ArticlePloS one2019
Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
113 citing papers in PubMed, 210 citations in OpenAlex.
- Review
- Interrogating the Escherichia coli Epitranscriptome Via CRISPR Interference and Nanopore Native RNA Sequencing.MicrobiologyOpen · 2026Article
- Integrating mass spectrometry with Nanopore direct RNA sequencing forbioRxiv : the preprint server for biology · 2026Article
- 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
- Assessment of nanopore RNA modification calling in human cell lines and synthetic systems.Genome biology · 2026Article
- CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing.Briefings in bioinformatics · 2026Article
- tRNA isodecoder analysis using Nanopore ionic current signals and deep learning.bioRxiv : the preprint server for biology · 2025Article
- Advances in Quantitative Techniques for Mapping RNA Modifications.Life (Basel, Switzerland) · 2025Review
- EIciRNAs in focus: current understanding and future perspectives.RNA biology · 2025Review
- mRNA vaccines: immunogenicity and quality characteristics.Journal of nanobiotechnology · 2025Review
- Saskemycin, a potent and selective antimycobacterial agent targeting a unique site on the ribosome.Research square · 2025Article
- DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.Genome biology · 2025Article
- De novo basecalling of RNA modifications at single molecule and nucleotide resolution.Genome biology · 2025Article
- TRMT1L-catalyzed mCell reports · 2025Article
- High-throughput detection of RNA modifications at single base resolution.FEBS letters · 2025Review
- When animal viruses meet NVeterinary research · 2024Review
- Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites.Nature communications · 2024Article
- Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models.Genome research · 2024Article
- Direct RNA sequencing in plants: Practical applications and future perspectives.Plant communications · 2024Review
53 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
5 authors at 2 institutions in 2 countries.
Funding
Abstract
The ribosome small subunit is expressed in all living cells. It performs numerous essential functions during translation, including formation of the initiation complex and proofreading of base-pairs between mRNA codons and tRNA anticodons. The core constituent of the small ribosomal subunit is a ~1.5 kb RNA strand in prokaryotes (16S rRNA) and a homologous ~1.8 kb RNA strand in eukaryotes (18S rRNA). Traditional sequencing-by-synthesis (SBS) of rRNA genes or rRNA cDNA copies has achieved wide use as a 'molecular chronometer' for phylogenetic studies, and as a tool for identifying infectious organisms in the clinic. However, epigenetic modifications on rRNA are erased by SBS methods. Here we describe direct MinION nanopore sequencing of individual, full-length 16S rRNA absent reverse transcription or amplification. As little as 5 picograms (~10 attomole) of purified E. coli 16S rRNA was detected in 4.5 micrograms of total human RNA. Nanopore ionic current traces that deviated from canonical patterns revealed conserved E. coli 16S rRNA 7-methylguanosine and pseudouridine modifications, and a 7-methylguanosine modification that confers aminoglycoside resistance to some pathological E. coli strains.
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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.