Reconstruction of regulatory network predicts transcription factors driving the dynamics of zebrafish heart regeneration
Autor(a) principal: | |
---|---|
Data de Publicação: | 2022 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/j.gene.2022.146242 http://hdl.handle.net/11449/230320 |
Resumo: | The limited regenerative capacity in mammals has serious implications for cardiac tissue damage. Meanwhile, zebrafish has a high regenerative capacity, but the regulation of the heart healing process has yet to be elucidated. The dynamic nature of cardiac regeneration requires consideration of the inherent temporal dimension of this process. Here, we conducted a systematic review to find genes that define the regenerative cell state of the zebrafish heart. We then performed an in silico temporal gene regulatory network analysis using transcriptomic data from the zebrafish heart regenerative process obtained from databases. In this analysis, the genes found in the systematic review were used to represent the final cell state of the transition process from a non-regenerative cell state to a regenerative state. We found 135 transcription factors driving the cellular state transition process during zebrafish cardiac regeneration, including Hand2, Nkx2.5, Tbx20, Fosl1, Fosb, Junb, Vdr, Wt1, and Tcf21 previously reported for playing a key role in tissue regeneration. Furthermore, we demonstrate that most regulators are activated in the first days post-injury, indicating that the transition from a non-regenerative to a regenerative state occurs promptly. |
id |
UNSP_8c355a79c3c8a66d643a4140f8d51cc7 |
---|---|
oai_identifier_str |
oai:repositorio.unesp.br:11449/230320 |
network_acronym_str |
UNSP |
network_name_str |
Repositório Institucional da UNESP |
repository_id_str |
2946 |
spelling |
Reconstruction of regulatory network predicts transcription factors driving the dynamics of zebrafish heart regenerationDanio rerioHeartRegenerationRegulationTranscription factorsThe limited regenerative capacity in mammals has serious implications for cardiac tissue damage. Meanwhile, zebrafish has a high regenerative capacity, but the regulation of the heart healing process has yet to be elucidated. The dynamic nature of cardiac regeneration requires consideration of the inherent temporal dimension of this process. Here, we conducted a systematic review to find genes that define the regenerative cell state of the zebrafish heart. We then performed an in silico temporal gene regulatory network analysis using transcriptomic data from the zebrafish heart regenerative process obtained from databases. In this analysis, the genes found in the systematic review were used to represent the final cell state of the transition process from a non-regenerative cell state to a regenerative state. We found 135 transcription factors driving the cellular state transition process during zebrafish cardiac regeneration, including Hand2, Nkx2.5, Tbx20, Fosl1, Fosb, Junb, Vdr, Wt1, and Tcf21 previously reported for playing a key role in tissue regeneration. Furthermore, we demonstrate that most regulators are activated in the first days post-injury, indicating that the transition from a non-regenerative to a regenerative state occurs promptly.Fundação de Amparo à Pesquisa do Estado do Rio Grande do SulLaboratório de Genômica Estrutural Programa de Pós-Graduação em Biotecnologia Centro de Desenvolvimento Tecnológico Universidade Federal de PelotasLaboratório de Bioinformática e Proteômica Programa de Pós-Graduação em Biotecnologia Centro de Desenvolvimento Tecnológico Universidade Federal de PelotasLaboratório Genômica e Evolução Molecular Departamento de Genética Instituto de Biociências de Botucatu Universidade Estadual Paulista (UNESP)Laboratório Genômica e Evolução Molecular Departamento de Genética Instituto de Biociências de Botucatu Universidade Estadual Paulista (UNESP)Universidade Federal de PelotasUniversidade Estadual Paulista (UNESP)Nunes, Leandro SilvaDomingues, William BorgesKremer, Frederico SchmittPinhal, Danillo [UNESP]Campos, Vinicius Farias2022-04-29T08:39:19Z2022-04-29T08:39:19Z2022-04-20info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1016/j.gene.2022.146242Gene, v. 819.1879-00380378-1119http://hdl.handle.net/11449/23032010.1016/j.gene.2022.1462422-s2.0-85123870560Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengGeneinfo:eu-repo/semantics/openAccess2022-04-29T08:39:19Zoai:repositorio.unesp.br:11449/230320Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462022-04-29T08:39:19Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Reconstruction of regulatory network predicts transcription factors driving the dynamics of zebrafish heart regeneration |
