ArticleBiomolecules2017
Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2'-O-Methylation.
Article in Biomolecules, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 67 citations in OpenAlex.
- Article
- Review
- Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies.Nucleic acids research · 2026Article
- RNA modifications in cancer: from biological insights to therapeutic targets.Bioorganic & medicinal chemistry · 2026Review
- tRNA-modifying enzymes in bacterial stress adaptation.Open biology · 2025Review
- The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae.PLoS genetics · 2025Article
- 2'-O-methylation and N6-methyladenosine enhance the oral delivery of small RNAs in mice.Molecular therapy. Nucleic acids · 2025Article
- Protein Functional Effector (pfe) Noncoding RNAS Are Identical to Fragments from Various Noncoding RNAs.International journal of molecular sciences · 2025Article
- RNA modification gene WDR4 facilitates tumor progression and immunotherapy resistance in breast cancer.Journal of advanced research · 2025Article
- The detection, function, and therapeutic potential of RNA 2'-O-methylation.The innovation life · 2025Article
- Differential redox sensitivity of tRNA dihydrouridylation.Nucleic acids research · 2024Article
- 2'-RNA (New York, N.Y.) · 2024Review
- Complicated target recognition by archaeal box C/D guide RNAs.Science China. Life sciences · 2024Article
- An integrative platform for detection of RNA 2'-O-methylation reveals its broad distribution on mRNA.Cell reports methods · 2024Article
- Base-Resolution Sequencing Methods for Whole-Transcriptome Quantification of mRNA Modifications.Accounts of chemical research · 2024Article
- Mapping the tRNA modification landscape ofFrontiers in microbiology · 2024Article
- Nm-Mut-seq: a base-resolution quantitative method for mapping transcriptome-wide 2'-O-methylation.Cell research · 2023Article
- Single-base resolution mapping of 2'-O-methylation sites by an exoribonuclease-enriched chemical method.Science China. Life sciences · 2023Article
- The ribose methylation enzyme FTSJ1 has a conserved role in neuron morphology and learning performance.Life science alliance · 2023Article
- Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications.International journal of molecular sciences · 2022Review
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analysis of RNA modifications by traditional physico-chemical approaches is labor intensive, requires substantial amounts of input material and only allows site-by-site measurements. The recent development of qualitative and quantitative approaches based on next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA species. The Illumina sequencing-based RiboMethSeq protocol was initially developed and successfully applied for mapping of ribosomal RNA (rRNA) 2'-O-methylations. This method also gives excellent results in the quantitative analysis of rRNA modifications in different species and under varying growth conditions. However, until now, RiboMethSeq was only employed for rRNA, and the whole sequencing and analysis pipeline was only adapted to this long and rather conserved RNA species. A deep understanding of RNA modification functions requires large and global analysis datasets for other important RNA species, namely for transfer RNAs (tRNAs), which are well known to contain a great variety of functionally-important modified residues. Here, we evaluated the application of the RiboMethSeq protocol for the analysis of tRNA 2'-O-methylation in Escherichia coli and in Saccharomyces cerevisiae. After a careful optimization of the bioinformatic pipeline, RiboMethSeq proved to be suitable for relative quantification of methylation rates for known modified positions in different tRNA species.
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