Nucleosome positions alone can be used to predict domains in yeast chromosomes
Depositor | dc.contributor | Brackley, Chris | |
Funder | dc.contributor.other | ERC - European Research Council | en_UK |
Data Creator | dc.creator | Wiese, Oliver | |
Data Creator | dc.creator | Marenduzzo, Davide | |
Data Creator | dc.creator | Brackley, Chris | |
Date Accessioned | dc.date.accessioned | 2019-08-21T10:26:14Z | |
Date Available | dc.date.available | 2019-08-21T10:26:14Z | |
Citation | dc.identifier.citation | Wiese, 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 Identifier | dc.identifier.uri | http://hdl.handle.net/10283/3401 | |
Persistent Identifier | dc.identifier.uri | https://doi.org/10.7488/ds/2610 | |
Dataset Description (abstract) | dc.description.abstract | Simulation 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.tableofcontents | This 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 |
Language | dc.language.iso | eng | en_UK |
Publisher | dc.publisher | University of Edinburgh. School of Physics and Astronomy | en_UK |
Relation (Is Referenced By) | dc.relation.isreferencedby | https://doi.org/10.1073/pnas.1817829116 | en_UK |
Rights | dc.rights | Creative Commons Attribution 4.0 International Public License | en |
Subject | dc.subject | chromatin domains | en_UK |
Subject | dc.subject | polymer simulations | en_UK |
Subject | dc.subject | MicroC | en_UK |
Subject Classification | dc.subject.classification | Physical Sciences | en_UK |
Title | dc.title | Nucleosome positions alone can be used to predict domains in yeast chromosomes | en_UK |
Type | dc.type | dataset | en_UK |
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