{"doi":"10.1093/nar/gkaf696","title":"tRNA modification profiling reveals epitranscriptome regulatory networks in <i>Pseudomonas aeruginosa</i>","abstract":"Transfer RNA (tRNA) modifications have emerged as critical post-transcriptional regulators of gene expression affecting diverse biological and disease processes. While there is extensive knowledge about the enzymes installing the dozens of post-transcriptional tRNA modifications-the tRNA epitranscriptome-very little is known about how metabolic, signaling, and other networks integrate to regulate tRNA modification levels. Here, we took a comprehensive first step at understanding epitranscriptome regulatory networks by developing a high-throughput tRNA isolation and mass spectrometry-based modification profiling platform and applying it to a Pseudomonas aeruginosa transposon insertion mutant library comprising 5746 strains. Analysis of >200,000 tRNA modification data points validated the annotations of predicted tRNA modification genes, uncovered novel tRNA-modifying enzymes, and revealed tRNA modification regulatory networks in P. aeruginosa. Platform adaptation for RNA-seq library preparation would complement epitranscriptome studies, while application to human cell and mouse tissue would facilitate biomarker and drug discovery and development.","journal":"Nucleic Acids Research","year":2025,"id":518625,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9558,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":730971,"name":"Junzhou Wu","orcid":"0000-0002-9195-7910","position":1,"is_corresponding":false},{"id":388659,"name":"Yifeng Yuan","orcid":"0000-0002-9549-2698","position":2,"is_corresponding":false},{"id":1329653,"name":"Leon Fan","orcid":"0009-0007-4357-1013","position":3,"is_corresponding":false},{"id":1330043,"name":"Wei Lin Patrina Chua","orcid":null,"position":4,"is_corresponding":false},{"id":1003246,"name":"Yan Han Sharon Ling","orcid":null,"position":5,"is_corresponding":false},{"id":1084188,"name":"Seetharamsing Balamkundu","orcid":null,"position":6,"is_corresponding":false},{"id":1330044,"name":"Dwijapriya","orcid":null,"position":7,"is_corresponding":false},{"id":1386521,"name":"Hazel Suen Suen Chay","orcid":null,"position":8,"is_corresponding":false},{"id":394551,"name":"Thomas J. Begley","orcid":"0000-0002-5641-7644","position":9,"is_corresponding":false},{"id":259550,"name":"Valérie de Crécy‐Lagard","orcid":"0000-0002-9955-3785","position":10,"is_corresponding":false},{"id":1275557,"name":"Agnieszka Dziergowska","orcid":"0000-0002-8888-380X","position":11,"is_corresponding":false},{"id":289582,"name":"Peter C. Dedon","orcid":"0000-0003-0011-3067","position":12,"is_corresponding":false},{"id":655448,"name":"Jingjing Sun","orcid":"0000-0002-6892-8177","position":0,"is_corresponding":true}],"reference_count":93,"raw_metadata":null,"created_at":"2026-07-19T02:49:09.679930Z","pmid":"40716780","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}