{rfName}
Qu

Indexed in

License and use

Icono OpenAccess

Citations

242

Altmetrics

Grant support

We thank all the members of the Novoa laboratory for their valuable insights and discussions. We thank V. Malhotra for providing us with the S. cerevisiae Pus4 KO strains used in this work. We thank the CRG Protein Technologies Unit for producing recombinant E. coli T4 RNA Ligase 2. We thank A. Delgado-Tejedor for help setting up simulations on bulk data from S. cerevisiae Pus1 and Pus7 KO Nano-tRNAseq runs. M.C.L. is supported by an FPI Severo Ochoa fellowship by the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC). L.P.P. is supported by funding from the European Union's H2020 Research and Innovation Programme under Marie Sklodowska-Curie grant agreement number 754422. I.M. is supported by 'la Caixa' InPhINIT PhD fellowship (LCF/BQ/DI18/11660028). This work was supported by funds from the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) (PID2021-128193NB-100 to E.M.N.). This project has received funding from the ERCEA program (ERC-StG-2021 under grant agreement number 101042103 to E.M.N.). We acknowledge the support of the MEIC to the EMBL partnership, Centro de Excelencia Severo Ochoa and CERCA Programme/Generalitat de Catalunya.

Analysis of institutional authors

Lucas McAuthorPryszcz LpAuthorMedina RAuthorMilenkovic IAuthorNovoa EmCorresponding Author

Share

April 11, 2023
Publications
>
Article
Sí

Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing

Publicated to:Nature Biotechnology. 42 (1): 72-86 - 2024-01-01 42(1), DOI: 10.1038/s41587-023-01743-6

Authors: Lucas, MC; Pryszcz, LP; Medina, R; Milenkovic, I; Camacho, N; Marchand, V; Motorin, Y; de Pouplana, LR; Novoa, EM

Affiliations

Barcelona Inst Sci & Technol, Ctr Genom Regulat CRG, Barcelona, Spain - Author
Catalan Inst Res & Adv Studies ICREA, Barcelona, Spain - Author
Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain. - Author
Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain. - Author
Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain. eva.novoa@crg.eu. - Author
CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France. - Author
Inst Res Biomed IRB, Barcelona, Spain - Author
Institute for Research in Biomedicine (IRB), Barcelona, Spain. - Author
Univ Lorraine, CNRS, UAR2008 IBSLor, UMR7365 IMoPA, Nancy, France - Author
Univ Pompeu Fabra UPF, Barcelona, Spain - Author
Universitat Pompeu Fabra (UPF), Barcelona, Spain. - Author
Universitat Pompeu Fabra (UPF), Barcelona, Spain. eva.novoa@crg.eu. - Author
See more

Abstract

Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both tRNA abundances and modification dynamics in a single experiment. We show that default nanopore sequencing settings discard the vast majority of tRNA reads, leading to poor sequencing yields and biased representations of tRNA abundances based on their transcript length. Re-processing of raw nanopore current intensity signals leads to a 12-fold increase in the number of recovered tRNA reads and enables recapitulation of accurate tRNA abundances. We then apply Nano-tRNAseq to Saccharomyces cerevisiae tRNA populations, revealing crosstalks and interdependencies between different tRNA modification types within the same molecule and changes in tRNA populations in response to oxidative stress.© 2023. The Author(s).

Keywords

anticodon loopbreast-cancercodon usageposttranscriptional modificationsrevealssynthaseu2 snrnauridine-5-oxyacetic acidyeastSaccharomyces-cerevisiae

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nature Biotechnology due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2024 there are still no calculated indicators, but in 2023, it was in position 2/174, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biotechnology & Applied Microbiology. Notably, the journal is positioned above the 90th percentile.

This publication has been distinguished as a “Highly Cited Paper” by the agencies WoS (ESI, Clarivate) and ESI (Clarivate), meaning that it ranks within the top 1% of the most cited articles in its thematic field during the year of its publication. In terms of the observed impact of the contribution, this work is considered one of the most influential worldwide, as it is recognized as highly cited. (source consulted: ESI Nov 14, 2024)

And this is evidenced by the extremely high normalized impacts through some of the main indicators of this type, which, although dynamic over time and dependent on the set of average global citations at the time of calculation, already indicate that they are well above the average in different agencies:

  • Field Citation Ratio (FCR) from Dimensions: 55.18 (source consulted: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-16, the following number of citations:

  • WoS: 64
  • Europe PMC: 91

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-16:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 224.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 279 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 369.85.
  • The number of mentions on the social network Facebook: 2 (Altmetric).
  • The number of mentions on the social network X (formerly Twitter): 294 (Altmetric).
  • The number of mentions in news outlets: 27 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: France.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Lucas, Morghan C) and Last Author (NOVOA PARDO, EVA MARIA).

the author responsible for correspondence tasks has been NOVOA PARDO, EVA MARIA.