Potential global cis and trans regulation of lncRNAs in Saccharomyces cerevisiae subjected to ethanol stress

Long noncoding RNAs (lncRNAs) are regulatory RNAs. Saccharomyces cerevisiae strains transcribe hundreds of lncRNAs. LncRNAs can regulate the expression of adjacent genes (cis-regulation) or distant genes from lncRNAs (trans-regulation). Here, we analyzed the potential global cis and trans-regulation...

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Detalhes bibliográficos
Autores: Schnepper, Amanda Piveta [UNESP], Marques, Lucas Farinazzo [UNESP], Wolf, Ivan Rodrigo [UNESP], Kubo, Agatha M.S. [UNESP], Valente, Guilherme Targino [UNESP]
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:Brasil
Recursos:Universidade Estadual Paulista (UNESP)
Repositorio:Repositório Institucional da UNESP
Idioma:inglés
OAI Identifier:oai:repositorio.unesp.br:11449/305499
Acesso em linha:http://dx.doi.org/10.1016/j.gene.2024.148521
https://hdl.handle.net/11449/305499
Access Level:acceso abierto
Palavra-chave:Cis and trans regulation
lncRNAs
Strain-specificity
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spelling Potential global cis and trans regulation of lncRNAs in Saccharomyces cerevisiae subjected to ethanol stressCis and trans regulationlncRNAsStrain-specificityLong noncoding RNAs (lncRNAs) are regulatory RNAs. Saccharomyces cerevisiae strains transcribe hundreds of lncRNAs. LncRNAs can regulate the expression of adjacent genes (cis-regulation) or distant genes from lncRNAs (trans-regulation). Here, we analyzed the potential global cis and trans-regulation of lncRNAs of yeast subjected to ethanol stress. For potential cis regulation, for BMA641-A and S288C strains, we observed that most lncRNA-neighbor gene pairs increased the expression at a certain point followed by a decrease, and vice versa. Based on the transcriptome profile and triple helix prediction between lncRNAs and promoters of coding genes, we observed nine different ways of potential trans regulation that work in a strain-specific manner. Our data provide an initial landscape of potential cis and trans regulation in yeast, which seems to be strain-specific.Department of Structural and Functional Biology Institute of Biosciences São Paulo State University (UNESP), São PauloDepartment of Bioprocess and Biotechnology School of Agriculture São Paulo State University (UNESP), SPLaboratory of Applied Biotechnology Sāo Paulo State University (UNESP), SPDepartment of Structural and Functional Biology Institute of Biosciences São Paulo State University (UNESP), São PauloDepartment of Bioprocess and Biotechnology School of Agriculture São Paulo State University (UNESP), SPLaboratory of Applied Biotechnology Sāo Paulo State University (UNESP), SPUniversidade Estadual Paulista (UNESP)2025-04-29T20:03:13Z2024-08-20info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1016/j.gene.2024.148521Gene, v. 920.1879-00380378-1119https://hdl.handle.net/11449/30549910.1016/j.gene.2024.1485212-s2.0-85192066169Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengGeneinfo:eu-repo/semantics/openAccessSchnepper, Amanda Piveta [UNESP]Marques, Lucas Farinazzo [UNESP]Wolf, Ivan Rodrigo [UNESP]Kubo, Agatha M.S. [UNESP]Valente, Guilherme Targino [UNESP]2025-04-30T14:32:54Zoai:repositorio.unesp.br:11449/305499Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestrepositoriounesp@unesp.bropendoar:29462025-04-30T14:32:54Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Potential global cis and trans regulation of lncRNAs in Saccharomyces cerevisiae subjected to ethanol stress
title Potential global cis and trans regulation of lncRNAs in Saccharomyces cerevisiae subjected to ethanol stress
spellingShingle Potential global cis and trans regulation of lncRNAs in Saccharomyces cerevisiae subjected to ethanol stress
Schnepper, Amanda Piveta [UNESP]
Cis and trans regulation
lncRNAs
Strain-specificity
title_short Potential global cis and trans regulation of lncRNAs in Saccharomyces cerevisiae subjected to ethanol stress
title_full Potential global cis and trans regulation of lncRNAs in Saccharomyces cerevisiae subjected to ethanol stress
title_fullStr Potential global cis and trans regulation of lncRNAs in Saccharomyces cerevisiae subjected to ethanol stress
title_full_unstemmed Potential global cis and trans regulation of lncRNAs in Saccharomyces cerevisiae subjected to ethanol stress
title_sort Potential global cis and trans regulation of lncRNAs in Saccharomyces cerevisiae subjected to ethanol stress
dc.creator.none.fl_str_mv Schnepper, Amanda Piveta [UNESP]
Marques, Lucas Farinazzo [UNESP]
Wolf, Ivan Rodrigo [UNESP]
Kubo, Agatha M.S. [UNESP]
Valente, Guilherme Targino [UNESP]
author Schnepper, Amanda Piveta [UNESP]
author_facet Schnepper, Amanda Piveta [UNESP]
Marques, Lucas Farinazzo [UNESP]
Wolf, Ivan Rodrigo [UNESP]
Kubo, Agatha M.S. [UNESP]
Valente, Guilherme Targino [UNESP]
author_role author
author2 Marques, Lucas Farinazzo [UNESP]
Wolf, Ivan Rodrigo [UNESP]
Kubo, Agatha M.S. [UNESP]
Valente, Guilherme Targino [UNESP]
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (UNESP)
dc.subject.por.fl_str_mv Cis and trans regulation
lncRNAs
Strain-specificity
topic Cis and trans regulation
lncRNAs
Strain-specificity
description Long noncoding RNAs (lncRNAs) are regulatory RNAs. Saccharomyces cerevisiae strains transcribe hundreds of lncRNAs. LncRNAs can regulate the expression of adjacent genes (cis-regulation) or distant genes from lncRNAs (trans-regulation). Here, we analyzed the potential global cis and trans-regulation of lncRNAs of yeast subjected to ethanol stress. For potential cis regulation, for BMA641-A and S288C strains, we observed that most lncRNA-neighbor gene pairs increased the expression at a certain point followed by a decrease, and vice versa. Based on the transcriptome profile and triple helix prediction between lncRNAs and promoters of coding genes, we observed nine different ways of potential trans regulation that work in a strain-specific manner. Our data provide an initial landscape of potential cis and trans regulation in yeast, which seems to be strain-specific.
publishDate 2024
dc.date.none.fl_str_mv 2024-08-20
2025-04-29T20:03:13Z
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.2024.148521
Gene, v. 920.
1879-0038
0378-1119
https://hdl.handle.net/11449/305499
10.1016/j.gene.2024.148521
2-s2.0-85192066169
url http://dx.doi.org/10.1016/j.gene.2024.148521
https://hdl.handle.net/11449/305499
identifier_str_mv Gene, v. 920.
1879-0038
0378-1119
10.1016/j.gene.2024.148521
2-s2.0-85192066169
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 repositoriounesp@unesp.br
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score 15,301629

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