Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation

Transfer RNA (tRNA) utilizes multiple properties of abundance, modification, and aminoacylation in translational regulation. These properties were typically studied one-by-one; however, recent advance in high throughput tRNA sequencing enables their simultaneous assessment in the same sequencing dat...

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Autores: Hernandez-Alias, Xavier, Katanski, Christopher D., Zhang, Wen, Assari, Mahdi, Watkins, Christopher P., Schaefer, Martin H., Serrano Pubull, Luis, 1982-, Pan, Tao
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/57319
Acceso en línea:http://hdl.handle.net/10230/57319
http://dx.doi.org/10.1093/nar/gkac1185
Access Level:acceso abierto
Palabra clave:Ribosomes
Protein Translation
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spelling Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentationHernandez-Alias, XavierKatanski, Christopher D.Zhang, WenAssari, MahdiWatkins, Christopher P.Schaefer, Martin H.Serrano Pubull, Luis, 1982-Pan, TaoRibosomesProtein TranslationTransfer RNA (tRNA) utilizes multiple properties of abundance, modification, and aminoacylation in translational regulation. These properties were typically studied one-by-one; however, recent advance in high throughput tRNA sequencing enables their simultaneous assessment in the same sequencing data. How these properties are coordinated at the transcriptome level is an open question. Here, we develop a single-read tRNA analysis pipeline that takes advantage of the pseudo single-molecule nature of tRNA sequencing in NGS libraries. tRNAs are short enough that a single NGS read can represent one tRNA molecule, and can simultaneously report on the status of multiple modifications, aminoacylation, and fragmentation of each molecule. We find correlations among modification-modification, modification-aminoacylation and modification-fragmentation. We identify interdependencies among one of the most common tRNA modifications, m1A58, as coordinators of tissue-specific gene expression. Our method, SingLe-read Analysis of Crosstalks (SLAC), reveals tRNAome-wide networks of modifications, aminoacylation, and fragmentation. We observe changes of these networks under different stresses, and assign a function for tRNA modification in translational regulation and fragment biogenesis. SLAC leverages the richness of the tRNA-seq data and provides new insights on the coordination of tRNA properties.Oxford University Press202320232023info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/57319http://dx.doi.org/10.1093/nar/gkac1185reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésNucleic Acids Res. 2023 Feb 22;51(3):e17© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. 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:10230/573192026-06-12T07:21:37Z
dc.title.none.fl_str_mv Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation
title Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation
spellingShingle Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation
Hernandez-Alias, Xavier
Ribosomes
Protein Translation
title_short Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation
title_full Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation
title_fullStr Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation
title_full_unstemmed Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation
title_sort Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation
dc.creator.none.fl_str_mv Hernandez-Alias, Xavier
Katanski, Christopher D.
Zhang, Wen
Assari, Mahdi
Watkins, Christopher P.
Schaefer, Martin H.
Serrano Pubull, Luis, 1982-
Pan, Tao
author Hernandez-Alias, Xavier
author_facet Hernandez-Alias, Xavier
Katanski, Christopher D.
Zhang, Wen
Assari, Mahdi
Watkins, Christopher P.
Schaefer, Martin H.
Serrano Pubull, Luis, 1982-
Pan, Tao
author_role author
author2 Katanski, Christopher D.
Zhang, Wen
Assari, Mahdi
Watkins, Christopher P.
Schaefer, Martin H.
Serrano Pubull, Luis, 1982-
Pan, Tao
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Ribosomes
Protein Translation
topic Ribosomes
Protein Translation
description Transfer RNA (tRNA) utilizes multiple properties of abundance, modification, and aminoacylation in translational regulation. These properties were typically studied one-by-one; however, recent advance in high throughput tRNA sequencing enables their simultaneous assessment in the same sequencing data. How these properties are coordinated at the transcriptome level is an open question. Here, we develop a single-read tRNA analysis pipeline that takes advantage of the pseudo single-molecule nature of tRNA sequencing in NGS libraries. tRNAs are short enough that a single NGS read can represent one tRNA molecule, and can simultaneously report on the status of multiple modifications, aminoacylation, and fragmentation of each molecule. We find correlations among modification-modification, modification-aminoacylation and modification-fragmentation. We identify interdependencies among one of the most common tRNA modifications, m1A58, as coordinators of tissue-specific gene expression. Our method, SingLe-read Analysis of Crosstalks (SLAC), reveals tRNAome-wide networks of modifications, aminoacylation, and fragmentation. We observe changes of these networks under different stresses, and assign a function for tRNA modification in translational regulation and fragment biogenesis. SLAC leverages the richness of the tRNA-seq data and provides new insights on the coordination of tRNA properties.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023
2023
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/10230/57319
http://dx.doi.org/10.1093/nar/gkac1185
url http://hdl.handle.net/10230/57319
http://dx.doi.org/10.1093/nar/gkac1185
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Nucleic Acids Res. 2023 Feb 22;51(3):e17
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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