ArticleThe Analyst2020
Improved RNA modification mapping of cellular non-coding RNAs using C- and U-specific RNases.
Article in The Analyst, 2020. 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, 39 citations in OpenAlex.
- Human 28S rRNA analysed by state-of-the-art oligonucleotide mass spectrometry: benchmarking current capabilities and a call to action for MS-Seq.bioRxiv : the preprint server for biology · 2026Article
- A nanogram-sensitive workflow for oligonucleotide mass spectrometry using ion-pair-free nanoflow HILIC and RNase benchmarking.Nucleic acids research · 2026Article
- Direct LC-HRMS/MS characterisation and RT-qPCR detection for potential mRNA-based doping agent.Analytical and bioanalytical chemistry · 2026Article
- Integrating mass spectrometry with Nanopore direct RNA sequencing forbioRxiv : the preprint server for biology · 2026Article
- tRNA modifications in viral replication.The Journal of biological chemistry · 2026Review
- Mapping the rRNA methylome reveals contributions of methyltransferases to ribosome function and antibiotic sensitivity.bioRxiv : the preprint server for biology · 2026Article
- RNase 4 improves bottom-up modification mapping ofbioRxiv : the preprint server for biology · 2026Article
- Pseudouridylation landscape across 42bioRxiv : the preprint server for biology · 2026Article
- Analysis of RNA and Its Modifications.Annual review of analytical chemistry (Palo Alto, Calif.) · 2024Review
- Mapping mMethods and protocols · 2024Article
- In-Gel Cyanoethylation for Pseudouridines Mass Spectrometry Detection of Bacterial Regulatory RNA.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Sample transformation in online separations: how chemical conversion advances analytical technology.Chemical communications (Cambridge, England) · 2023Review
- Direct sequencing of totalRNA (New York, N.Y.) · 2023Article
- Challenges and emerging trends in liquid chromatography-based analyses of mRNA pharmaceuticals.Journal of pharmaceutical and biomedical analysis · 2023Review
- Human RNase 4 improves mRNA sequence characterization by LC-MS/MS.Nucleic acids research · 2022Article
- RNA Cleavage Properties of Nucleobase-Specific RNase MC1 and Cusativin Are Determined by the Dinucleotide-Binding Interactions in the Enzyme-Active Site.International journal of molecular sciences · 2022Article
- Pytheas: a software package for the automated analysis of RNA sequences and modifications via tandem mass spectrometry.Nature communications · 2022Article
- Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcriptRNA (New York, N.Y.) · 2022Article
- Review
- Epigenetics: Roles and therapeutic implications of non-coding RNA modifications in human cancers.Molecular therapy. Nucleic acids · 2021Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Locating ribonucleoside modifications within an RNA sequence requires digestion of the RNA into oligoribonucleotides of amenable size for subsequent analysis by LC-MS (liquid chromatography-mass spectrometry). This approach, widely referred to as RNA modification mapping, is facilitated through ribonucleases (RNases) such as T1 (guanosine-specific), U2 (purine-selective) and A (pyrimidine-specific) among others. Sequence coverage by these enzymes depends on positioning of the recognized nucleobase (such as guanine or purine or pyrimidine) in the sequence and its ribonucleotide composition. Using E. coli transfer RNA (tRNA) and ribosomal RNA (rRNA) as model samples, we demonstrate the ability of complementary nucleobase-specific ribonucleases cusativin (C-specific) and MC1 (U-specific) to generate digestion products that facilitate confident mapping of modifications in regions such as G-rich and pyrimidine-rich segments of RNA, and to distinguish C to U sequence differences. These enzymes also increase the number of oligonucleotide digestion products that are unique to a specific RNA sequence. Further, with these additional RNases, multiple modifications can be localized with high confidence in a single set of experiments with minimal dependence on the individual tRNA abundance in a mixture. The sequence overlaps observed with these complementary digestion products and that of RNase T1 improved sequence coverage to 75% or above. A similar level of sequence coverage was also observed for the 2904 nt long 23S rRNA indicating their utility has no dependence on RNA size. Wide-scale adoption of these additional modification mapping tools could help expedite the characterization of modified RNA sequences to understand their structural and functional role in various living systems.
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Registered trials
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.