Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing

Autores
Fuchs, Armin; Riegler, Stefan; Ayatollahi, Zahra; Cavallari, Nicola; Giono, Luciana Eugenia; Nimeth, Barbara A.; Mutanwad, Krishna V.; Schweighofer, Alois; Lucyshyn, Doris; Barta, Andrea; Petrillo, Ezequiel; Kalyna, Maria
Año de publicación
2021
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interactions with alternative splicing are poorly understood. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression.
Fil: Fuchs, Armin. Universidad de Viena; Austria
Fil: Riegler, Stefan. Universidad de Viena; Austria
Fil: Ayatollahi, Zahra. Universidad de Viena; Austria
Fil: Cavallari, Nicola. Universidad de Viena; Austria
Fil: Giono, Luciana Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina
Fil: Nimeth, Barbara A.. University of Natural Resources and Life Sciences ; Austria
Fil: Mutanwad, Krishna V.. University of Natural Resources and Life Sciences ; Austria
Fil: Schweighofer, Alois. Universidad de Viena; Austria
Fil: Lucyshyn, Doris. Universitat Fur Bodenkultur Wien; Austria
Fil: Barta, Andrea. University of Natural Resources and Life Sciences ; Austria
Fil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina
Fil: Kalyna, Maria. University of Natural Resources and Life Sciences ; Austria
Materia
splicing
RNA interference
decay
translation
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:11336/175296
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/175296
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicingFuchs, ArminRiegler, StefanAyatollahi, ZahraCavallari, NicolaGiono, Luciana EugeniaNimeth, Barbara A.Mutanwad, Krishna V.Schweighofer, AloisLucyshyn, DorisBarta, AndreaPetrillo, EzequielKalyna, MariasplicingRNA interferencedecaytranslationhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interactions with alternative splicing are poorly understood. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression.Fil: Fuchs, Armin. Universidad de Viena; AustriaFil: Riegler, Stefan. Universidad de Viena; AustriaFil: Ayatollahi, Zahra. Universidad de Viena; AustriaFil: Cavallari, Nicola. Universidad de Viena; AustriaFil: Giono, Luciana Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Nimeth, Barbara A.. University of Natural Resources and Life Sciences ; AustriaFil: Mutanwad, Krishna V.. University of Natural Resources and Life Sciences ; AustriaFil: Schweighofer, Alois. Universidad de Viena; AustriaFil: Lucyshyn, Doris. Universitat Fur Bodenkultur Wien; AustriaFil: Barta, Andrea. University of Natural Resources and Life Sciences ; AustriaFil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; ArgentinaFil: Kalyna, Maria. University of Natural Resources and Life Sciences ; AustriaOxford University Press2021-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/175296Fuchs, Armin; Riegler, Stefan; Ayatollahi, Zahra; Cavallari, Nicola; Giono, Luciana Eugenia; et al.; Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing; Oxford University Press; Nucleic Acids Research; 49; 2; 1-2021; 1133-11511362-4962CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkaa1260info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:46:03Zoai:ri.conicet.gov.ar:11336/175296instacron: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:34982025-10-15 14:46:03.434CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing
title Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing
spellingShingle Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing
Fuchs, Armin
splicing
RNA interference
decay
translation
title_short Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing
title_full Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing
title_fullStr Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing
title_full_unstemmed Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing
title_sort Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing
dc.creator.none.fl_str_mv Fuchs, Armin
Riegler, Stefan
Ayatollahi, Zahra
Cavallari, Nicola
Giono, Luciana Eugenia
Nimeth, Barbara A.
Mutanwad, Krishna V.
Schweighofer, Alois
Lucyshyn, Doris
Barta, Andrea
Petrillo, Ezequiel
Kalyna, Maria
author Fuchs, Armin
author_facet Fuchs, Armin
Riegler, Stefan
Ayatollahi, Zahra
Cavallari, Nicola
Giono, Luciana Eugenia
Nimeth, Barbara A.
Mutanwad, Krishna V.
Schweighofer, Alois
Lucyshyn, Doris
Barta, Andrea
Petrillo, Ezequiel
Kalyna, Maria
author_role author
author2 Riegler, Stefan
Ayatollahi, Zahra
Cavallari, Nicola
Giono, Luciana Eugenia
Nimeth, Barbara A.
Mutanwad, Krishna V.
Schweighofer, Alois
Lucyshyn, Doris
Barta, Andrea
Petrillo, Ezequiel
Kalyna, Maria
author2_role author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv splicing
RNA interference
decay
translation
topic splicing
RNA interference
decay
translation
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interactions with alternative splicing are poorly understood. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression.
Fil: Fuchs, Armin. Universidad de Viena; Austria
Fil: Riegler, Stefan. Universidad de Viena; Austria
Fil: Ayatollahi, Zahra. Universidad de Viena; Austria
Fil: Cavallari, Nicola. Universidad de Viena; Austria
Fil: Giono, Luciana Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina
Fil: Nimeth, Barbara A.. University of Natural Resources and Life Sciences ; Austria
Fil: Mutanwad, Krishna V.. University of Natural Resources and Life Sciences ; Austria
Fil: Schweighofer, Alois. Universidad de Viena; Austria
Fil: Lucyshyn, Doris. Universitat Fur Bodenkultur Wien; Austria
Fil: Barta, Andrea. University of Natural Resources and Life Sciences ; Austria
Fil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina
Fil: Kalyna, Maria. University of Natural Resources and Life Sciences ; Austria
description Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interactions with alternative splicing are poorly understood. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression.
publishDate 2021
dc.date.none.fl_str_mv 2021-01
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/11336/175296
Fuchs, Armin; Riegler, Stefan; Ayatollahi, Zahra; Cavallari, Nicola; Giono, Luciana Eugenia; et al.; Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing; Oxford University Press; Nucleic Acids Research; 49; 2; 1-2021; 1133-1151
1362-4962
CONICET Digital
CONICET
url http://hdl.handle.net/11336/175296
identifier_str_mv Fuchs, Armin; Riegler, Stefan; Ayatollahi, Zahra; Cavallari, Nicola; Giono, Luciana Eugenia; et al.; Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing; Oxford University Press; Nucleic Acids Research; 49; 2; 1-2021; 1133-1151
1362-4962
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkaa1260
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
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
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 13.22299

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