domain formation are not fully understood. Here we use computer simulations to investigate domain formation in yeast. Our model reproduces the experimentally observed domains using only nucleosome positioning information as an input, implying that (unlike in higher eukaryotes) domain boundary locations are largely determined at this level. Our results reveal how irregular nucleosome spacing impacts the 3D chromosome organization, pointing to a direct link between nucleosome positioning and genome regulation at the large scale.en_UK
Dataset Description (TOC)dc.description.tableofcontentsThis deposit includes the source data for all figures in the publication. Simulations were performed using the LAMMPS molecular dynamics software; the full set of LAMMPS output trajectories used in the paper are included. Example LAMMPS initial condition and input scripts are included. LAMMPS version 31Mar17 was used. Experimental data used in the work was previously published elsewhere. Full details are given in the README file.en_UK
Languagedc.language.isoengen_UK
Publisherdc.publisherUniversity of Edinburgh. School of Physics and Astronomyen_UK
Relation (Is Referenced By)dc.relation.isreferencedbyhttps://doi.org/10.1073/pnas.1817829116en_UK
Rightsdc.rightsCreative Commons Attribution 4.0 International Public Licenseen
Subjectdc.subjectchromatin domainsen_UK
Subjectdc.subjectpolymer simulationsen_UK
Subjectdc.subjectMicroCen_UK
Subject Classificationdc.subject.classificationPhysical Sciencesen_UK
Titledc.titleNucleosome positions alone can be used to predict domains in yeast chromosomesen_UK
Typedc.typedataseten_UK

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