A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin

Autores
Diaz, Maria Candelaria; Oses Oliveto, Camila Maite; Vázquez Lareu, Alejo; Roberti, Sabrina Lorena; Guberman, Alejandra Sonia; Levi, Valeria
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
In recent years, a wealth of evidence revealed that many transcription-related molecules concentrate in membrane less nuclear compartments which are now recognized as relevant for transcription regulation. However, many aspects of this relationship remain unclear partly due to the experimental challenges of manipulating the distribution of transcription factors (TFs) in a controlled fashion.Here, we introduce a simple procedure to generate in live cells light-induced clusters (LICs) of TFs labeled with Janelia Fluor® probes through the HaloTag. When irradiated with the appropriate laser, the photooxidation/photobleaching of fluorescent molecules leads to the formation of a cluster which grows by incorporating other TF molecules, some through weak interactions. While the method was mostly tested with OCT4, other TFs such as SOX2 and the hormone-stimulated glucocorticoid receptor also form LICs. Relevantly, the inactive receptor in stem cells fails to form LICs suggesting that the process requires certain TF conformations and/or cellular contexts.Finally, we show that the recruitment of OCT4 to large LICs lowers its nucleoplasmic concentration and modifies both the overall distribution of the TF and its interactions with chromatin. In contrast, the generation of smaller LICs triggers the dissolution of nearby natural condensates of OCT4 but does not affect its nucleoplasmic concentration and OCT4-chromatin interactions. These results suggest that OCT4 condensates act as reservoirs, buffering variations in the nucleoplasmic concentration of this TF. This new method could be a valuable tool for exploring the relation between TFs distribution, landscape of interactions with chromatin and transcriptional output.
Fil: Diaz, Maria Candelaria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Oses Oliveto, Camila Maite. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Vázquez Lareu, Alejo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Roberti, Sabrina Lorena. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Guberman, Alejandra Sonia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Levi, Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina
Materia
embryonic stem cells
light-induced clusters
nuclear compartments
pluripotency transcription factors
transcriptional condensates
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:11336/280665
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/280665
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With ChromatinDiaz, Maria CandelariaOses Oliveto, Camila MaiteVázquez Lareu, AlejoRoberti, Sabrina LorenaGuberman, Alejandra SoniaLevi, Valeriaembryonic stem cellslight-induced clustersnuclear compartmentspluripotency transcription factorstranscriptional condensateshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1In recent years, a wealth of evidence revealed that many transcription-related molecules concentrate in membrane less nuclear compartments which are now recognized as relevant for transcription regulation. However, many aspects of this relationship remain unclear partly due to the experimental challenges of manipulating the distribution of transcription factors (TFs) in a controlled fashion.Here, we introduce a simple procedure to generate in live cells light-induced clusters (LICs) of TFs labeled with Janelia Fluor® probes through the HaloTag. When irradiated with the appropriate laser, the photooxidation/photobleaching of fluorescent molecules leads to the formation of a cluster which grows by incorporating other TF molecules, some through weak interactions. While the method was mostly tested with OCT4, other TFs such as SOX2 and the hormone-stimulated glucocorticoid receptor also form LICs. Relevantly, the inactive receptor in stem cells fails to form LICs suggesting that the process requires certain TF conformations and/or cellular contexts.Finally, we show that the recruitment of OCT4 to large LICs lowers its nucleoplasmic concentration and modifies both the overall distribution of the TF and its interactions with chromatin. In contrast, the generation of smaller LICs triggers the dissolution of nearby natural condensates of OCT4 but does not affect its nucleoplasmic concentration and OCT4-chromatin interactions. These results suggest that OCT4 condensates act as reservoirs, buffering variations in the nucleoplasmic concentration of this TF. This new method could be a valuable tool for exploring the relation between TFs distribution, landscape of interactions with chromatin and transcriptional output.Fil: Diaz, Maria Candelaria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Oses Oliveto, Camila Maite. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Vázquez Lareu, Alejo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Roberti, Sabrina Lorena. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Guberman, Alejandra Sonia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Levi, Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; ArgentinaAcademic Press Ltd - Elsevier Science Ltd2025-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/280665Diaz, Maria Candelaria; Oses Oliveto, Camila Maite; Vázquez Lareu, Alejo; Roberti, Sabrina Lorena; Guberman, Alejandra Sonia; et al.; A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin; Academic Press Ltd - Elsevier Science Ltd; Journal of Molecular Biology; 437; 12; 6-2025; 1-220022-2836CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://linkinghub.elsevier.com/retrieve/pii/S0022283625001846info:eu-repo/semantics/altIdentifier/doi/10.1016/j.jmb.2025.169118info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2026-02-06T13:14:06Zoai:ri.conicet.gov.ar:11336/280665instacron: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:34982026-02-06 13:14:06.636CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin
title A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin
spellingShingle A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin
Diaz, Maria Candelaria
embryonic stem cells
light-induced clusters
nuclear compartments
pluripotency transcription factors
transcriptional condensates
