Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)

Cèl·lules mare embrionàries; Seqüenciació d'alt rendiment

Detalles Bibliográficos
Autores: Tian, Tian V, Vidal, Enrique, Graf, Thomas, Stik, Grégoire
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2020
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:11351/6485
Acceso en línea:https://hdl.handle.net/11351/6485
http://hdl.handle.net/11351/6485
Access Level:acceso abierto
Palabra clave:Embriologia
Seqüència de nucleòtids
ANATOMY::Cells::Stem Cells::Pluripotent Stem Cells::Embryonic Stem Cells::Embryoid Bodies
ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT::Investigative Techniques::Genetic Techniques::Sequence Analysis::High-Throughput Nucleotide Sequencing
ANATOMÍA::células::células madre::células madre pluripotentes::células madre embrionarias::cuerpos embrioides
TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS::técnicas de investigación::técnicas genéticas::análisis de secuencias::secuenciación de nucleótidos de alto rendimiento
id ES_4e1d660dfce641dc15311d6de34a3cff
oai_identifier_str oai:recercat.cat:11351/6485
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)
title Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)
spellingShingle Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)
Tian, Tian V
Embriologia
Seqüència de nucleòtids
ANATOMY::Cells::Stem Cells::Pluripotent Stem Cells::Embryonic Stem Cells::Embryoid Bodies
ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT::Investigative Techniques::Genetic Techniques::Sequence Analysis::High-Throughput Nucleotide Sequencing
ANATOMÍA::células::células madre::células madre pluripotentes::células madre embrionarias::cuerpos embrioides
TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS::técnicas de investigación::técnicas genéticas::análisis de secuencias::secuenciación de nucleótidos de alto rendimiento
title_short Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)
title_full Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)
title_fullStr Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)
title_full_unstemmed Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)
title_sort Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)
dc.creator.none.fl_str_mv Tian, Tian V
Vidal, Enrique
Graf, Thomas
Stik, Grégoire
author Tian, Tian V
author_facet Tian, Tian V
Vidal, Enrique
Graf, Thomas
Stik, Grégoire
author_role author
author2 Vidal, Enrique
Graf, Thomas
Stik, Grégoire
author2_role author
author
author
dc.contributor.none.fl_str_mv Institut Català de la Salut
[Tian TV] Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain. [Vidal E, Graf T, Stik G] Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
Vall d'Hebron Barcelona Hospital Campus
dc.subject.none.fl_str_mv Embriologia
Seqüència de nucleòtids
ANATOMY::Cells::Stem Cells::Pluripotent Stem Cells::Embryonic Stem Cells::Embryoid Bodies
ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT::Investigative Techniques::Genetic Techniques::Sequence Analysis::High-Throughput Nucleotide Sequencing
ANATOMÍA::células::células madre::células madre pluripotentes::células madre embrionarias::cuerpos embrioides
TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS::técnicas de investigación::técnicas genéticas::análisis de secuencias::secuenciación de nucleótidos de alto rendimiento
topic Embriologia
Seqüència de nucleòtids
ANATOMY::Cells::Stem Cells::Pluripotent Stem Cells::Embryonic Stem Cells::Embryoid Bodies
ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT::Investigative Techniques::Genetic Techniques::Sequence Analysis::High-Throughput Nucleotide Sequencing
ANATOMÍA::células::células madre::células madre pluripotentes::células madre embrionarias::cuerpos embrioides
TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS::técnicas de investigación::técnicas genéticas::análisis de secuencias::secuenciación de nucleótidos de alto rendimiento
description Cèl·lules mare embrionàries; Seqüenciació d'alt rendiment
publishDate 2020
dc.date.none.fl_str_mv 2020
2021
2021
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 https://hdl.handle.net/11351/6485
http://hdl.handle.net/11351/6485
url https://hdl.handle.net/11351/6485
http://hdl.handle.net/11351/6485
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Journal of Visualized Experiments;158
https://doi.org/10.3791/60960
