Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features

Bibliographic Details
Main Author: Caldas, Paulo
Publication Date: 2024
Other Authors: Luz, Mariana, Baseggio, Simone, Andrade, Rita, Sobral, Daniel, Grosso, Ana Rita
Format: Article
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/10362/166844
Summary: We thank João Neto, Silvia Carvalho, and the remaining Computational Multi-Omics Lab members at UCIBIO for their helpful comments and suggestions. Paulo Caldas was a recipient of a Marie Skłodowska-Curie Postdoctoral Fellowship (FOX-MTN-HORIZON-MSCA - 2021-PF-01-01). This work was financed by national funds from Fundação para a Ciência e Tecnologia (FCT), in the scope of the projects UIDP/04378/2020 and UIDB/04378/2020 of the Research Unit on Applied Molecular Biosciences (UCIBIO) and the project LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy - i4HB. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. Publisher Copyright: © 2024, The Author(s).
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spelling Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic featuresMedicine (miscellaneous)Biochemistry, Genetics and Molecular Biology(all)Agricultural and Biological Sciences(all)SDG 3 - Good Health and Well-beingWe thank João Neto, Silvia Carvalho, and the remaining Computational Multi-Omics Lab members at UCIBIO for their helpful comments and suggestions. Paulo Caldas was a recipient of a Marie Skłodowska-Curie Postdoctoral Fellowship (FOX-MTN-HORIZON-MSCA - 2021-PF-01-01). This work was financed by national funds from Fundação para a Ciência e Tecnologia (FCT), in the scope of the projects UIDP/04378/2020 and UIDB/04378/2020 of the Research Unit on Applied Molecular Biosciences (UCIBIO) and the project LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy - i4HB. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. Publisher Copyright: © 2024, The Author(s).Transcription termination is a crucial step in the production of conforming mRNAs and functional proteins. Under cellular stress conditions, the transcription machinery fails to identify the termination site and continues transcribing beyond gene boundaries, a phenomenon designated as transcription readthrough. However, the prevalence and impact of this phenomenon in healthy human tissues remain unexplored. Here, we assessed transcription readthrough in almost 3000 transcriptome profiles representing 23 human tissues and found that 34% of the expressed protein-coding genes produced readthrough transcripts. The production of readthrough transcripts was restricted in genomic regions with high transcriptional activity and was associated with inefficient splicing and increased chromatin accessibility in terminal regions. In addition, we showed that these transcripts contained several binding sites for the same miRNA, unravelling a potential role as miRNA sponges. Overall, this work provides evidence that transcription readthrough is pervasive and non-stochastic, not only in abnormal conditions but also in healthy tissues. This suggests a potential role for such transcripts in modulating normal cellular functions.UCIBIO - Applied Molecular Biosciences UnitDCV - Departamento de Ciências da VidaRUNCaldas, PauloLuz, MarianaBaseggio, SimoneAndrade, RitaSobral, DanielGrosso, Ana Rita2024-05-01T01:09:05Z2024-122024-12-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article12application/pdfhttp://hdl.handle.net/10362/166844engPURE: 89600326https://doi.org/10.1038/s42003-024-05779-5info:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2024-12-02T01:35:16Zoai:run.unl.pt:10362/166844Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-28T17:51:46.035290Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
dc.title.none.fl_str_mv Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features
title Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features
spellingShingle Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features
Caldas, Paulo
Medicine (miscellaneous)
Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)
SDG 3 - Good Health and Well-being
title_short Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features
title_full Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features
title_fullStr Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features
title_full_unstemmed Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features
title_sort Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features
author Caldas, Paulo
author_facet Caldas, Paulo
Luz, Mariana
Baseggio, Simone
Andrade, Rita
Sobral, Daniel
Grosso, Ana Rita
author_role author
author2 Luz, Mariana
Baseggio, Simone
Andrade, Rita
Sobral, Daniel
Grosso, Ana Rita
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv UCIBIO - Applied Molecular Biosciences Unit
DCV - Departamento de Ciências da Vida
RUN
dc.contributor.author.fl_str_mv Caldas, Paulo
Luz, Mariana
Baseggio, Simone
Andrade, Rita
Sobral, Daniel
Grosso, Ana Rita
dc.subject.por.fl_str_mv Medicine (miscellaneous)
Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)
SDG 3 - Good Health and Well-being
topic Medicine (miscellaneous)
Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)
SDG 3 - Good Health and Well-being
description We thank João Neto, Silvia Carvalho, and the remaining Computational Multi-Omics Lab members at UCIBIO for their helpful comments and suggestions. Paulo Caldas was a recipient of a Marie Skłodowska-Curie Postdoctoral Fellowship (FOX-MTN-HORIZON-MSCA - 2021-PF-01-01). This work was financed by national funds from Fundação para a Ciência e Tecnologia (FCT), in the scope of the projects UIDP/04378/2020 and UIDB/04378/2020 of the Research Unit on Applied Molecular Biosciences (UCIBIO) and the project LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy - i4HB. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. Publisher Copyright: © 2024, The Author(s).
publishDate 2024
dc.date.none.fl_str_mv 2024-05-01T01:09:05Z
2024-12
2024-12-01T00:00:00Z
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://hdl.handle.net/10362/166844
url http://hdl.handle.net/10362/166844
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv PURE: 89600326
https://doi.org/10.1038/s42003-024-05779-5
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 12
application/pdf
dc.source.none.fl_str_mv reponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
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