Studying relative RNA localization from nucleus to the cytosol

The precise coordination of important biological processes, such as differentiation and development, relies heavily on the regulation of gene expression. In eukaryotic cells, understanding the distribution of RNA transcripts between the nucleus and cytosol is essential for gaining valuable insights...

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Detalles Bibliográficos
Autores: Ntasis, Vasilis F., Guigó Serra, Roderic
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/71198
Acceso en línea:http://hdl.handle.net/10230/71198
http://dx.doi.org/10.1093/nargab/lqaf032
Access Level:acceso abierto
Palabra clave:RNA
Cèl·lules eucariotes
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spelling Studying relative RNA localization from nucleus to the cytosolNtasis, Vasilis F.Guigó Serra, RodericRNACèl·lules eucariotesThe precise coordination of important biological processes, such as differentiation and development, relies heavily on the regulation of gene expression. In eukaryotic cells, understanding the distribution of RNA transcripts between the nucleus and cytosol is essential for gaining valuable insights into the process of protein production. The most efficient way to estimate the levels of RNA species genome-wide is through RNA sequencing (RNAseq). While RNAseq can be performed separately in the nucleus and in the cytosol, comparing transcript levels between compartments is challenging since measurements are relative to the unknown total RNA volume. Here, we show theoretically that if, in addition to nuclear and cytosolic RNAseq, whole-cell RNAseq is also performed, then accurate estimations of the localization of transcripts can be obtained. Based on this, we designed a method that estimates, first the fraction of the total RNA volume in the cytosol (nucleus), and then, this fraction for every transcript. We evaluate our methodology on simulated data and nuclear and cytosolic single-cell data available. Finally, we use our method to investigate the subcellular localization of transcripts using bulk RNAseq data from the ENCODE project.Oxford University Press202520252025info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/71198http://dx.doi.org/10.1093/nargab/lqaf032reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésNAR Genom Bioinform. 2025 Jun 20;7(2):lqaf032© The Author(s) 2025. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/711982026-06-12T07:21:37Z
dc.title.none.fl_str_mv Studying relative RNA localization from nucleus to the cytosol
title Studying relative RNA localization from nucleus to the cytosol
spellingShingle Studying relative RNA localization from nucleus to the cytosol
Ntasis, Vasilis F.
RNA
Cèl·lules eucariotes
title_short Studying relative RNA localization from nucleus to the cytosol
title_full Studying relative RNA localization from nucleus to the cytosol
title_fullStr Studying relative RNA localization from nucleus to the cytosol
title_full_unstemmed Studying relative RNA localization from nucleus to the cytosol
title_sort Studying relative RNA localization from nucleus to the cytosol
dc.creator.none.fl_str_mv Ntasis, Vasilis F.
Guigó Serra, Roderic
author Ntasis, Vasilis F.
author_facet Ntasis, Vasilis F.
Guigó Serra, Roderic
author_role author
author2 Guigó Serra, Roderic
author2_role author
dc.subject.none.fl_str_mv RNA
Cèl·lules eucariotes
topic RNA
Cèl·lules eucariotes
description The precise coordination of important biological processes, such as differentiation and development, relies heavily on the regulation of gene expression. In eukaryotic cells, understanding the distribution of RNA transcripts between the nucleus and cytosol is essential for gaining valuable insights into the process of protein production. The most efficient way to estimate the levels of RNA species genome-wide is through RNA sequencing (RNAseq). While RNAseq can be performed separately in the nucleus and in the cytosol, comparing transcript levels between compartments is challenging since measurements are relative to the unknown total RNA volume. Here, we show theoretically that if, in addition to nuclear and cytosolic RNAseq, whole-cell RNAseq is also performed, then accurate estimations of the localization of transcripts can be obtained. Based on this, we designed a method that estimates, first the fraction of the total RNA volume in the cytosol (nucleus), and then, this fraction for every transcript. We evaluate our methodology on simulated data and nuclear and cytosolic single-cell data available. Finally, we use our method to investigate the subcellular localization of transcripts using bulk RNAseq data from the ENCODE project.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/71198
http://dx.doi.org/10.1093/nargab/lqaf032
url http://hdl.handle.net/10230/71198
http://dx.doi.org/10.1093/nargab/lqaf032
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv NAR Genom Bioinform. 2025 Jun 20;7(2):lqaf032
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
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:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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