ChIP-Seq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem Cells

The Prep1 (Pknox1) homeodomain transcription factor is essential at multiple stages of embryo development. In the E11.5 embryo trunk, we previously estimated that Prep1 binds about 3,300 genomic sites at a highly specific decameric consensus sequence, mainly governing basal cellular functions. We no...

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Detalles Bibliográficos
Autores: Laurent, Audrey, Calabrese, Manuela, Warnatz, Hans-Joerg, Yaspo, Marie-Laure, Tkachuk, Vsevolod, Torres, Miguel, Blasi, Francesco, Penkov, Dmitry
Tipo de recurso: artículo
Fecha de publicación:2015
País:España
Institución:Instituto de Salud Carlos III (ISCIII)
Repositorio:Repisalud
Idioma:inglés
OAI Identifier:oai:repisalud.isciii.es:20.500.12105/5410
Acceso en línea:http://hdl.handle.net/20.500.12105/5410
Access Level:acceso abierto
Palabra clave:HOMEODOMAIN TRANSCRIPTION FACTOR
HOX PROTEIN
PBX
DNA
COMPLEX
PKNOX1
DIFFERENTIATION
EMBRYOGENESIS
PLURIPOTENT
EXPRESSION
id ES_ceace2eb3e0414152becaf2ad448e438
oai_identifier_str oai:repisalud.isciii.es:20.500.12105/5410
network_acronym_str ES
network_name_str España
repository_id_str
spelling ChIP-Seq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem CellsLaurent, AudreyCalabrese, ManuelaWarnatz, Hans-JoergYaspo, Marie-LaureTkachuk, VsevolodTorres, MiguelBlasi, FrancescoPenkov, DmitryHOMEODOMAIN TRANSCRIPTION FACTORHOX PROTEINPBXDNACOMPLEXPKNOX1DIFFERENTIATIONEMBRYOGENESISPLURIPOTENTEXPRESSIONThe Prep1 (Pknox1) homeodomain transcription factor is essential at multiple stages of embryo development. In the E11.5 embryo trunk, we previously estimated that Prep1 binds about 3,300 genomic sites at a highly specific decameric consensus sequence, mainly governing basal cellular functions. We now show that in embryonic stem (ES) cells Prep1 binding pattern only partly overlaps that of the embryo trunk, with about 2,000 novel sites. Moreover, in ES cells Prep1 still binds mostly to promoters, as in total embryo trunk but, among the peaks bound exclusively in ES cells, the percentage of enhancers was threefold higher. RNA-seq identifies about 1800 genes down-regulated in Prep1(-/-) ES cells which belong to gene ontology categories not enriched in the E11.5 Prep1(i/i) differentiated embryo, including in particular essential components of the Wnt and Fgf pathways. These data agree with aberrant Wnt and Fgf expression levels in the Prep1(-/-) ES cells with a deficient embryoid bodies (EBs) formation and differentiation. Re-establishment of the Prep1 level rescues the phenotype.Public Library of Science (PLOS)Fondazione Umberto VeronesiItalian Association for Cancer ResearchFondazione CariploMinistero della Salute (Italia)Max Planck SocietyUnión Europea. Comisión EuropeaMinisterio de Economía y Competitividad (España)Russian Foundation for Basic Research20172017-11-2720152015-01-0120152015-01-01journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfapplication/pdfapplication/vnd.ms-excelapplication/pdfapplication/vnd.openxmlformats-officedocument.spreadsheetml.sheetapplication/pdfapplication/vnd.openxmlformats-officedocument.spreadsheetml.sheetapplication/vnd.openxmlformats-officedocument.spreadsheetml.sheetapplication/vnd.ms-excelapplication/vnd.openxmlformats-officedocument.wordprocessingml.documentapplication/vnd.openxmlformats-officedocument.wordprocessingml.documenthttp://hdl.handle.net/20.500.12105/5410reponame:Repisaludinstname:Instituto de Salud Carlos III (ISCIII)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2Atribución 4.0 Internacionalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repisalud.isciii.es:20.500.12105/54102026-06-12T12:43:37Z
dc.title.none.fl_str_mv ChIP-Seq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem Cells
title ChIP-Seq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem Cells
spellingShingle ChIP-Seq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem Cells
Laurent, Audrey
