ArticleNature communications2023
Quantitative analysis of C. elegans transcripts by Nanopore direct-cDNA sequencing reveals terminal hairpins in non trans-spliced mRNAs.
Article in Nature communications, 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, 14 citations in OpenAlex.
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- The "cutting edge" of non-canonical RNA splicing.Frontiers in molecular biosciences · 2026Review
- Evolution of SL-RNA Genes and Their Splicing Targets in Parasitic Flatworms.Molecular biology and evolution · 2025Article
- SLRanger: an integrated approach for spliced leader detection and operon prediction using long RNA reads.Briefings in bioinformatics · 2025Article
- Detecting gene expression in Caenorhabditis elegans.Genetics · 2025Review
- High-resolution reconstruction of aRNA (New York, N.Y.) · 2024Article
- Neurogenesis in Caenorhabditis elegans.Genetics · 2024Review
- Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA fromMicrobial genomics · 2024Article
- U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs.Nucleic acids research · 2024Article
- A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs.Nucleic acids research · 2024Article
- Molecular insights and antibody response to Dr20/22 in dogs naturally infected with Dirofilaria repens.Scientific reports · 2024Article
- AdvancingPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Characterizing short germline-specific promoters with a range of expression levels inmicroPublication biology · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In nematodes and kinetoplastids, mRNA processing involves a trans-splicing step through which a short sequence from a snRNP replaces the original 5' end of the primary transcript. It has long been held that 70% of C. elegans mRNAs are submitted to trans-splicing. Our recent work suggested that the mechanism is more pervasive but not fully captured by mainstream transcriptome sequencing methods. Here we use Oxford Nanopore's long-read amplification-free sequencing technology to perform a comprehensive analysis of trans-splicing in worms. We demonstrate that spliced leader (SL) sequences at the 5' end of the mRNAs affect library preparation and generate sequencing artefacts due to their self-complementarity. Consistent with our previous observations, we find evidence of trans-splicing for most genes. However, a subset of genes appears to be only marginally trans-spliced. These mRNAs all share the capacity to generate a 5' terminal hairpin structure mimicking the SL structure and offering a mechanistic explanation for their non conformity. Altogether, our data provide a comprehensive quantitative analysis of SL usage in C. elegans.
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