Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conforma...

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Autores: Serra, François, Baù, Davide, Goodstadt, Michael, Castillo Andreo, David, Filion, Guillaume, Martí Renom, Marc A.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/35026
Acceso en línea:http://hdl.handle.net/10230/35026
http://dx.doi.org/10.1371/journal.pcbi.1005665
Access Level:acceso abierto
Palabra clave:Chromatin
Drosophila melanogaster
Chromosome mapping
Structural genomics
Invertebrate genomics
Mammalian genomics
Genome analysis
Genomic libraries
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spelling Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colorsSerra, FrançoisBaù, DavideGoodstadt, MichaelCastillo Andreo, DavidFilion, GuillaumeMartí Renom, Marc A.ChromatinDrosophila melanogasterChromosome mappingStructural genomicsInvertebrate genomicsMammalian genomicsGenome analysisGenomic librariesThe sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights in the spatial organization of genomes. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions. Our package takes as input the sequencing reads of 3C-based experiments and performs the following main tasks: (i) pre-process the reads, (ii) map the reads to a reference genome, (iii) filter and normalize the interaction data, (iv) analyze the resulting interaction matrices, (v) build 3D models of selected genomic domains, and (vi) analyze the resulting models to characterize their structural properties. To illustrate the use of TADbit, we automatically modeled 50 genomic domains from the fly genome revealing differential structural features of the previously defined chromatin colors, establishing a link between the conformation of the genome and the local chromatin composition. TADbit provides three-dimensional models built from 3C-based experiments, which are ready for visualization and for characterizing their relation to gene expression and epigenetic states. TADbit is an open-source Python library available for download from https://github.com/3DGenomes/tadbit.The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement 609989, the Spanish Ministry of Economy and Competitiveness (BFU2013-47736-P) and the Human Frontiers Science Program (RGP0044). We acknowledge support of the CERCA Programme / Generalitat de Catalunya and the Spanish Ministry of Economy and Competitiveness, 'Centro de Excelencia Severo Ochoa 2013-2017', SEV-2012-0208 to the CRG.Public Library of Science (PLoS)201820182017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/35026http://dx.doi.org/10.1371/journal.pcbi.1005665reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésPLOS Computational Biology. 2017 Jul 19;13(7):e1005665info:eu-repo/grantAgreement/EC/FP7/609989info:eu-repo/grantAgreement/ES/1PE/BFU2013-47736-P© 2017 Serra et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/350262026-05-29T05:05:01Z
dc.title.none.fl_str_mv Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
title Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
spellingShingle Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
Serra, François
Chromatin
Drosophila melanogaster
Chromosome mapping
Structural genomics
Invertebrate genomics
Mammalian genomics
Genome analysis
Genomic libraries
title_short Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
title_full Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
title_fullStr Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
title_full_unstemmed Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
title_sort Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
dc.creator.none.fl_str_mv Serra, François
Baù, Davide
Goodstadt, Michael
Castillo Andreo, David
Filion, Guillaume
Martí Renom, Marc A.
author Serra, François
author_facet Serra, François
Baù, Davide
Goodstadt, Michael
Castillo Andreo, David
Filion, Guillaume
Martí Renom, Marc A.
author_role author
author2 Baù, Davide
Goodstadt, Michael
Castillo Andreo, David
Filion, Guillaume
Martí Renom, Marc A.
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Chromatin
Drosophila melanogaster
Chromosome mapping
Structural genomics
Invertebrate genomics
Mammalian genomics
Genome analysis
Genomic libraries
topic Chromatin
Drosophila melanogaster
Chromosome mapping
Structural genomics
Invertebrate genomics
Mammalian genomics
Genome analysis
Genomic libraries
description The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights in the spatial organization of genomes. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions. Our package takes as input the sequencing reads of 3C-based experiments and performs the following main tasks: (i) pre-process the reads, (ii) map the reads to a reference genome, (iii) filter and normalize the interaction data, (iv) analyze the resulting interaction matrices, (v) build 3D models of selected genomic domains, and (vi) analyze the resulting models to characterize their structural properties. To illustrate the use of TADbit, we automatically modeled 50 genomic domains from the fly genome revealing differential structural features of the previously defined chromatin colors, establishing a link between the conformation of the genome and the local chromatin composition. TADbit provides three-dimensional models built from 3C-based experiments, which are ready for visualization and for characterizing their relation to gene expression and epigenetic states. TADbit is an open-source Python library available for download from https://github.com/3DGenomes/tadbit.
publishDate 2017
dc.date.none.fl_str_mv 2017
2018
2018
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/10230/35026
http://dx.doi.org/10.1371/journal.pcbi.1005665
url http://hdl.handle.net/10230/35026
http://dx.doi.org/10.1371/journal.pcbi.1005665
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv PLOS Computational Biology. 2017 Jul 19;13(7):e1005665
info:eu-repo/grantAgreement/EC/FP7/609989
info:eu-repo/grantAgreement/ES/1PE/BFU2013-47736-P
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science (PLoS)
publisher.none.fl_str_mv Public Library of Science (PLoS)
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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