Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines
- Publikationstyp:
- Zeitschriftenaufsatz
- Metadaten:
-
- Autoren
- Florian Pichot
- Marion C Hogg
- Virginie Marchand
- Valerie Bourguignon
- Elisabeth Jirstrom
- Cliona Farrell
- Hesham A Gibriel
- Jochen HM Prehn
- Yuri Motorin
- Mark Helm
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000909090200001&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1016/j.csbj.2022.12.020
- Externe Identifier
- Clarivate Analytics Document Solution ID: 7Q0ME
- PubMed Identifier: 36618980
- ISSN
- 2001-0370
- Zeitschrift
- COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
- Schlüsselwörter
- TRNA
- Modification
- TRNA fragments
- Angiogenin
- Modification mapping
- RNAseq
- Paginierung
- 401 - 417
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Titel
- Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines
- Sub types
- Article
- Ausgabe der Zeitschrift
- 21
Datenquelle: Web of Science (Lite)
- Andere Metadatenquellen:
-
- Autoren
- Florian Pichot
- Marion C Hogg
- Virginie Marchand
- Valérie Bourguignon
- Elisabeth Jirström
- Cliona Farrell
- Hesham A Gibriel
- Jochen HM Prehn
- Yuri Motorin
- Mark Helm
- DOI
- 10.1016/j.csbj.2022.12.020
- ISSN
- 2001-0370
- Zeitschrift
- Computational and Structural Biotechnology Journal
- Sprache
- en
- Paginierung
- 401 - 417
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Herausgeber
- Elsevier BV
- Herausgeber URL
- http://dx.doi.org/10.1016/j.csbj.2022.12.020
- Datum der Datenerfassung
- 2024
- Titel
- Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines
- Ausgabe der Zeitschrift
- 21
Datenquelle: Crossref
- Abstract
- Modification of tRNA is an integral part of the epitranscriptome with a particularly pronounced potential to generate diversity in RNA expression. Eukaryotic tRNA contains modifications in up to 20% of their nucleotides, but not all sites are always fully modified. Combinations and permutations of partially modified sites in tRNAs can generate a plethora of tRNA isoforms, termed modivariants. Here, we investigate the stoichiometry of incompletely modified sites in tRNAs from human cell lines for their information content. Using a panel of RNA modification mapping methods, we assess the stoichiometry of sites that contain the modifications 5-methylcytidine (m<sup>5</sup>C), 2'-O-ribose methylation (Nm), 3-methylcytidine (m<sup>3</sup>C), 7-methylguanosine (m<sup>7</sup>G), and Dihydrouridine (D). We discovered that up to 75% of sites can be incompletely modified and that the differential modification status of a cellular tRNA population holds information that allows to discriminate e.g. different cell lines. As a further aspect, we investigated potential causal connectivity between tRNA modification and its processing into tRNA fragments (tiRNAs and tRFs). Upon exposure of cultured living cells to cell-penetrating angiogenin, the modification patterns of the corresponding RNA populations was changed. Importantly, we also found that tsRNAs were significantly less modified than their parent tRNAs at numerous sites, suggesting that tsRNAs might derive chiefly from hypomodified tRNAs.
- Addresses
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany.
- Autoren
- Florian Pichot
- Marion C Hogg
- Virginie Marchand
- Valérie Bourguignon
- Elisabeth Jirström
- Cliona Farrell
- Hesham A Gibriel
- Jochen HM Prehn
- Yuri Motorin
- Mark Helm
- DOI
- 10.1016/j.csbj.2022.12.020
- eISSN
- 2001-0370
- Externe Identifier
- PubMed Identifier: 36618980
- PubMed Central ID: PMC9798144
- Funding acknowledgements
- Federal Ministry of Education and Research Bonn Office:
- European Regional Development Fund: 17/JPND/3455
- EU Joint Programme Neurodegenerative Disease Research:
- Science Foundation Ireland: 16/RC/3948
- Deutsche Forschungsgemeinschaft: HE 3397/21-1
- Royal College of Surgeons in Ireland: 01ED1804
- Open access
- true
- ISSN
- 2001-0370
- Zeitschrift
- Computational and structural biotechnology journal
- Sprache
- eng
- Medium
- Electronic-eCollection
- Online publication date
- 2022
- Open access status
- Open Access
- Paginierung
- 401 - 417
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Publisher licence
- CC BY
- Datum der Datenerfassung
- 2023
- Titel
- Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines.
- Sub types
- research-article
- Journal Article
- Ausgabe der Zeitschrift
- 21
Files
http://www.csbj.org/article/S2001037022005773/pdf https://europepmc.org/articles/PMC9798144?pdf=render
Datenquelle: Europe PubMed Central
- Abstract
- Modification of tRNA is an integral part of the epitranscriptome with a particularly pronounced potential to generate diversity in RNA expression. Eukaryotic tRNA contains modifications in up to 20% of their nucleotides, but not all sites are always fully modified. Combinations and permutations of partially modified sites in tRNAs can generate a plethora of tRNA isoforms, termed modivariants. Here, we investigate the stoichiometry of incompletely modified sites in tRNAs from human cell lines for their information content. Using a panel of RNA modification mapping methods, we assess the stoichiometry of sites that contain the modifications 5-methylcytidine (m5C), 2'-O-ribose methylation (Nm), 3-methylcytidine (m3C), 7-methylguanosine (m7G), and Dihydrouridine (D). We discovered that up to 75% of sites can be incompletely modified and that the differential modification status of a cellular tRNA population holds information that allows to discriminate e.g. different cell lines. As a further aspect, we investigated potential causal connectivity between tRNA modification and its processing into tRNA fragments (tiRNAs and tRFs). Upon exposure of cultured living cells to cell-penetrating angiogenin, the modification patterns of the corresponding RNA populations was changed. Importantly, we also found that tsRNAs were significantly less modified than their parent tRNAs at numerous sites, suggesting that tsRNAs might derive chiefly from hypomodified tRNAs.
- Date of acceptance
- 2022
- Autoren
- Florian Pichot
- Marion C Hogg
- Virginie Marchand
- Valérie Bourguignon
- Elisabeth Jirström
- Cliona Farrell
- Hesham A Gibriel
- Jochen HM Prehn
- Yuri Motorin
- Mark Helm
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/36618980
- DOI
- 10.1016/j.csbj.2022.12.020
- Externe Identifier
- PubMed Central ID: PMC9798144
- ISSN
- 2001-0370
- Zeitschrift
- Comput Struct Biotechnol J
- Schlüsselwörter
- Angiogenin
- Modification
- Modification mapping
- RNAseq
- TRNA
- TRNA fragments
- Sprache
- eng
- Country
- Netherlands
- Paginierung
- 401 - 417
- PII
- S2001-0370(22)00577-3
- Datum der Veröffentlichung
- 2023
- Status
- Published online
- Titel
- Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines.
- Sub types
- Journal Article
- Ausgabe der Zeitschrift
- 21
Datenquelle: PubMed
- Beziehungen:
- Eigentum von