A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process

Different convergent evolutionary strategies adopted by angiosperm fruits lead to diverse functional seed dispersal units. Dry dehiscent fruits are a common type of fruit, characterized by their lack of fleshy pericarp and the release of seeds at maturity through openings (dehiscence zones, DZs) in...

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Autores: Moya-Cuevas, José, Ortiz-Gutiérrez, Elizabeth, López-Sánchez, Patricio, Simon‐Moya, Miguel, Ballester, Patricia, Álvarez-Buylla, Elena R., Ferrándiz, Cristina
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:10261/370796
Acceso en línea:http://hdl.handle.net/10261/370796
Access Level:acceso abierto
Palabra clave:Fruit
Dehiscence
Systems biology
Boolean modeling
GRN
Arabidopsis
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spelling A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter ProcessMoya-Cuevas, JoséOrtiz-Gutiérrez, ElizabethLópez-Sánchez, PatricioSimon‐Moya, MiguelBallester, PatriciaÁlvarez-Buylla, Elena R.Ferrándiz, CristinaFruitDehiscenceSystems biologyBoolean modelingGRNArabidopsisDifferent convergent evolutionary strategies adopted by angiosperm fruits lead to diverse functional seed dispersal units. Dry dehiscent fruits are a common type of fruit, characterized by their lack of fleshy pericarp and the release of seeds at maturity through openings (dehiscence zones, DZs) in their structure. In previous decades, a set of core players in DZ formation have been intensively characterized in Arabidopsis and integrated in a gene regulatory network (GRN) that explains the morphogenesis of these tissues. In this work, we compile all the experimental data available to date to build a discrete Boolean model as a mechanistic approach to validate the network and, if needed, to identify missing components of the GRN and/or propose new hypothetical regulatory interactions, but also to provide a new formal framework to feed further work in Brassicaceae fruit development and the evolution of seed dispersal mechanisms. Hence, by means of exhaustive in-silico validations and experimental evidence, we are able to incorporate both the NO TRANSMITTING TRACT (NTT) transcription factor as a new additional node, and a new set of regulatory hypothetical rules to uncover the dynamics of Arabidopsis DZ specification.This work was supported by the Spanish MINECO/FEDER grants n◦ BIO2012- 32902, BIO2015-64531-R, FRUITLOOK, EU.FP7-PEOPLE-PIRSES- 2013-612640 and Ministerio de Ciencia e Innovación/Agencia Estatal de Investigación (AEI)/10.13039/501100011033 and by Fondo Europeo de Desarrollo Regional (FEDER) ‘A way of making Europe’ (grant no. PID2021-122754OB-I00 to C.F.). José Moya-Cuevas was supported by a predoctoral contract of the Spanish MINECO n◦ BES-2013-066219.Peer reviewedMultidisciplinary Digital Publishing InstituteMinisterio de Economía y Competitividad (España)European CommissionMinisterio de Ciencia e Innovación (España)Agencia Estatal de Investigación (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2024202420242024info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/370796reponame: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##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-122754OB-I00info:eu-repo/grantAgreement/MINECO//BIO2012-32902info:eu-repo/grantAgreement/MINECO//BIO2015-64531-Rinfo:eu-repo/grantAgreement/EC/FP7/2013-612640info:eu-repo/grantAgreement/MINECO//BES-2013-066219The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.3390/plants13202927https://doi.org/10.3390/plants13202927Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3707962026-05-22T06:33:51Z
dc.title.none.fl_str_mv A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process
title A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process
spellingShingle A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process
Moya-Cuevas, José
Fruit
Dehiscence
Systems biology
Boolean modeling
GRN
Arabidopsis
title_short A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process
title_full A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process
title_fullStr A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process
title_full_unstemmed A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process
title_sort A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process
dc.creator.none.fl_str_mv Moya-Cuevas, José
Ortiz-Gutiérrez, Elizabeth
López-Sánchez, Patricio
Simon‐Moya, Miguel
Ballester, Patricia
Álvarez-Buylla, Elena R.
Ferrándiz, Cristina
author Moya-Cuevas, José
author_facet Moya-Cuevas, José
Ortiz-Gutiérrez, Elizabeth
López-Sánchez, Patricio
Simon‐Moya, Miguel
Ballester, Patricia
Álvarez-Buylla, Elena R.
Ferrándiz, Cristina
author_role author
author2 Ortiz-Gutiérrez, Elizabeth
López-Sánchez, Patricio
Simon‐Moya, Miguel
Ballester, Patricia
Álvarez-Buylla, Elena R.
Ferrándiz, Cristina
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Economía y Competitividad (España)
European Commission
Ministerio de Ciencia e Innovación (España)
Agencia Estatal de Investigación (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Fruit
Dehiscence
Systems biology
Boolean modeling
GRN
Arabidopsis
topic Fruit
Dehiscence
Systems biology
Boolean modeling
GRN
Arabidopsis
description Different convergent evolutionary strategies adopted by angiosperm fruits lead to diverse functional seed dispersal units. Dry dehiscent fruits are a common type of fruit, characterized by their lack of fleshy pericarp and the release of seeds at maturity through openings (dehiscence zones, DZs) in their structure. In previous decades, a set of core players in DZ formation have been intensively characterized in Arabidopsis and integrated in a gene regulatory network (GRN) that explains the morphogenesis of these tissues. In this work, we compile all the experimental data available to date to build a discrete Boolean model as a mechanistic approach to validate the network and, if needed, to identify missing components of the GRN and/or propose new hypothetical regulatory interactions, but also to provide a new formal framework to feed further work in Brassicaceae fruit development and the evolution of seed dispersal mechanisms. Hence, by means of exhaustive in-silico validations and experimental evidence, we are able to incorporate both the NO TRANSMITTING TRACT (NTT) transcription factor as a new additional node, and a new set of regulatory hypothetical rules to uncover the dynamics of Arabidopsis DZ specification.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024
2024
2024
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/10261/370796
url http://hdl.handle.net/10261/370796
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#
#PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-122754OB-I00
info:eu-repo/grantAgreement/MINECO//BIO2012-32902
info:eu-repo/grantAgreement/MINECO//BIO2015-64531-R
info:eu-repo/grantAgreement/EC/FP7/2013-612640
info:eu-repo/grantAgreement/MINECO//BES-2013-066219
The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI https://doi.org/10.3390/plants13202927
https://doi.org/10.3390/plants13202927
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
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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