{"doi":"10.1261/rna.079966.124","title":"Chemical manipulation of m<sup>1</sup>A mediates its detection in human tRNA","abstract":"N 1 -methyl adenosine (m 1 A) is a widespread RNA modification present in tRNA, rRNA, and mRNA. m 1 A modification sites in tRNAs are evolutionarily conserved and its formation on tRNA is catalyzed by methyltransferase TRMT61A and TRMT6 complex. m 1 A promotes translation initiation and elongation. Due to its positive charge under physiological conditions, m 1 A can notably modulate RNA structure. It also blocks Watson–Crick–Franklin base-pairing and causes mutation and truncation during reverse transcription. Several misincorporation-based high-throughput sequencing methods have been developed to sequence m 1 A. In this study, we introduce a reduction-based m 1 A sequencing (red-m 1 A-seq). We report that NaBH 4 reduction of m 1 A can improve the mutation and readthrough rates using commercially available RT enzymes to give a better positive signature, while alkaline-catalyzed Dimroth rearrangement can efficiently convert m 1 A to m 6 A to provide good controls, allowing the detection of m 1 A with higher sensitivity and accuracy. We applied red-m 1 A-seq to sequence human small RNA, and we not only detected all the previously reported tRNA m 1 A sites, but also new m 1 A sites in mt-tRNA Asn-GTT and 5.8S rRNA.","journal":"RNA","year":2024,"id":432103,"datarank":0.42498200160843247,"base_score":2.833213344056216,"endowment":2.833213344056216,"self_citation_contribution":0.42498200160843247,"citation_network_contribution":0.0,"self_endowment_contribution":0.42498200160843247,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":16,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9587,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":262498,"name":"Ruitu Lyu","orcid":"0000-0003-4597-1604","position":1,"is_corresponding":false},{"id":109070,"name":"Xiaoyang Dou","orcid":"0000-0003-3742-1813","position":2,"is_corresponding":false},{"id":841799,"name":"Chang Ye","orcid":"0000-0003-0236-5671","position":3,"is_corresponding":false},{"id":243495,"name":"Li-Sheng Zhang","orcid":null,"position":4,"is_corresponding":false},{"id":233670,"name":"Qing Dai","orcid":"0000-0002-8578-1568","position":5,"is_corresponding":false},{"id":21408,"name":"Chuan He","orcid":"0000-0003-4319-7424","position":6,"is_corresponding":false},{"id":622153,"name":"Kinga Pajdzik","orcid":null,"position":0,"is_corresponding":true}],"reference_count":40,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:59:35.267142Z","pmid":"38531647","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":[]}