Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development

Autores
Pajoro, Alice; Madrigal, Pedro; Muiño, Jose M.; Matus, José Tomás; Jin, Jian; Mecchia, Martin Alejandro; Debernardi, Juan Manuel; Palatnik, Javier Fernando; Balazadeh, Salma; Arif, Muhammad; Ó’Maoiléidigh, Diarmuid S.; Wellmer, Frank; Krajewsk, Pawel; Riechmann, José Luis; Angenent, Gerco C.; Kaufmann, Kerstin
Año de publicación
2014
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility
Fil: Pajoro, Alice. Wageningen University. Laboratory of Molecular Biology; Países Bajos
Fil: Madrigal, Pedro. Polish Academy of Sciences. Institute of Plant Genetics; Polonia
Fil: Muiño, Jose M.. Max-Planck Institute for Molecular Genetics. Department of Computational Molecular Biology; Alemania
Fil: Matus, José Tomás. Universidad de Barcelona. Center for Research in Agricultural Genomics; España
Fil: Jin, Jian. Universidad de Barcelona. Center for Research in Agricultural Genomics; España
Fil: Mecchia, Martin Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Debernardi, Juan Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Palatnik, Javier Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Balazadeh, Salma. University of Potsdam. Institute of Biochemistry and Biology; Alemania
Fil: Arif, Muhammad. University of Potsdam. Institute of Biochemistry and Biology; Alemania
Fil: Ó’Maoiléidigh, Diarmuid S.. Trinity College Dublin. Smurfit Institute of Genetics; Irlanda
Fil: Wellmer, Frank. Trinity College Dublin. Smurfit Institute of Genetics; Irlanda
Fil: Krajewsk, Pawel. Polish Academy of Sciences. Institute of Plant Genetics; Polonia
Fil: Riechmann, José Luis . Universidad de Barcelona. Center for Research in Agricultural Genomics; España. Institució Catalana de Recerca i Estudis Avançats; España
Fil: Angenent, Gerco C.. Wageningen University. Laboratory of Molecular Biology; Países Bajos. Plant Research International. Business Unit Bioscience; Países Bajos
Fil: Kaufmann, Kerstin. Wageningen University. Laboratory of Molecular Biology; Países Bajos. University of Potsdam. Institute of Biochemistry and Biology; Alemania
Materia
MADS box
Chromatin Remodelling
miR396
GRF
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/4835
Acceder
id CONICETDig_1d9383b5ede44fdb8c915805b16a65e7
oai_identifier_str oai:ri.conicet.gov.ar:11336/4835
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower developmentPajoro, AliceMadrigal, PedroMuiño, Jose M.Matus, José TomásJin, JianMecchia, Martin AlejandroDebernardi, Juan ManuelPalatnik, Javier FernandoBalazadeh, SalmaArif, MuhammadÓ’Maoiléidigh, Diarmuid S.Wellmer, FrankKrajewsk, PawelRiechmann, José Luis Angenent, Gerco C.Kaufmann, KerstinMADS boxChromatin RemodellingmiR396GRFhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibilityFil: Pajoro, Alice. Wageningen University. Laboratory of Molecular Biology; Países BajosFil: Madrigal, Pedro. Polish Academy of Sciences. Institute of Plant Genetics; PoloniaFil: Muiño, Jose M.. Max-Planck Institute for Molecular Genetics. Department of Computational Molecular Biology; AlemaniaFil: Matus, José Tomás. Universidad de Barcelona. Center for Research in Agricultural Genomics; EspañaFil: Jin, Jian. Universidad de Barcelona. Center for Research in Agricultural Genomics; EspañaFil: Mecchia, Martin Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Debernardi, Juan Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Palatnik, Javier Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Balazadeh, Salma. University of Potsdam. Institute of Biochemistry and Biology; AlemaniaFil: Arif, Muhammad. University of Potsdam. Institute of Biochemistry and Biology; AlemaniaFil: Ó’Maoiléidigh, Diarmuid S.. Trinity College Dublin. Smurfit Institute of Genetics; IrlandaFil: Wellmer, Frank. Trinity College Dublin. Smurfit Institute of Genetics; IrlandaFil: Krajewsk, Pawel. Polish Academy of Sciences. Institute of Plant Genetics; PoloniaFil: Riechmann, José Luis . Universidad de Barcelona. Center for Research in Agricultural Genomics; España. Institució Catalana de Recerca i Estudis Avançats; EspañaFil: Angenent, Gerco C.. Wageningen University. Laboratory of Molecular Biology; Países Bajos. Plant Research International. Business Unit Bioscience; Países BajosFil: Kaufmann, Kerstin. Wageningen University. Laboratory of Molecular Biology; Países Bajos. University of Potsdam. Institute of Biochemistry and Biology; AlemaniaBiomed Central2014-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/4835Pajoro, Alice; Madrigal, Pedro; Muiño, Jose M.; Matus, José Tomás; Jin, Jian; et al.; Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development; Biomed Central; Genome Biology; 15; 3; 3-2014; 1-181474-760Xenginfo:eu-repo/semantics/altIdentifier/url/https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r41info:eu-repo/semantics/altIdentifier/url/http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054849/info:eu-repo/semantics/altIdentifier/pmid/PMC4054849info:eu-repo/semantics/altIdentifier/doi/10.1186%2Fgb-2014-15-3-r41info:eu-repo/semantics/altIdentifier/doi/info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-10T13:08:29Zoai:ri.conicet.gov.ar:11336/4835instacron: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:34982025-09-10 13:08:29.788CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
title Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
spellingShingle Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
Pajoro, Alice
MADS box
Chromatin Remodelling
miR396
GRF
title_short Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
title_full Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
title_fullStr Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
title_full_unstemmed Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
title_sort Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
dc.creator.none.fl_str_mv Pajoro, Alice
Madrigal, Pedro
Muiño, Jose M.
