ArticleJournal of molecular biology2023
MRT-ModSeq - Rapid Detection of RNA Modifications with MarathonRT.
Article in Journal of molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Production of MarathonRT and its comparison with commercial reverse transcriptases for tRNA sequencing library preparation.RNA biology · 2026Article
- A B1 SINE element within the mouseScience advances · 2026Article
- Identifying RNA acInterdisciplinary sciences, computational life sciences · 2026Article
- One-Step Affinity Purification of MarathonRT Reverse Transcriptase for RNA Sequencing Applications.Bio-protocol · 2026Article
- Nanopore Sequencing Reveals rRNA Modification Changes in Human Cells Experiencing Oxidative or Inflammatory Stress.ACS chemical biology · 2026Article
- SnoRNA Expression and RNA 2'-O-Methylation inbioRxiv : the preprint server for biology · 2026Article
- Conserved structural features of the lncRNA HOTAIR in breast cancer cells.bioRxiv : the preprint server for biology · 2026Article
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- Post-Transcriptional Modifications of the Large Ribosome Subunit Assembly Intermediates inBiochemistry · 2025Article
- All the sites we cannot see: Sources and mitigation of false negatives in RNA modification studies.Nature reviews. Molecular cell biology · 2025Review
- Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes.Nature communications · 2025Article
- Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-seq.RNA (New York, N.Y.) · 2024Article
- Pan-cancer analysis of m1A writer gene RRP8: implications for immune infiltration and prognosis in human cancers.Discover oncology · 2024Article
- ac4C: a fragile modification with stabilizing functions in RNA metabolism.RNA (New York, N.Y.) · 2024Review
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Authors and funding
4 authors.
Funding
Abstract
Chemical modifications are essential regulatory elements that modulate the behavior and function of cellular RNAs. Despite recent advances in sequencing-based RNA modification mapping, methods combining accuracy and speed are still lacking. Here, we introduce MRT-ModSeq for rapid, simultaneous detection of multiple RNA modifications using MarathonRT. MRT-ModSeq employs distinct divalent cofactors to generate 2-D mutational profiles that are highly dependent on nucleotide identity and modification type. As a proof of concept, we use the MRT fingerprints of well-studied rRNAs to implement a general workflow for detecting RNA modifications. MRT-ModSeq rapidly detects positions of diverse modifications across a RNA transcript, enabling assignment of m1acp3Y, m1A, m3U, m7G and 2'-OMe locations through mutation-rate filtering and machine learning. m1A sites in sparsely modified targets, such as MALAT1 and PRUNE1 could also be detected. MRT-ModSeq can be trained on natural and synthetic transcripts to expedite detection of diverse RNA modification subtypes across targets of interest.
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Registered trials
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