ArticleNucleic acids research2025
MoDorado: enhanced detection of tRNA modifications in nanopore sequencing by off-label use of modification callers.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Emerging Roles of tRNA Modifications in Translational Adaptation of Human Fungal Pathogens.Microorganisms · 2026Review
- QutRNA2: robust tRNA modification discovery from Nanopore direct tRNA sequencing.NAR genomics and bioinformatics · 2026Article
- Review
- Evaluation of Dorado v5.2.0 de novo basecalling models for the detection of tRNA modifications using RNA004 chemistry.BMC genomics · 2026Article
- Systematic benchmarking of dorado basecalling models for RNA modification detection with highly multiplexed nanopore sequencing.Nucleic acids research · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- 5-Methylcytidine RNA Epitranscriptomics in Women's Health and Disease: Mechanisms and Clinical Implications.Cells · 2026Review
- Pseudouridylation landscape across 42bioRxiv : the preprint server for biology · 2026Article
- tRNA modification genes are associated with genomic instability, proliferative programs, and poor prognosis in breast cancer.Breast cancer (Tokyo, Japan) · 2026Article
- Veterinary Herpesviruses: Experimental Tools for Transcriptomics and Neuroscience.Veterinary sciences · 2026Review
- Hidden in plain sight: illuminating the tRNA landscape by sequencing.Genome biology · 2026Review
- ADAM-tRNA-seq: an optimized approach for demultiplexing and enhanced hierarchal mapping in direct tRNA sequencing.Nucleic acids research · 2026Article
- Advances in molecular tools for elucidating nucleic acid biology in fungal pathogens.microLife · 2026Review
- tRNA isodecoder analysis using Nanopore ionic current signals and deep learning.bioRxiv : the preprint server for biology · 2025Article
- WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing.Nucleic acids research · 2025Article
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Authors and funding
9 authors.
Funding
Abstract
Rapid and accurate identification of transfer RNA (tRNA) modifications is crucial for understanding their role in protein translation and disease. However, their detection on tRNAs is challenging due to high modification density. With the release of the nanopore direct RNA sequencing kit SQK-RNA004, de novo modification calling models became available for pseudouridine (Ψ), m6A, inosine, and m5C, as part of the Dorado basecaller. By applying the Ψ model to tRNAs, we mapped both known and previously uncharacterized Ψ sites in Schizosaccharomyces pombe, and identified the corresponding pseudouridine synthases. This led to the discovery of two novel modification sites, Pus7-dependent Ψ8 and Pus1-dependent Ψ22. Furthermore, we have developed MoDorado, an algorithm to detect modifications beyond those used in model training ("off-label use"). It does so by assessing differences in modification predictions between modified and nonmodified samples using pre-trained, modification-specific models. By repurposing the Ψ/m6A/inosine/m5C models, MoDorado detected seven additional modifications (ncm5U, mcm5U, mcm5s2U, m7G, queuosine, m1A, and i6A), thus generating an expanded map of these tRNA modifications in S. pombe. This work provides a generalized framework for leveraging pre-trained models in determining the intricate landscape of tRNA modifications.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.