Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes
Deuterostomes are one major group of bilaterians composed by hemichordates and echinoderms (collectively called Ambulacraria) and chordates. Comparative studies between these groups can provide valuable insights into the nature of the last common ancestor of deuterostomes and that of bilaterians. In...
| Autores: | , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2024 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/384517 |
| Acceso en línea: | http://hdl.handle.net/10261/384517 |
| Access Level: | acceso abierto |
| Palabra clave: | Epigenetics Evolutionary biology Evolutionary developmental biology Evolutionary genetics |
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Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes |
| title |
Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes |
| spellingShingle |
Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes Pérez-Posada, Alberto Epigenetics Evolutionary biology Evolutionary developmental biology Evolutionary genetics |
| title_short |
Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes |
| title_full |
Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes |
| title_fullStr |
Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes |
| title_full_unstemmed |
Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes |
| title_sort |
Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes |
| dc.creator.none.fl_str_mv |
Pérez-Posada, Alberto Lin, Che-Yi Fan, Tzu-Pei Lin, Ching-Yi Chen, Yi-Chih Gómez-Skarmeta, José Luis Yu, Jr-Kai Su, Yi-Hsien Tena, Juan J. |
| author |
Pérez-Posada, Alberto |
| author_facet |
Pérez-Posada, Alberto Lin, Che-Yi Fan, Tzu-Pei Lin, Ching-Yi Chen, Yi-Chih Gómez-Skarmeta, José Luis Yu, Jr-Kai Su, Yi-Hsien Tena, Juan J. |
| author_role |
author |
| author2 |
Lin, Che-Yi Fan, Tzu-Pei Lin, Ching-Yi Chen, Yi-Chih Gómez-Skarmeta, José Luis Yu, Jr-Kai Su, Yi-Hsien Tena, Juan J. |
| author2_role |
author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Ministerio de Ciencia y Tecnología (España) Academia Sinica (Taiwan) European Research Council European Commission Ministerio de Ciencia, Innovación y Universidades (España) Agencia Estatal de Investigación (España) Ministerio de Ciencia e Innovación (España) Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] |
| dc.subject.none.fl_str_mv |
Epigenetics Evolutionary biology Evolutionary developmental biology Evolutionary genetics |
| topic |
Epigenetics Evolutionary biology Evolutionary developmental biology Evolutionary genetics |
| description |
Deuterostomes are one major group of bilaterians composed by hemichordates and echinoderms (collectively called Ambulacraria) and chordates. Comparative studies between these groups can provide valuable insights into the nature of the last common ancestor of deuterostomes and that of bilaterians. Indirect development of hemichordates, with larval phases similar to echinoderms and an adult body plan with an anteroposterior polarity like chordates and other bilaterians, makes them a suitable model for studying the molecular basis of development among deuterostomes. However, a comprehensive, quantitative catalogue of gene expression and chromatin dynamics in hemichordates is still lacking. In this study, we analysed the transcriptomes and chromatin accessibility of multiple developmental stages of the indirect-developing hemichordate Ptychodera flava. We observed that P. flava development is underpinned by a biphasic transcriptional program probably controlled by distinct genetic networks. Comparisons with other bilaterian species revealed similar transcriptional and regulatory dynamics during hemichordate gastrulation, cephalochordate neurulation and elongation stages of annelids. By means of regulatory networks analysis and functional validations by transgenesis experiments in echinoderms, we propose that gastrulation is the stage of highest molecular resemblance in deuterostomes and that much of the molecular basis of deuterostome development was probably present in the bilaterian last common ancestor. |
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2024 |
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2024 2025 2025 |
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info:eu-repo/semantics/article http://purl.org/coar/resource_type/c_6501 Publisher's version info:eu-repo/semantics/publishedVersion |
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article |
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publishedVersion |
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http://hdl.handle.net/10261/384517 |
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http://hdl.handle.net/10261/384517 |
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Inglés |
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Inglés |
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#PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/EC/H2020/740041 info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-103921GB-I00 info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2022-141288NB-I00 The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.1038/s41559-024-02562-x Pérez-Posada, Alberto; Lin, Che-Yi; Fan, Tzu-Pei; Lin, Ching-Yi; Chen, Yi-Chih; Gómez-Skarmeta, José Luis; Yu, Jr-Kai; Su, Yi-Hsien; Tena, Juan J.; 2024; Ptychodera flava genomics and transcriptomics data [Dataset]; DIGITAL.CSIC; https://doi.org/10.20350/digitalCSIC/16340 Pérez-Posada, Alberto; Lin, Che-Yi; Fan, Tzu-Pei; Lin, Ching-Yi; Chen, Yi-Chih; Gómez-Skarmeta, José Luis; Yu, Jr-Kai; Su, Yi-Hsien; Tena, Juan J.; 2024; Insights into deuterostome evolution from the biphasic transcriptional programmes of hemichordates [Dataset]; GEO - Gene Expression Omnibus; https://doi.org/10.1038/s41559-024-02562-x Pérez-Posada, Alberto; Lin, Che-Yi; Fan, Tzu-Pei; Lin, Ching-Yi; Chen, Yi-Chih; Gómez-Skarmeta, José Luis; Yu, Jr-Kai; Su, Yi-Hsien; Tena, Juan J.; 2024; Analyses of the Ptychodera flava RNASeq+ATACSeq project [Dataset]; GitHub; https://doi.org/10.1038/s41559-024-02562-x https://doi.org/10.1038/s41559-024-02562-x Sí |
