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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Detalhes bibliográficos
Autores: Madrid, Miguel|||0000-0002-3998-5316, Raineri, Emanuele, Cao, Tran Bich Ngoc, Pancaldi, Vera|||0000-0002-7433-624X
Tipo de documento: artigo
Data de publicação:2020
País:España
Recursos:Universitat Politècnica de Catalunya (UPC)
Repositório:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglês
OAI Identifier:oai:upcommons.upc.edu:2117/189644
Acesso em linha:https://hdl.handle.net/2117/189644
https://dx.doi.org/10.1093/nar/gkaa159
Access Level:Acceso aberto
Palavra-chave:Chromatin
Epigenetics
Bone marrow cell
Chromatin assembly and disassembly
Chromatin structure
DNA methylation
DNA replication timing
Gene expression level
Hematopoietic cell
Histone modification
ADN
ADN -- Estructura -- Mètodes de simulació
Cèl·lules
Epigenètica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
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repository_id_str
spelling Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networksMadrid, Miguel|||0000-0002-3998-5316Raineri, EmanueleCao, Tran Bich NgocPancaldi, Vera|||0000-0002-7433-624XChromatinEpigeneticsBone marrow cellChromatin assembly and disassemblyChromatin structureDNA methylationDNA replication timingEpigeneticsGene expression levelHematopoietic cellHistone modificationADNADN -- Estructura -- Mètodes de simulacióCèl·lulesEpigenèticaÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::BioinformàticaWe 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. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.INSERM; Fondation Toulouse Cancer Santé and Pierre Fabre Research Institute as part of the Chair of Bioinformatics in Oncology of the CRCT [to M.M., V.P.]; BioInfo4Women programme at the Barcelona Supercomputing Center [to V.P.]; 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.]. Funding for open access charge: Chair of Bioinformatics in Oncology of the CRCT [to V.P.].Peer ReviewedOxford University Press (OUP)20202020-05-0720202020-06-01journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfapplication/pdfhttps://hdl.handle.net/2117/189644https://dx.doi.org/10.1093/nar/gkaa159reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2https://creativecommons.org/licenses/by-nc/3.0/es/https://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/1896442026-05-27T15:37:01Z
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, Miguel|||0000-0002-3998-5316
Chromatin
Epigenetics
Bone marrow cell
Chromatin assembly and disassembly
Chromatin structure
DNA methylation
DNA replication timing
Epigenetics
Gene expression level
Hematopoietic cell
Histone modification
ADN
ADN -- Estructura -- Mètodes de simulació
Cèl·lules
Epigenètica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
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, Miguel|||0000-0002-3998-5316
Raineri, Emanuele
Cao, Tran Bich Ngoc
Pancaldi, Vera|||0000-0002-7433-624X
author Madrid, Miguel|||0000-0002-3998-5316
author_facet Madrid, Miguel|||0000-0002-3998-5316
Raineri, Emanuele
Cao, Tran Bich Ngoc
Pancaldi, Vera|||0000-0002-7433-624X
author_role author
author2 Raineri, Emanuele
Cao, Tran Bich Ngoc
Pancaldi, Vera|||0000-0002-7433-624X
author2_role author
author
author
dc.subject.none.fl_str_mv Chromatin
Epigenetics
Bone marrow cell
Chromatin assembly and disassembly
Chromatin structure
DNA methylation
DNA replication timing
Epigenetics
Gene expression level
Hematopoietic cell
Histone modification
ADN
ADN -- Estructura -- Mètodes de simulació
Cèl·lules
Epigenètica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
topic Chromatin
Epigenetics
Bone marrow cell
Chromatin assembly and disassembly
Chromatin structure
DNA methylation
DNA replication timing
Epigenetics
Gene expression level
Hematopoietic cell
Histone modification
ADN
ADN -- Estructura -- Mètodes de simulació
Cèl·lules
Epigenètica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
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. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020-05-07
2020
2020-06-01
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/189644
https://dx.doi.org/10.1093/nar/gkaa159
url https://hdl.handle.net/2117/189644
https://dx.doi.org/10.1093/nar/gkaa159
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2

https://creativecommons.org/licenses/by-nc/3.0/es/

https://creativecommons.org/licenses/by-nc/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2

https://creativecommons.org/licenses/by-nc/3.0/es/
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:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.301603

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