title_short A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin
title_full A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin
title_fullStr A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin
title_full_unstemmed A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin
title_sort A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin
dc.creator.none.fl_str_mv Diaz, Maria Candelaria
Oses Oliveto, Camila Maite
Vázquez Lareu, Alejo
Roberti, Sabrina Lorena
Guberman, Alejandra Sonia
Levi, Valeria
author Diaz, Maria Candelaria
author_facet Diaz, Maria Candelaria
Oses Oliveto, Camila Maite
Vázquez Lareu, Alejo
Roberti, Sabrina Lorena
Guberman, Alejandra Sonia
Levi, Valeria
author_role author
author2 Oses Oliveto, Camila Maite
Vázquez Lareu, Alejo
Roberti, Sabrina Lorena
Guberman, Alejandra Sonia
Levi, Valeria
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv embryonic stem cells
light-induced clusters
nuclear compartments
pluripotency transcription factors
transcriptional condensates
topic embryonic stem cells
light-induced clusters
nuclear compartments
pluripotency transcription factors
transcriptional condensates
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv In recent years, a wealth of evidence revealed that many transcription-related molecules concentrate in membrane less nuclear compartments which are now recognized as relevant for transcription regulation. However, many aspects of this relationship remain unclear partly due to the experimental challenges of manipulating the distribution of transcription factors (TFs) in a controlled fashion.Here, we introduce a simple procedure to generate in live cells light-induced clusters (LICs) of TFs labeled with Janelia Fluor® probes through the HaloTag. When irradiated with the appropriate laser, the photooxidation/photobleaching of fluorescent molecules leads to the formation of a cluster which grows by incorporating other TF molecules, some through weak interactions. While the method was mostly tested with OCT4, other TFs such as SOX2 and the hormone-stimulated glucocorticoid receptor also form LICs. Relevantly, the inactive receptor in stem cells fails to form LICs suggesting that the process requires certain TF conformations and/or cellular contexts.Finally, we show that the recruitment of OCT4 to large LICs lowers its nucleoplasmic concentration and modifies both the overall distribution of the TF and its interactions with chromatin. In contrast, the generation of smaller LICs triggers the dissolution of nearby natural condensates of OCT4 but does not affect its nucleoplasmic concentration and OCT4-chromatin interactions. These results suggest that OCT4 condensates act as reservoirs, buffering variations in the nucleoplasmic concentration of this TF. This new method could be a valuable tool for exploring the relation between TFs distribution, landscape of interactions with chromatin and transcriptional output.
Fil: Diaz, Maria Candelaria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Oses Oliveto, Camila Maite. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Vázquez Lareu, Alejo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Roberti, Sabrina Lorena. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Guberman, Alejandra Sonia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Levi, Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina
description In recent years, a wealth of evidence revealed that many transcription-related molecules concentrate in membrane less nuclear compartments which are now recognized as relevant for transcription regulation. However, many aspects of this relationship remain unclear partly due to the experimental challenges of manipulating the distribution of transcription factors (TFs) in a controlled fashion.Here, we introduce a simple procedure to generate in live cells light-induced clusters (LICs) of TFs labeled with Janelia Fluor® probes through the HaloTag. When irradiated with the appropriate laser, the photooxidation/photobleaching of fluorescent molecules leads to the formation of a cluster which grows by incorporating other TF molecules, some through weak interactions. While the method was mostly tested with OCT4, other TFs such as SOX2 and the hormone-stimulated glucocorticoid receptor also form LICs. Relevantly, the inactive receptor in stem cells fails to form LICs suggesting that the process requires certain TF conformations and/or cellular contexts.Finally, we show that the recruitment of OCT4 to large LICs lowers its nucleoplasmic concentration and modifies both the overall distribution of the TF and its interactions with chromatin. In contrast, the generation of smaller LICs triggers the dissolution of nearby natural condensates of OCT4 but does not affect its nucleoplasmic concentration and OCT4-chromatin interactions. These results suggest that OCT4 condensates act as reservoirs, buffering variations in the nucleoplasmic concentration of this TF. This new method could be a valuable tool for exploring the relation between TFs distribution, landscape of interactions with chromatin and transcriptional output.
publishDate 2025
dc.date.none.fl_str_mv 2025-06
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/11336/280665
Diaz, Maria Candelaria; Oses Oliveto, Camila Maite; Vázquez Lareu, Alejo; Roberti, Sabrina Lorena; Guberman, Alejandra Sonia; et al.; A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin; Academic Press Ltd - Elsevier Science Ltd; Journal of Molecular Biology; 437; 12; 6-2025; 1-22
0022-2836
CONICET Digital
CONICET
url http://hdl.handle.net/11336/280665
identifier_str_mv Diaz, Maria Candelaria; Oses Oliveto, Camila Maite; Vázquez Lareu, Alejo; Roberti, Sabrina Lorena; Guberman, Alejandra Sonia; et al.; A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin; Academic Press Ltd - Elsevier Science Ltd; Journal of Molecular Biology; 437; 12; 6-2025; 1-22
0022-2836
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://linkinghub.elsevier.com/retrieve/pii/S0022283625001846
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.jmb.2025.169118
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
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Academic Press Ltd - Elsevier Science Ltd
publisher.none.fl_str_mv Academic Press Ltd - Elsevier Science Ltd
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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