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info:eu-repo/semantics/openAccess |
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openAccess |
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Springer Nature |
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Springer Nature |
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reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC instname:Consejo Superior de Investigaciones Científicas (CSIC) |
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Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomesPérez-Posada, AlbertoLin, Che-YiFan, Tzu-PeiLin, Ching-YiChen, Yi-ChihGómez-Skarmeta, José LuisYu, Jr-KaiSu, Yi-HsienTena, Juan J.EpigeneticsEvolutionary biologyEvolutionary developmental biologyEvolutionary geneticsDeuterostomes are one major group of bilaterians composed by hemichordates and echinoderms (collectively called Ambulacraria) and chordates. Comparative studies between these groups can provide valuable insights into the nature of the last common ancestor of deuterostomes and that of bilaterians. Indirect development of hemichordates, with larval phases similar to echinoderms and an adult body plan with an anteroposterior polarity like chordates and other bilaterians, makes them a suitable model for studying the molecular basis of development among deuterostomes. However, a comprehensive, quantitative catalogue of gene expression and chromatin dynamics in hemichordates is still lacking. In this study, we analysed the transcriptomes and chromatin accessibility of multiple developmental stages of the indirect-developing hemichordate Ptychodera flava. We observed that P. flava development is underpinned by a biphasic transcriptional program probably controlled by distinct genetic networks. Comparisons with other bilaterian species revealed similar transcriptional and regulatory dynamics during hemichordate gastrulation, cephalochordate neurulation and elongation stages of annelids. By means of regulatory networks analysis and functional validations by transgenesis experiments in echinoderms, we propose that gastrulation is the stage of highest molecular resemblance in deuterostomes and that much of the molecular basis of deuterostome development was probably present in the bilaterian last common ancestor.This study was supported by the Ministry of Science and Technology, Taiwan (grant no. MOST-110-2326-B-001-006 to Y.-H.S. and grant no. MOST-110-2621-B-001-001-MY3 to J.-K.Y.) and Academia Sinica (AS-GC-111-L01 to Y.-H.S. and J.-K.Y.). J.J.T. and J.L.G.S. were supported by the European Research Council (grant agreement no. 740041) and the Spanish Ministerio de Economía y Competitividad (grant no. PID2019-103921GB-I00). J.J.T. was also funded by the Spanish Ministerio de Ciencia e Innovación (grant no. PID2022-141288NB-I00). We thank A. G. Galvez and P. Firbas for advice with the analyses and M. Van der Sande, S. Frolich and S. Van Heeringen, for their advice with ANANSE. A.P.-P. thanks the rest of the authors and all the members of the Skarmeta/Tena laboratory, as well as J. Solana, D. Salamanca-Diaz and M. Rosselló, for their support during the difficult times of this project.Peer reviewedSpringer NatureMinisterio de Ciencia y Tecnología (España)Academia Sinica (Taiwan)European Research CouncilEuropean CommissionMinisterio de Ciencia, Innovación y Universidades (España)Agencia Estatal de Investigación (España)Ministerio de Ciencia e Innovación (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202520252024info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/384517reponame: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/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-103921GB-I00info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2022-141288NB-I00The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.1038/s41559-024-02562-xPérez-Posada, Alberto; Lin, Che-Yi; Fan, Tzu-Pei; Lin, Ching-Yi; Chen, Yi-Chih; Gómez-Skarmeta, José Luis; Yu, Jr-Kai; Su, Yi-Hsien; Tena, Juan J.; 2024; Ptychodera flava genomics and transcriptomics data [Dataset]; DIGITAL.CSIC; https://doi.org/10.20350/digitalCSIC/16340Pérez-Posada, Alberto; Lin, Che-Yi; Fan, Tzu-Pei; Lin, Ching-Yi; Chen, Yi-Chih; Gómez-Skarmeta, José Luis; Yu, Jr-Kai; Su, Yi-Hsien; Tena, Juan J.; 2024; Insights into deuterostome evolution from the biphasic transcriptional programmes of hemichordates [Dataset]; GEO - Gene Expression Omnibus; https://doi.org/10.1038/s41559-024-02562-xPérez-Posada, Alberto; Lin, Che-Yi; Fan, Tzu-Pei; Lin, Ching-Yi; Chen, Yi-Chih; Gómez-Skarmeta, José Luis; Yu, Jr-Kai; Su, Yi-Hsien; Tena, Juan J.; 2024; Analyses of the Ptychodera flava RNASeq+ATACSeq project [Dataset]; GitHub; https://doi.org/10.1038/s41559-024-02562-xhttps://doi.org/10.1038/s41559-024-02562-xSíinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3845172026-05-22T06:33:51Z |
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