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

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,...

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Authors: Madrid-Mencía, Miguel, Raineri, Emanuele, Cao, Tran Bich Ngoc, Pancaldi, Vera
Format: article
Status:Published version
Publication Date:2020
Country:España
Institution:Universitat Pompeu Fabra
Repository:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/45556
Online Access:http://hdl.handle.net/10230/45556
http://dx.doi.org/10.1093/nar/gkaa159
Access Level:Open access
Keyword:Epigenòmica
Cromatina
Expressió gènica
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spelling Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networksMadrid-Mencía, MiguelRaineri, EmanueleCao, Tran Bich NgocPancaldi, VeraEpigenòmicaCromatinaExpressió gènicaWe 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.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.]Oxford University Press (OUP)202020202020info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/45556http://dx.doi.org/10.1093/nar/gkaa159reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésNucleic Acids Research. 2020 May 7;48(8):4066-80info:eu-repo/grantAgreement/ES/1PE/BIO2015-71792-P© 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 citedhttps://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/455562026-06-12T07:21:37Z
dc.title.none.fl_str_mv Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks
title Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks
spellingShingle Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks
Madrid-Mencía, Miguel
Epigenòmica
Cromatina
Expressió gènica
title_short Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks
title_full Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks
title_fullStr Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks
title_full_unstemmed Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks
title_sort Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks
dc.creator.none.fl_str_mv Madrid-Mencía, Miguel
Raineri, Emanuele
Cao, Tran Bich Ngoc
Pancaldi, Vera
author Madrid-Mencía, Miguel
author_facet Madrid-Mencía, Miguel
Raineri, Emanuele
Cao, Tran Bich Ngoc
Pancaldi, Vera
author_role author
author2 Raineri, Emanuele
Cao, Tran Bich Ngoc
Pancaldi, Vera
author2_role author
author
author
dc.subject.none.fl_str_mv Epigenòmica
Cromatina
Expressió gènica
topic Epigenòmica
Cromatina
Expressió gènica
description 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.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/45556
http://dx.doi.org/10.1093/nar/gkaa159
url http://hdl.handle.net/10230/45556
http://dx.doi.org/10.1093/nar/gkaa159
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Nucleic Acids Research. 2020 May 7;48(8):4066-80
info:eu-repo/grantAgreement/ES/1PE/BIO2015-71792-P
dc.rights.none.fl_str_mv https://creativecommons.org/licenses/by-nc/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press (OUP)
publisher.none.fl_str_mv Oxford University Press (OUP)
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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