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Quantitative analysis of C. elegans transcripts by Nanopore direct-cDNA sequencing reveals terminal hairpins in non trans-spliced mRNAs

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  • Florian Bernard

    (Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie et Biologie (IECB)
    Tel Aviv University)

  • Delphine Dargère

    (Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie et Biologie (IECB))

  • Oded Rechavi

    (Tel Aviv University)

  • Denis Dupuy

    (Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie et Biologie (IECB))

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.

Suggested Citation

  • Florian Bernard & Delphine Dargère & Oded Rechavi & Denis Dupuy, 2023. "Quantitative analysis of C. elegans transcripts by Nanopore direct-cDNA sequencing reveals terminal hairpins in non trans-spliced mRNAs," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36915-0
    DOI: 10.1038/s41467-023-36915-0
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    1. Thomas Blumenthal & Donald Evans & Christopher D. Link & Alessandro Guffanti & Daniel Lawson & Jean Thierry-Mieg & Danielle Thierry-Mieg & Wei Lu Chiu & Kyle Duke & Moni Kiraly & Stuart K. Kim, 2002. "A global analysis of Caenorhabditis elegans operons," Nature, Nature, vol. 417(6891), pages 851-854, June.
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