info:eu-repo/grantAgreement/ES/PE2013-2016/FJCI-2014-22946
info:eu-repo/grantAgreement/EC/FP7/609989
dc.rights.none.fl_str_mv Attribution-NonCommercial-NoDerivatives 3.0 International
https://creativecommons.org/licenses/by-nc-nd/3.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Attribution-NonCommercial-NoDerivatives 3.0 International
https://creativecommons.org/licenses/by-nc-nd/3.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv MyJove Corporation
publisher.none.fl_str_mv MyJove Corporation
dc.source.none.fl_str_mv Scientia
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
_version_ 1869407735337975808
spelling Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)Tian, Tian VVidal, EnriqueGraf, ThomasStik, GrégoireEmbriologiaSeqüència de nucleòtidsANATOMY::Cells::Stem Cells::Pluripotent Stem Cells::Embryonic Stem Cells::Embryoid BodiesANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT::Investigative Techniques::Genetic Techniques::Sequence Analysis::High-Throughput Nucleotide SequencingANATOMÍA::células::células madre::células madre pluripotentes::células madre embrionarias::cuerpos embrioidesTÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS::técnicas de investigación::técnicas genéticas::análisis de secuencias::secuenciación de nucleótidos de alto rendimientoCèl·lules mare embrionàries; Seqüenciació d'alt rendimentCélulas madre embrionarias; Secuenciación de alto rendimientoEmbryonic stem cells; High-throughput sequencingDuring mammalian development, cell fates are determined through the establishment of regulatory networks that define the specificity, timing, and spatial patterns of gene expression. Embryoid bodies (EBs) derived from pluripotent stem cells have been a popular model to study the differentiation of the main three germ layers and to define regulatory circuits during cell fate specification. Although it is well-known that tissue-specific enhancers play an important role in these networks by interacting with promoters, assigning them to their relevant target genes still remains challenging. To make this possible, quantitative approaches are needed to study enhancer-promoter contacts and their dynamics during development. Here, we adapted a 4C method to define enhancers and their contacts with cognate promoters in the EB differentiation model. The method uses frequently cutting restriction enzymes, sonication, and a nested-ligation-mediated PCR protocol compatible with commercial DNA library preparation kits. Subsequently, the 4C libraries are subjected to high-throughput sequencing and analyzed bioinformatically, allowing detection and quantification of all sequences that have contacts with a chosen promoter. The resulting sequencing data can also be used to gain information about the dynamics of enhancer-promoter contacts during differentiation. The technique described for the EB differentiation model is easy to implement.We would like to thank F. Le Dily, R. Stadhouders and members of the Graf laboratory for their advice and discussions. G.S. was supported by a Marie Sklodowska-Curie fellowship (H2020-MSCA-IF-2016, miRStem), T.V.T by a Juan de la Cierva postdoctoral fellowship (MINECO, FJCI-2014-22946). This work was supported by the European Research Council under the 7th Framework Programme FP7 (ERC Synergy Grant 4D-Genome, grant agreement 609989 to T.G.), the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, Centro de Excelencia Severo Ochoa 2013-2017 and CERCA Program Generalitat de Catalunya.MyJove CorporationInstitut Català de la Salut[Tian TV] Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain. [Vidal E, Graf T, Stik G] Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, SpainVall d'Hebron Barcelona Hospital Campus202120212020info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttps://hdl.handle.net/11351/6485http://hdl.handle.net/11351/6485Scientiareponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésJournal of Visualized Experiments;158https://doi.org/10.3791/60960info:eu-repo/grantAgreement/ES/PE2013-2016/FJCI-2014-22946info:eu-repo/grantAgreement/EC/FP7/609989Attribution-NonCommercial-NoDerivatives 3.0 Internationalhttps://creativecommons.org/licenses/by-nc-nd/3.0/info:eu-repo/semantics/openAccessoai:recercat.cat:11351/64852026-05-29T05:05:01Z
score 15.812429

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