ArticleNucleic acids research2020
Machine learning of reverse transcription signatures of variegated polymerases allows mapping and discrimination of methylated purines in limited transcriptomes.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 57 citations in OpenAlex.
- Defining cell surface and glycosylated RNAs.Trends in genetics : TIG · 2026Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling.Genome biology · 2026Article
- Remodeling of tRNA modification in Trypanosoma cruzi life forms.PLoS pathogens · 2026Article
- RNA modifications and cancer ferroptosis.Cancer cell international · 2026Review
- Emerging role of N-acetyltransferase 10 in diseases: RNA ac4C modification and beyond.Molecular biomedicine · 2025Review
- The Mysterious World of Non-Canonical Caps - What We Know and Why We Need New Sequencing Techniques.Chembiochem : a European journal of chemical biology · 2025Review
- Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes.Nature communications · 2025Article
- tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development.Nucleic acids research · 2024Article
- Enhanced ac4C detection in RNA via chemical reduction and cDNA synthesis with modified dNTPs.RNA (New York, N.Y.) · 2024Article
- N1-methylation of adenosine (mMolecular psychiatry · 2024Article
- Advances in methods for tRNA sequencing and quantification.Trends in genetics : TIG · 2024Review
- General Principles and Limitations for Detection of RNA Modifications by Sequencing.Accounts of chemical research · 2024Article
- Mapping the tRNA modification landscape ofFrontiers in microbiology · 2024Article
- Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing.Nature biotechnology · 2024Article
- Artifacts and biases of the reverse transcription reaction in RNA sequencing.RNA (New York, N.Y.) · 2023Review
- MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT.bioRxiv : the preprint server for biology · 2023Article
- Extracellular RNA: mechanisms of secretion and potential functions.Journal of experimental botany · 2023Article
- ALL-tRNAseq enables robust tRNA profiling in tissue samples.Genes & development · 2023Article
- Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing.Nature methods · 2023Article
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Authors and funding
13 authors at 4 institutions in 3 countries.
Funding
Abstract
Reverse transcription (RT) of RNA templates containing RNA modifications leads to synthesis of cDNA containing information on the modification in the form of misincorporation, arrest, or nucleotide skipping events. A compilation of such events from multiple cDNAs represents an RT-signature that is typical for a given modification, but, as we show here, depends also on the reverse transcriptase enzyme. A comparison of 13 different enzymes revealed a range of RT-signatures, with individual enzymes exhibiting average arrest rates between 20 and 75%, as well as average misincorporation rates between 30 and 75% in the read-through cDNA. Using RT-signatures from individual enzymes to train a random forest model as a machine learning regimen for prediction of modifications, we found strongly variegated success rates for the prediction of methylated purines, as exemplified with N1-methyladenosine (m1A). Among the 13 enzymes, a correlation was found between read length, misincorporation, and prediction success. Inversely, low average read length was correlated to high arrest rate and lower prediction success. The three most successful polymerases were then applied to the characterization of RT-signatures of other methylated purines. Guanosines featuring methyl groups on the Watson-Crick face were identified with high confidence, but discrimination between m1G and m22G was only partially successful. In summary, the results suggest that, given sufficient coverage and a set of specifically optimized reaction conditions for reverse transcription, all RNA modifications that impede Watson-Crick bonds can be distinguished by their RT-signature.
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