ArticleJournal of the American Chemical Society2024
Mass Spectrometry-Based Direct Sequencing of tRNAs De Novo and Quantitative Mapping of Multiple RNA Modifications.
Article in Journal of the American Chemical Society, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- qMAP decodes RNA fragmentation dynamics in development and disease.Molecular systems biology · 2026Article
- Compendium of RNA modifications for bacterial stress adaptation.Microbiology and molecular biology reviews : MMBR · 2026Review
- Rapid Exonuclease-Based De Novo Sequencing Strategy for Long Oligonucleotides via Liquid-Phase Ion Trap Coupled With Mass Spectrometry.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Quantitative RNA modification mapping by mass spectrometry with isobaric tags and nucleobase fragment analysis.Nature communications · 2026Article
- Article
- De novo direct sequencing of small therapeutic RNAs by layer-by-layer intensity-resolved mass spectrometry.Nucleic acids research · 2026Article
- Integrating mass spectrometry with Nanopore direct RNA sequencing forbioRxiv : the preprint server for biology · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Mapping the rRNA methylome reveals contributions of methyltransferases to ribosome function and antibiotic sensitivity.bioRxiv : the preprint server for biology · 2026Article
- SnoRNA Expression and RNA 2'-O-Methylation inbioRxiv : the preprint server for biology · 2026Article
- Deciphering tRNA repertoires and translation coordination during mouse early embryogenesis by ORACLE-tRNAseq.Nature communications · 2026Article
- Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent mbioRxiv : the preprint server for biology · 2026Article
- Purification of post-transcriptionally modified tRNAs for enhanced cell-free translation systems.Nucleic acids research · 2026Article
- Hidden in plain sight: illuminating the tRNA landscape by sequencing.Genome biology · 2026Review
- Conserved shifts in sperm small non-coding RNA profiles during mouse and human aging.The EMBO journal · 2026Article
- MODOMICS: a database of RNA modifications and related information. 2025 update and 20th anniversary.Nucleic acids research · 2026Article
- A cholesterol-responsive hepatic tRNA-derived small RNA regulates cholesterol homeostasis and atherosclerosis development.Nature communications · 2025Article
- Peripheral blood RNA modifications as a novel diagnostic signature for polycystic ovary syndrome.Science China. Life sciences · 2025Article
- Unlocking the regulatory code of RNA: launching the Human RNome Project.Genome biology · 2025Article
- The Life of MicroRNAs: Biogenesis, Function and Decay in Cancer.Biomolecules · 2025Review
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Despite the extensive use of next-generation sequencing (NGS) of RNA, simultaneous direct sequencing and quantitative mapping of multiple RNA nucleotide modifications remains challenging. Mass spectrometry (MS)-based sequencing can directly sequence all RNA modifications without being limited to specific ones, but it requires a perfect MS ladder that few tRNAs can provide. Here, we describe an MS ladder complementation sequencing approach (MLC-Seq) that circumvents the perfect ladder requirement, allowing de novo MS sequencing of full-length heterogeneous cellular tRNAs with multiple nucleotide modifications at single-nucleotide precision. Unlike NGS-based methods, which lose RNA modification information, MLC-Seq preserves RNA sequence diversity and modification information, revealing new detailed stoichiometric tRNA modification profiles and their changes upon treatment with the dealkylating enzyme AlkB. It can also be combined with reference sequences to provide quantitative analysis of diverse tRNAs and modifications in total tRNA samples. MLC-Seq enables systematic, quantitative, and site-specific mapping of RNA modifications, revealing the truly complete informational content of tRNA.
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Registered trials
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