Matus, José Tomás
Jin, Jian
Mecchia, Martin Alejandro
Debernardi, Juan Manuel
Palatnik, Javier Fernando
Balazadeh, Salma
Arif, Muhammad
Ó’Maoiléidigh, Diarmuid S.
Wellmer, Frank
Krajewsk, Pawel
Riechmann, José Luis
Angenent, Gerco C.
Kaufmann, Kerstin
author Pajoro, Alice
author_facet Pajoro, Alice
Madrigal, Pedro
Muiño, Jose M.
Matus, José Tomás
Jin, Jian
Mecchia, Martin Alejandro
Debernardi, Juan Manuel
Palatnik, Javier Fernando
Balazadeh, Salma
Arif, Muhammad
Ó’Maoiléidigh, Diarmuid S.
Wellmer, Frank
Krajewsk, Pawel
Riechmann, José Luis
Angenent, Gerco C.
Kaufmann, Kerstin
author_role author
author2 Madrigal, Pedro
Muiño, Jose M.
Matus, José Tomás
Jin, Jian
Mecchia, Martin Alejandro
Debernardi, Juan Manuel
Palatnik, Javier Fernando
Balazadeh, Salma
Arif, Muhammad
Ó’Maoiléidigh, Diarmuid S.
Wellmer, Frank
Krajewsk, Pawel
Riechmann, José Luis
Angenent, Gerco C.
Kaufmann, Kerstin
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv MADS box
Chromatin Remodelling
miR396
GRF
topic MADS box
Chromatin Remodelling
miR396
GRF
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility
Fil: Pajoro, Alice. Wageningen University. Laboratory of Molecular Biology; Países Bajos
Fil: Madrigal, Pedro. Polish Academy of Sciences. Institute of Plant Genetics; Polonia
Fil: Muiño, Jose M.. Max-Planck Institute for Molecular Genetics. Department of Computational Molecular Biology; Alemania
Fil: Matus, José Tomás. Universidad de Barcelona. Center for Research in Agricultural Genomics; España
Fil: Jin, Jian. Universidad de Barcelona. Center for Research in Agricultural Genomics; España
Fil: Mecchia, Martin Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Debernardi, Juan Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Palatnik, Javier Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; Argentina
Fil: Balazadeh, Salma. University of Potsdam. Institute of Biochemistry and Biology; Alemania
Fil: Arif, Muhammad. University of Potsdam. Institute of Biochemistry and Biology; Alemania
Fil: Ó’Maoiléidigh, Diarmuid S.. Trinity College Dublin. Smurfit Institute of Genetics; Irlanda
Fil: Wellmer, Frank. Trinity College Dublin. Smurfit Institute of Genetics; Irlanda
Fil: Krajewsk, Pawel. Polish Academy of Sciences. Institute of Plant Genetics; Polonia
Fil: Riechmann, José Luis . Universidad de Barcelona. Center for Research in Agricultural Genomics; España. Institució Catalana de Recerca i Estudis Avançats; España
Fil: Angenent, Gerco C.. Wageningen University. Laboratory of Molecular Biology; Países Bajos. Plant Research International. Business Unit Bioscience; Países Bajos
Fil: Kaufmann, Kerstin. Wageningen University. Laboratory of Molecular Biology; Países Bajos. University of Potsdam. Institute of Biochemistry and Biology; Alemania
description Background: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Results: We characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Conclusions: Our findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility
publishDate 2014
dc.date.none.fl_str_mv 2014-03
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/11336/4835
Pajoro, Alice; Madrigal, Pedro; Muiño, Jose M.; Matus, José Tomás; Jin, Jian; et al.; Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development; Biomed Central; Genome Biology; 15; 3; 3-2014; 1-18
1474-760X
url http://hdl.handle.net/11336/4835
identifier_str_mv Pajoro, Alice; Madrigal, Pedro; Muiño, Jose M.; Matus, José Tomás; Jin, Jian; et al.; Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development; Biomed Central; Genome Biology; 15; 3; 3-2014; 1-18
1474-760X
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r41
info:eu-repo/semantics/altIdentifier/url/http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054849/
info:eu-repo/semantics/altIdentifier/pmid/PMC4054849
info:eu-repo/semantics/altIdentifier/doi/10.1186%2Fgb-2014-15-3-r41
info:eu-repo/semantics/altIdentifier/doi/
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Biomed Central
publisher.none.fl_str_mv Biomed Central
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 12.993085

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