Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice

Autores
Reynoso, Mauricio Alberto; Borowsky, Alexander T.; Pauluzzi, Germain; Yeung, Elaine; Zhang, Jianhai; Formentin, Elide; Velasco, Joel; Cabanlit, Sean; Duvenjian, Christine; Prior, Matthew J.; Akmakjian, Garo Z.; Deal, Roger; Sinha, Neelima; Brady, Siobhan M.; Girke, Thomas; Bailey Serres, Julia
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience.
Fil: Reynoso, Mauricio Alberto. University of California; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Borowsky, Alexander T.. University of California; Estados Unidos
Fil: Pauluzzi, Germain. University of California; Estados Unidos
Fil: Yeung, Elaine. University of California; Estados Unidos
Fil: Zhang, Jianhai. University of California; Estados Unidos
Fil: Formentin, Elide. Università di Padova; Italia. University of California; Estados Unidos
Fil: Velasco, Joel. University of California; Estados Unidos
Fil: Cabanlit, Sean. University of California; Estados Unidos
Fil: Duvenjian, Christine. University of California; Estados Unidos
Fil: Prior, Matthew J.. University of California; Estados Unidos
Fil: Akmakjian, Garo Z.. University of California; Estados Unidos
Fil: Deal, Roger. University of Emory; Estados Unidos
Fil: Sinha, Neelima. University of California at Davis; Estados Unidos
Fil: Brady, Siobhan M.. University of California at Davis; Estados Unidos
Fil: Girke, Thomas. University of California; Estados Unidos
Fil: Bailey Serres, Julia. Utrecht University; Países Bajos. University of Utrecht; Países Bajos. University of California; Estados Unidos
Materia
CHROMATIN
DROUGHT
ORYZA SATIVA
ROOTS
SUBMERGENCE
TRANSCRIPTIONAL REGULATORY NETWORKS
TRANSLATOME
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/213272
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/213272
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Gene regulatory networks shape developmental plasticity of root cell types under water extremes in riceReynoso, Mauricio AlbertoBorowsky, Alexander T.Pauluzzi, GermainYeung, ElaineZhang, JianhaiFormentin, ElideVelasco, JoelCabanlit, SeanDuvenjian, ChristinePrior, Matthew J.Akmakjian, Garo Z.Deal, RogerSinha, NeelimaBrady, Siobhan M.Girke, ThomasBailey Serres, JuliaCHROMATINDROUGHTORYZA SATIVAROOTSSUBMERGENCETRANSCRIPTIONAL REGULATORY NETWORKSTRANSLATOMEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience.Fil: Reynoso, Mauricio Alberto. University of California; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Borowsky, Alexander T.. University of California; Estados UnidosFil: Pauluzzi, Germain. University of California; Estados UnidosFil: Yeung, Elaine. University of California; Estados UnidosFil: Zhang, Jianhai. University of California; Estados UnidosFil: Formentin, Elide. Università di Padova; Italia. University of California; Estados UnidosFil: Velasco, Joel. University of California; Estados UnidosFil: Cabanlit, Sean. University of California; Estados UnidosFil: Duvenjian, Christine. University of California; Estados UnidosFil: Prior, Matthew J.. University of California; Estados UnidosFil: Akmakjian, Garo Z.. University of California; Estados UnidosFil: Deal, Roger. University of Emory; Estados UnidosFil: Sinha, Neelima. University of California at Davis; Estados UnidosFil: Brady, Siobhan M.. University of California at Davis; Estados UnidosFil: Girke, Thomas. University of California; Estados UnidosFil: Bailey Serres, Julia. Utrecht University; Países Bajos. University of Utrecht; Países Bajos. University of California; Estados UnidosCell Press2022-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/213272Reynoso, Mauricio Alberto; Borowsky, Alexander T.; Pauluzzi, Germain; Yeung, Elaine; Zhang, Jianhai; et al.; Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice; Cell Press; Developmental Cell; 57; 9; 5-2022; 1177-11921534-5807CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1016/j.devcel.2022.04.013info:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S1534580722002532info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:39:15Zoai:ri.conicet.gov.ar:11336/213272instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:39:15.859CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice
title Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice
spellingShingle Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice
Reynoso, Mauricio Alberto
CHROMATIN
DROUGHT
ORYZA SATIVA
ROOTS
SUBMERGENCE
TRANSCRIPTIONAL REGULATORY NETWORKS
TRANSLATOME
title_short Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice
title_full Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice
title_fullStr Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice
title_full_unstemmed Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice
title_sort Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice
dc.creator.none.fl_str_mv Reynoso, Mauricio Alberto
Borowsky, Alexander T.
