Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks

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• dc.contributor.author Madrid-Mencía, Miguel
• dc.contributor.author Raineri, Emanuele
• dc.contributor.author Cao, Tran Bich Ngoc
• dc.contributor.author Pancaldi, Vera
• dc.date.accessioned 2020-10-22T06:28:34Z
• dc.date.available 2020-10-22T06:28:34Z
• dc.date.issued 2020
• dc.description.abstract We introduce an R package and a web-based visualization tool for the representation, analysis and integration of epigenomic data in the context of 3D chromatin interaction networks. GARDEN-NET allows for the projection of user-submitted genomic features on pre-loaded chromatin interaction networks, exploiting the functionalities of the ChAseR package to explore the features in combination with chromatin network topology properties. We demonstrate the approach using published epigenomic and chromatin structure datasets in haematopoietic cells, including a collection of gene expression, DNA methylation and histone modifications data in primary healthy myeloid cells from hundreds of individuals. These datasets allow us to test the robustness of chromatin assortativity, which highlights which epigenomic features, alone or in combination, are more strongly associated with 3D genome architecture. We find evidence for genomic regions with specific histone modifications, DNA methylation, and gene expression levels to be forming preferential contacts in 3D nuclear space, to a different extent depending on the cell type and lineage. Finally, we examine replication timing data and find it to be the genomic feature most strongly associated with overall 3D chromatin organization at multiple scales, consistent with previous results from the literature.
• dc.description.sponsorship N.C. acknowledges an Internship scholarship from University of Science and Technology of Hanoi, Vietnam; Spanish Ministry of Economy, Industry and Competitiveness (MEIC) through the Instituto de Salud Carlos III and the 2014–2020 Smart Growth Operating Program [to E.R.]; EMBL partnership and co-financing with the European Regional Development Fund (MINECO/FEDER) [BIO2015-71792-P to E.R.]; Centro de Excelencia Severo Ochoa, and the Generalitat de Catalunya through the Departament de Salut, Departament d’Empresa i Coneixement and the CERCA Programme [to E.R.]; Plan Nacional [PGC2018-099640-B-I00 to E.R.]
• dc.format.mimetype application/pdf
• dc.identifier.citation Madrid-Mencía M, Raineri E, Cao TBN, Pancaldi V. Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks. Nucleic Acids Res. 2020 May 7; 48(8): 4066-4080. DOI: 10.1093/nar/gkaa159
• dc.identifier.doi http://dx.doi.org/10.1093/nar/gkaa159
• dc.identifier.issn 0305-1048
• dc.identifier.uri http://hdl.handle.net/10230/45556
• dc.language.iso eng
• dc.publisher Oxford University Press (OUP)
• dc.relation.ispartof Nucleic Acids Research. 2020 May 7;48(8):4066-80
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BIO2015-71792-P
• dc.rights © Miguel Madrid-Mencía et al 2020. 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
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri https://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.other Epigenòmica
• dc.subject.other Cromatina
• dc.subject.other Expressió gènica
• dc.title Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion