ArticleNucleic acids research2022
Nanopore ReCappable sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- NanoPrePro: a fully equipped, fast, and memory-efficient preprocessor for nanopore transcriptomic sequencing.Briefings in bioinformatics · 2026Article
- Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.Bioinformatics advances · 2026Article
- Novel non-coding FOXP3 transcript isoform associated to potential transcriptional interference in human regulatory T cells.RNA biology · 2025Article
- Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications.Nucleic acids research · 2025Article
- Highly Recurrent Multinucleotide Mutations in SARS-CoV-2.Molecular biology and evolution · 2025Article
- Long-read sequencing-based analyses of the adult Drosophila brain transcriptome in physiological and pathological settings.BMC genomics · 2025Article
- True length of diverse capped RNA sequencing (TLDR-seq): 5'-3'-end sequencing of capped RNAs regardless of 3'-end status.Nucleic acids research · 2025Article
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- Nanopore guided annotation of transcriptome architectures.mSystems · 2024Article
- The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research.Viruses · 2024Review
- Nanopore Guided Annotation of Transcriptome Architectures.bioRxiv : the preprint server for biology · 2024Article
- Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome.Molecular therapy. Nucleic acids · 2023Article
- Biochemical characterization of mRNA capping enzyme from Faustovirus.RNA (New York, N.Y.) · 2023Article
- The Local Anaesthetic Procaine Prodrugs ProcClusterInternational journal of molecular sciences · 2023Article
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- News from around the RNA world: new avenues in RNA biology, biotechnology and therapeutics from the 2022 SIBBM meeting.Biology open · 2022Article
- Advances in nanopore direct RNA sequencing.Nature methods · 2022Article
- STArS (STrain-Amplicon-Seq), a targeted nanopore sequencing workflow for SARS-CoV-2 diagnostics and genotyping.Biology methods & protocols · 2022Article
Corrections and comments
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Authors and funding
25 authors.
Funding
Abstract
The SARS-CoV-2 virus has a complex transcriptome characterised by multiple, nested subgenomic RNAsused to express structural and accessory proteins. Long-read sequencing technologies such as nanopore direct RNA sequencing can recover full-length transcripts, greatly simplifying the assembly of structurally complex RNAs. However, these techniques do not detect the 5' cap, thus preventing reliable identification and quantification of full-length, coding transcript models. Here we used Nanopore ReCappable Sequencing (NRCeq), a new technique that can identify capped full-length RNAs, to assemble a complete annotation of SARS-CoV-2 sgRNAs and annotate the location of capping sites across the viral genome. We obtained robust estimates of sgRNA expression across cell lines and viral isolates and identified novel canonical and non-canonical sgRNAs, including one that uses a previously un-annotated leader-to-body junction site. The data generated in this work constitute a useful resource for the scientific community and provide important insights into the mechanisms that regulate the transcription of SARS-CoV-2 sgRNAs.
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