Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning

Buitrago, Diana; Codó, Laia; Illa, Ricard; Jorge, Pau de; Battistini, Federica; Flores, Oscar; Bayarri, Genis; Royo, Romina; Pino, Marc del; Heath, Simon; Hospital, Adam; Gelpí, Josep Lluís; Brun-Heath, Isabelle; Orozco, Modesto

Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning

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dc.contributor.author Buitrago, Diana
dc.contributor.author Codó, Laia
dc.contributor.author Illa, Ricard
dc.contributor.author Jorge, Pau de
dc.contributor.author Battistini, Federica
dc.contributor.author Flores, Oscar
dc.contributor.author Bayarri, Genis
dc.contributor.author Royo, Romina
dc.contributor.author Pino, Marc del
dc.contributor.author Heath, Simon
dc.contributor.author Hospital, Adam
dc.contributor.author Gelpí, Josep Lluís
dc.contributor.author Brun-Heath, Isabelle
dc.contributor.author Orozco, Modesto
dc.date.accessioned 2020-04-06T10:06:31Z
dc.date.available 2020-04-06T10:06:31Z
dc.date.issued 2019
dc.description.abstract We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models.
dc.description.sponsorship M.O. is an ICREA (Institució Catalana de Recerca i Estudis Avancats) academia researcher; Spanish Ministry of Science [RTI2018-096704-B-100]; Catalan Government [2017-SGR-134]; Instituto de Salud Carlos III–Instituto Nacional de Bioinformática, the European Union's Horizon 2020 research and innovation program, and the Biomolecular and Bioinformatics Resources Platform [ISCIII PT 17/0009/0007 co-funded by the Fondo Europeo de Desarrollo Regional FEDER; Grants Elixir-Excelerate: 676559 and BioExcel2: 823830; ERC:812850; MuG-676566]; MINECO Severo Ochoa Award of Excellence from the Government of Spain (awarded to IRB Barcelona). Funding for open access charge: Spanish Ministry of Science [RTI2018-096704-B-100].
dc.format.mimetype application/pdf
dc.identifier.citation Buitrago D, Codó L, Illa R, de Jorge P, Battistini F, Flores O, Bayarri G, Royo R, Del Pino M, Heath S, Hospital A, Gelpí JL, Heath IB, Orozco M. Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning. Nucleic Acids Res. 2019; 47(18):9511-23. DOI: 10.1093/nar/gkz759
dc.identifier.doi http://dx.doi.org/10.1093/nar/gkz759
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10230/44159
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Nucleic Acids Res. 2019; 47(18):9511-23
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/676559
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/823830
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/812850
dc.rights © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
dc.subject.keyword Computational methods
dc.subject.keyword Chromatin and epigenetics
dc.subject.keyword Genomics
dc.title Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning
dc.type info:eu-repo/semantics/article
dc.type.version info:eu-repo/semantics/publishedVersion

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