Assaying chromatin accessibility using ATAC-seq in invertebrate chordate embryos

Cis-regulatory elements (CREs) are non-coding DNA regions involved in the spatio-temporal regulation of gene expression. Gene regulatory changes drive animal development and play major roles during evolution of animal body plans. Therefore, we believe that determining CREs at different developmental...

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Autores: Magri, Marta Silvia, Jiménez-Gancedo, Sandra, Bertrand, Stephanie, Madgwick, Alicia, Escrivá, Héctor, Lemaire, Patrick, Gómez-Skarmeta, José Luis
Tipo de documento: artigo
Estado:Versão publicada
Data de publicação:2020
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositório:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/198912
Acesso em linha:http://hdl.handle.net/10261/198912
Access Level:Acceso aberto
Palavra-chave:ATAC-seq
Cis-regulatory elements
Invertebrate chordates
Amphioxus
Tunicates
Development
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spelling Assaying chromatin accessibility using ATAC-seq in invertebrate chordate embryosMagri, Marta SilviaJiménez-Gancedo, SandraBertrand, StephanieMadgwick, AliciaEscrivá, HéctorLemaire, PatrickGómez-Skarmeta, José LuisATAC-seqCis-regulatory elementsInvertebrate chordatesAmphioxusTunicatesDevelopmentCis-regulatory elements (CREs) are non-coding DNA regions involved in the spatio-temporal regulation of gene expression. Gene regulatory changes drive animal development and play major roles during evolution of animal body plans. Therefore, we believe that determining CREs at different developmental stages and across animal lineages is critical to understand how evolution operates through development. The Assay for Transposase-Accessible Chromatin followed by high-throughput sequencing (ATAC-seq) is a powerful technique for the study of CREs that takes advantage of Tn5 transposase activity. Starting from fewer than 105 cells, in a 1-day procedure, it is possible to detect, at a genome-wide level, CREs located in open chromatin regions with high resolution. Here, we describe a detailed step-by-step ATAC-seq protocol for invertebrate chordate marine embryos. We have successfully applied this technique to amphioxus and two species of tunicate embryos. We also show an easy workflow to analyze data generated with this technique. Moreover, we point out that this method and our bioinformatic pipeline are efficient to detect CREs associated with Wnt signaling pathway by simply using embryos treated with a drug that perturbs this pathway. This approach can be extended to other signaling pathways and also to embryo mutants for critical genes. Our results therefore demonstrate the power of ATAC-seq for the identification of CREs that play essential functions during animal development in a wide range of invertebrate or vertebrate animals.This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Program (Grant Agreement No. 740041), the Spanish Ministerio de Economía y Competitividad (Grant No. BFU2016-74961-P), and the Andalusian Government (Grant No. BIO-396). This work was also supported by the institutional grant Unidad de Excelencia María de Maeztu (MDM-2016-0687 to the Department of Gene regulation and morphogenesis of Centro Andaluz de Biología del Desarrollo) and by the EMBO short-term fellowship. The laboratory of HE and SB was supported by the Centre National de la Recherche Scientifique (CNRS) and the Agence Nationale de la Recherche (Grant No. ANR-16-CE12-0008-01).Peer reviewedFrontiers MediaEuropean Research CouncilEuropean CommissionMinisterio de Economía y Competitividad (España)Centre National de la Recherche Scientifique (France)Junta de AndalucíaEMBOAgence Nationale de la Recherche (France)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202020202020info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/198912reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/H2020/740041info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2016-74961-Pinfo:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/MDM-2016-0687https://doi.org/10.3389/fcell.2019.00372Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1989122026-05-22T06:33:51Z
dc.title.none.fl_str_mv Assaying chromatin accessibility using ATAC-seq in invertebrate chordate embryos
title Assaying chromatin accessibility using ATAC-seq in invertebrate chordate embryos
spellingShingle Assaying chromatin accessibility using ATAC-seq in invertebrate chordate embryos
Magri, Marta Silvia
ATAC-seq
Cis-regulatory elements
Invertebrate chordates
Amphioxus
Tunicates
Development
title_short Assaying chromatin accessibility using ATAC-seq in invertebrate chordate embryos
title_full Assaying chromatin accessibility using ATAC-seq in invertebrate chordate embryos
title_fullStr Assaying chromatin accessibility using ATAC-seq in invertebrate chordate embryos
title_full_unstemmed Assaying chromatin accessibility using ATAC-seq in invertebrate chordate embryos
title_sort Assaying chromatin accessibility using ATAC-seq in invertebrate chordate embryos
dc.creator.none.fl_str_mv Magri, Marta Silvia
Jiménez-Gancedo, Sandra
Bertrand, Stephanie
Madgwick, Alicia
Escrivá, Héctor
Lemaire, Patrick
Gómez-Skarmeta, José Luis
author Magri, Marta Silvia
author_facet Magri, Marta Silvia
Jiménez-Gancedo, Sandra
Bertrand, Stephanie
Madgwick, Alicia
Escrivá, Héctor
Lemaire, Patrick
Gómez-Skarmeta, José Luis
author_role author
author2 Jiménez-Gancedo, Sandra
Bertrand, Stephanie
Madgwick, Alicia
Escrivá, Héctor
Lemaire, Patrick
Gómez-Skarmeta, José Luis
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv European Research Council
European Commission
Ministerio de Economía y Competitividad (España)
Centre National de la Recherche Scientifique (France)
Junta de Andalucía
EMBO
Agence Nationale de la Recherche (France)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv ATAC-seq
Cis-regulatory elements
Invertebrate chordates
Amphioxus
Tunicates
Development
topic ATAC-seq
Cis-regulatory elements
Invertebrate chordates
Amphioxus
Tunicates
Development
description Cis-regulatory elements (CREs) are non-coding DNA regions involved in the spatio-temporal regulation of gene expression. Gene regulatory changes drive animal development and play major roles during evolution of animal body plans. Therefore, we believe that determining CREs at different developmental stages and across animal lineages is critical to understand how evolution operates through development. The Assay for Transposase-Accessible Chromatin followed by high-throughput sequencing (ATAC-seq) is a powerful technique for the study of CREs that takes advantage of Tn5 transposase activity. Starting from fewer than 105 cells, in a 1-day procedure, it is possible to detect, at a genome-wide level, CREs located in open chromatin regions with high resolution. Here, we describe a detailed step-by-step ATAC-seq protocol for invertebrate chordate marine embryos. We have successfully applied this technique to amphioxus and two species of tunicate embryos. We also show an easy workflow to analyze data generated with this technique. Moreover, we point out that this method and our bioinformatic pipeline are efficient to detect CREs associated with Wnt signaling pathway by simply using embryos treated with a drug that perturbs this pathway. This approach can be extended to other signaling pathways and also to embryo mutants for critical genes. Our results therefore demonstrate the power of ATAC-seq for the identification of CREs that play essential functions during animal development in a wide range of invertebrate or vertebrate animals.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/198912
url http://hdl.handle.net/10261/198912
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/EC/H2020/740041
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2016-74961-P
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/MDM-2016-0687
https://doi.org/10.3389/fcell.2019.00372
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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