HOMEODOMAIN TRANSCRIPTION FACTOR
HOX PROTEIN
PBX
DNA
COMPLEX
PKNOX1
DIFFERENTIATION
EMBRYOGENESIS
PLURIPOTENT
EXPRESSION
title_short ChIP-Seq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem Cells
title_full ChIP-Seq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem Cells
title_fullStr ChIP-Seq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem Cells
title_full_unstemmed ChIP-Seq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem Cells
title_sort ChIP-Seq and RNA-Seq Analyses Identify Components of the Wnt and Fgf Signaling Pathways as Prep1 Target Genes in Mouse Embryonic Stem Cells
dc.creator.none.fl_str_mv Laurent, Audrey
Calabrese, Manuela
Warnatz, Hans-Joerg
Yaspo, Marie-Laure
Tkachuk, Vsevolod
Torres, Miguel
Blasi, Francesco
Penkov, Dmitry
author Laurent, Audrey
author_facet Laurent, Audrey
Calabrese, Manuela
Warnatz, Hans-Joerg
Yaspo, Marie-Laure
Tkachuk, Vsevolod
Torres, Miguel
Blasi, Francesco
Penkov, Dmitry
author_role author
author2 Calabrese, Manuela
Warnatz, Hans-Joerg
Yaspo, Marie-Laure
Tkachuk, Vsevolod
Torres, Miguel
Blasi, Francesco
Penkov, Dmitry
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Fondazione Umberto Veronesi
Italian Association for Cancer Research
Fondazione Cariplo
Ministero della Salute (Italia)
Max Planck Society
Unión Europea. Comisión Europea
Ministerio de Economía y Competitividad (España)
Russian Foundation for Basic Research
dc.subject.none.fl_str_mv HOMEODOMAIN TRANSCRIPTION FACTOR
HOX PROTEIN
PBX
DNA
COMPLEX
PKNOX1
DIFFERENTIATION
EMBRYOGENESIS
PLURIPOTENT
EXPRESSION
topic HOMEODOMAIN TRANSCRIPTION FACTOR
HOX PROTEIN
PBX
DNA
COMPLEX
PKNOX1
DIFFERENTIATION
EMBRYOGENESIS
PLURIPOTENT
EXPRESSION
description The Prep1 (Pknox1) homeodomain transcription factor is essential at multiple stages of embryo development. In the E11.5 embryo trunk, we previously estimated that Prep1 binds about 3,300 genomic sites at a highly specific decameric consensus sequence, mainly governing basal cellular functions. We now show that in embryonic stem (ES) cells Prep1 binding pattern only partly overlaps that of the embryo trunk, with about 2,000 novel sites. Moreover, in ES cells Prep1 still binds mostly to promoters, as in total embryo trunk but, among the peaks bound exclusively in ES cells, the percentage of enhancers was threefold higher. RNA-seq identifies about 1800 genes down-regulated in Prep1(-/-) ES cells which belong to gene ontology categories not enriched in the E11.5 Prep1(i/i) differentiated embryo, including in particular essential components of the Wnt and Fgf pathways. These data agree with aberrant Wnt and Fgf expression levels in the Prep1(-/-) ES cells with a deficient embryoid bodies (EBs) formation and differentiation. Re-establishment of the Prep1 level rescues the phenotype.
publishDate 2015
dc.date.none.fl_str_mv 2015
2015-01-01
2015
2015-01-01
2017
2017-11-27
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12105/5410
url http://hdl.handle.net/20.500.12105/5410
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Atribución 4.0 Internacional
http://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Atribución 4.0 Internacional
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
application/vnd.ms-excel
application/pdf
application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
application/pdf
application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
application/vnd.ms-excel
application/vnd.openxmlformats-officedocument.wordprocessingml.document
application/vnd.openxmlformats-officedocument.wordprocessingml.document
dc.publisher.none.fl_str_mv Public Library of Science (PLOS)
publisher.none.fl_str_mv Public Library of Science (PLOS)
dc.source.none.fl_str_mv reponame:Repisalud
instname:Instituto de Salud Carlos III (ISCIII)
instname_str Instituto de Salud Carlos III (ISCIII)
reponame_str Repisalud
collection Repisalud
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869420012619431936
score 15,812429

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