ArticleRNA biology2023
Comprehensive identification of diverse ribosomal RNA modifications by targeted nanopore direct RNA sequencing and JACUSA2.
Article in RNA biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 19 citations in OpenAlex.
- QutRNA2: robust tRNA modification discovery from Nanopore direct tRNA sequencing.NAR genomics and bioinformatics · 2026Article
- ModiCal: A Targeted Calibration Workflow for Site-Specific mACS chemical biology · 2026Article
- Systematic benchmarking of dorado basecalling models for RNA modification detection with highly multiplexed nanopore sequencing.Nucleic acids research · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Mapping human pre-rRNA processing and modification at single nucleotide resolution using long read nanopore sequencing.Nature communications · 2026Article
- Review
- Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications.Nucleic acids research · 2025Article
- A direct RNA-seq-based EBV latency transcriptome offers insights into the biogenesis of EBV gene products.The Journal of general virology · 2025Article
- Detecting a wide range of epitranscriptomic modifications using a nanopore-sequencing-based computational approach with 1D score-clustering.Nucleic acids research · 2025Article
- Visualizing the modification landscape of the human 60S ribosomal subunit at close to atomic resolution.Nucleic acids research · 2025Article
- Article
- NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs.Genome biology · 2024Article
- Detecting mNature communications · 2024Article
- Detection of queuosine and queuosine precursors in tRNAs by direct RNA sequencing.Nucleic acids research · 2023Article
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Authors and funding
8 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ribosomal RNAs are decorated by numerous post-transcriptional modifications whose exact roles in ribosome biogenesis, function, and human pathophysiology remain largely unknown. Here, we report a targeted direct rRNA sequencing approach involving a substrate selection step and demonstrate its suitability to identify differential modification sites in combination with the JACUSA2 software. We compared JACUSA2 to other tools designed for RNA modification detection and show that JACUSA2 outperforms other software with regard to detection of base modifications such as methylation, acetylation and aminocarboxypropylation. To illustrate its widespread usability, we applied our method to a collection of CRISPR-Cas9 engineered colon carcinoma cells lacking specific enzymatic activities responsible for particular rRNA modifications and systematically compared them to isogenic wild-type RNAs. Besides the numerous 2'-O methylated riboses and pseudouridylated residues, our approach was suitable to reliably identify differential base methylation and acetylation events. Importantly, our method does not require any prior knowledge of modification sites or the need to train complex models. We further report for the first time detection of human rRNA modifications by direct RNA-sequencing on Flongle flow cells, the smallest-scale nanopore flow cell available to date. The use of these smaller flow cells reduces RNA input requirements, making our workflow suitable for the analysis of samples with limited availability and clinical work.
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