title |
Reconstruction of regulatory network predicts transcription factors driving the dynamics of zebrafish heart regeneration |
spellingShingle |
Reconstruction of regulatory network predicts transcription factors driving the dynamics of zebrafish heart regeneration Nunes, Leandro Silva Danio rerio Heart Regeneration Regulation Transcription factors |
title_short |
Reconstruction of regulatory network predicts transcription factors driving the dynamics of zebrafish heart regeneration |
title_full |
Reconstruction of regulatory network predicts transcription factors driving the dynamics of zebrafish heart regeneration |
title_fullStr |
Reconstruction of regulatory network predicts transcription factors driving the dynamics of zebrafish heart regeneration |
title_full_unstemmed |
Reconstruction of regulatory network predicts transcription factors driving the dynamics of zebrafish heart regeneration |
title_sort |
Reconstruction of regulatory network predicts transcription factors driving the dynamics of zebrafish heart regeneration |
author |
Nunes, Leandro Silva |
author_facet |
Nunes, Leandro Silva Domingues, William Borges Kremer, Frederico Schmitt Pinhal, Danillo [UNESP] Campos, Vinicius Farias |
author_role |
author |
author2 |
Domingues, William Borges Kremer, Frederico Schmitt Pinhal, Danillo [UNESP] Campos, Vinicius Farias |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Universidade Federal de Pelotas Universidade Estadual Paulista (UNESP) |
dc.contributor.author.fl_str_mv |
Nunes, Leandro Silva Domingues, William Borges Kremer, Frederico Schmitt Pinhal, Danillo [UNESP] Campos, Vinicius Farias |
dc.subject.por.fl_str_mv |
Danio rerio Heart Regeneration Regulation Transcription factors |
topic |
Danio rerio Heart Regeneration Regulation Transcription factors |
description |
The limited regenerative capacity in mammals has serious implications for cardiac tissue damage. Meanwhile, zebrafish has a high regenerative capacity, but the regulation of the heart healing process has yet to be elucidated. The dynamic nature of cardiac regeneration requires consideration of the inherent temporal dimension of this process. Here, we conducted a systematic review to find genes that define the regenerative cell state of the zebrafish heart. We then performed an in silico temporal gene regulatory network analysis using transcriptomic data from the zebrafish heart regenerative process obtained from databases. In this analysis, the genes found in the systematic review were used to represent the final cell state of the transition process from a non-regenerative cell state to a regenerative state. We found 135 transcription factors driving the cellular state transition process during zebrafish cardiac regeneration, including Hand2, Nkx2.5, Tbx20, Fosl1, Fosb, Junb, Vdr, Wt1, and Tcf21 previously reported for playing a key role in tissue regeneration. Furthermore, we demonstrate that most regulators are activated in the first days post-injury, indicating that the transition from a non-regenerative to a regenerative state occurs promptly. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-04-29T08:39:19Z 2022-04-29T08:39:19Z 2022-04-20 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1016/j.gene.2022.146242 Gene, v. 819. 1879-0038 0378-1119 http://hdl.handle.net/11449/230320 10.1016/j.gene.2022.146242 2-s2.0-85123870560 |
url |
http://dx.doi.org/10.1016/j.gene.2022.146242 http://hdl.handle.net/11449/230320 |
identifier_str_mv |
Gene, v. 819. 1879-0038 0378-1119 10.1016/j.gene.2022.146242 2-s2.0-85123870560 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Gene |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1799965558070837248 |