ArticleRNA (New York, N.Y.)2013
HAMR: high-throughput annotation of modified ribonucleotides.
Article in RNA (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
92 citing papers in PubMed, 145 citations in OpenAlex.
- Article
- The mRNA covalent modification dihydrouridine regulates transcript turnover and photosynthetic capacity during plant abiotic stress.The Plant cell · 2026Article
- 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
- Identification of tRNA-Derived Fragments in Legumes.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- Block sparse Bayes-based fuzzy system for RNA N6-methyladenosine sites prediction.PLoS computational biology · 2025Article
- Transcriptome-wide mapping of N3-methylcytidine modification at single-base resolution.Nucleic acids research · 2025Article
- Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework.Genome research · 2024Article
- A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3' termini.Molecular cell · 2024Article
- Comparative analyses suggest a link between mRNA splicing, stability, and RNA covalent modifications in flowering plants.BMC plant biology · 2024Article
- General Principles and Limitations for Detection of RNA Modifications by Sequencing.Accounts of chemical research · 2024Article
- Detecting m6A RNA modification from nanopore sequencing using a semi-supervised learning framework.bioRxiv : the preprint server for biology · 2024Article
- Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing.Nature biotechnology · 2024Article
- mScience advances · 2023Article
- Analysis approaches for the identification and prediction ofEpigenetics · 2023Review
- Identifying N6-Methyladenosine Sites in HepG2 Cell Lines Using Oxford Nanopore Technology.International journal of molecular sciences · 2023Article
- Epitranscriptomic subtyping, visualization, and denoising by global motif visualization.Nature communications · 2023Article
- Artifacts and biases of the reverse transcription reaction in RNA sequencing.RNA (New York, N.Y.) · 2023Review
- A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3' termini.bioRxiv : the preprint server for biology · 2023Article
32 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
RNA is often altered post-transcriptionally by the covalent modification of particular nucleotides; these modifications are known to modulate the structure and activity of their host RNAs. The recent discovery that an RNA methyl-6 adenosine demethylase (FTO) is a risk gene in obesity has brought to light the significance of RNA modifications to human biology. These noncanonical nucleotides, when converted to cDNA in the course of RNA sequencing, can produce sequence patterns that are distinguishable from simple base-calling errors. To determine whether these modifications can be detected in RNA sequencing data, we developed a method that can not only locate these modifications transcriptome-wide with single nucleotide resolution, but can also differentiate between different classes of modifications. Using small RNA-seq data we were able to detect 92% of all known human tRNA modification sites that are predicted to affect RT activity. We also found that different modifications produce distinct patterns of cDNA sequence, allowing us to differentiate between two classes of adenosine and two classes of guanine modifications with 98% and 79% accuracy, respectively. To show the robustness of this method to sample preparation and sequencing methods, as well as to organismal diversity, we applied it to a publicly available yeast data set and achieved similar levels of accuracy. We also experimentally validated two novel and one known 3-methylcytosine (3mC) sites predicted by HAMR in human tRNAs. Researchers can now use our method to identify and characterize RNA modifications using only RNA-seq data, both retrospectively and when asking questions specifically about modified RNA.
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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.