Pauluzzi, Germain
Yeung, Elaine
Zhang, Jianhai
Formentin, Elide
Velasco, Joel
Cabanlit, Sean
Duvenjian, Christine
Prior, Matthew J.
Akmakjian, Garo Z.
Deal, Roger
Sinha, Neelima
Brady, Siobhan M.
Girke, Thomas
Bailey Serres, Julia
author Reynoso, Mauricio Alberto
author_facet Reynoso, Mauricio Alberto
Borowsky, Alexander T.
Pauluzzi, Germain
Yeung, Elaine
Zhang, Jianhai
Formentin, Elide
Velasco, Joel
Cabanlit, Sean
Duvenjian, Christine
Prior, Matthew J.
Akmakjian, Garo Z.
Deal, Roger
Sinha, Neelima
Brady, Siobhan M.
Girke, Thomas
Bailey Serres, Julia
author_role author
author2 Borowsky, Alexander T.
Pauluzzi, Germain
Yeung, Elaine
Zhang, Jianhai
Formentin, Elide
Velasco, Joel
Cabanlit, Sean
Duvenjian, Christine
Prior, Matthew J.
Akmakjian, Garo Z.
Deal, Roger
Sinha, Neelima
Brady, Siobhan M.
Girke, Thomas
Bailey Serres, Julia
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv CHROMATIN
DROUGHT
ORYZA SATIVA
ROOTS
SUBMERGENCE
TRANSCRIPTIONAL REGULATORY NETWORKS
TRANSLATOME
topic CHROMATIN
DROUGHT
ORYZA SATIVA
ROOTS
SUBMERGENCE
TRANSCRIPTIONAL REGULATORY NETWORKS
TRANSLATOME
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience.
Fil: Reynoso, Mauricio Alberto. University of California; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Borowsky, Alexander T.. University of California; Estados Unidos
Fil: Pauluzzi, Germain. University of California; Estados Unidos
Fil: Yeung, Elaine. University of California; Estados Unidos
Fil: Zhang, Jianhai. University of California; Estados Unidos
Fil: Formentin, Elide. Università di Padova; Italia. University of California; Estados Unidos
Fil: Velasco, Joel. University of California; Estados Unidos
Fil: Cabanlit, Sean. University of California; Estados Unidos
Fil: Duvenjian, Christine. University of California; Estados Unidos
Fil: Prior, Matthew J.. University of California; Estados Unidos
Fil: Akmakjian, Garo Z.. University of California; Estados Unidos
Fil: Deal, Roger. University of Emory; Estados Unidos
Fil: Sinha, Neelima. University of California at Davis; Estados Unidos
Fil: Brady, Siobhan M.. University of California at Davis; Estados Unidos
Fil: Girke, Thomas. University of California; Estados Unidos
Fil: Bailey Serres, Julia. Utrecht University; Países Bajos. University of Utrecht; Países Bajos. University of California; Estados Unidos
description Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience.
publishDate 2022
dc.date.none.fl_str_mv 2022-05
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/213272
Reynoso, Mauricio Alberto; Borowsky, Alexander T.; Pauluzzi, Germain; Yeung, Elaine; Zhang, Jianhai; et al.; Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice; Cell Press; Developmental Cell; 57; 9; 5-2022; 1177-1192
1534-5807
CONICET Digital
CONICET
url http://hdl.handle.net/11336/213272
identifier_str_mv Reynoso, Mauricio Alberto; Borowsky, Alexander T.; Pauluzzi, Germain; Yeung, Elaine; Zhang, Jianhai; et al.; Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice; Cell Press; Developmental Cell; 57; 9; 5-2022; 1177-1192
1534-5807
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1016/j.devcel.2022.04.013
info:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S1534580722002532
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Cell Press
publisher.none.fl_str_mv Cell Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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