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The full-length transcriptome of C. elegans using direct RNA sequencing

View ORCID ProfileNathan P. Roach, View ORCID ProfileNorah Sadowski, Amelia F. Alessi, View ORCID ProfileWinston Timp, View ORCID ProfileJames Taylor, John K. Kim
doi: https://doi.org/10.1101/598763
Nathan P. Roach
Department of Biology, Johns Hopkins University, Baltimore 21218, USA
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Norah Sadowski
Department of Biomedical Engineering, Johns Hopkins University, Baltimore 21218, USA
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Amelia F. Alessi
Department of Biology, Johns Hopkins University, Baltimore 21218, USA
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Winston Timp
Department of Biomedical Engineering, Johns Hopkins University, Baltimore 21218, USA
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  • For correspondence: wtimp@jhu.edu james@taylorlab.org jnkim@jhu.edu
James Taylor
Department of Biology, Johns Hopkins University, Baltimore 21218, USADepartment of Computer Science, Johns Hopkins University, Baltimore 21218, USA
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  • For correspondence: wtimp@jhu.edu james@taylorlab.org jnkim@jhu.edu
John K. Kim
Department of Biology, Johns Hopkins University, Baltimore 21218, USA
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  • For correspondence: wtimp@jhu.edu james@taylorlab.org jnkim@jhu.edu
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Abstract

Current transcriptome annotations have largely relied on short read lengths intrinsic to most widely used high-throughput cDNA sequencing technologies. For example, in the annotation of the Caenorhabditis elegans transcriptome, more than half of the transcript isoforms lack full-length support and instead rely on inference from short reads that do not span the full length of the isoform. We applied nanopore-based direct RNA sequencing to characterize the developmental polyadenylated transcriptome of C. elegans. Taking advantage of long reads spanning the full length of mRNA transcripts, we provide support for 20,902 splice isoforms across 14,115 genes, without the need for computational reconstruction of gene models. Of the isoforms identified, 2,188 are novel splice isoforms not present in the Wormbase WS265 annotation. Furthermore, we identified 16,325 3’ untranslated region (3’UTR) isoforms, 2,304 of which are novel and do not fall within 10 bp of existing 3’UTR datasets and annotations. Combining 3’UTRs and splice isoforms we identified 25,944 full-length isoforms. We also determined that poly(A) tail lengths of transcripts vary across development, as do the strengths of previously reported correlations between poly(A) tail length and expression level, and poly(A) tail length and 3’UTR length. Finally, we have formatted this data as a publically accessible track hub, enabling researchers to explore this dataset easily in a genome browser.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 09, 2019.
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The full-length transcriptome of C. elegans using direct RNA sequencing
Nathan P. Roach, Norah Sadowski, Amelia F. Alessi, Winston Timp, James Taylor, John K. Kim
bioRxiv 598763; doi: https://doi.org/10.1101/598763
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The full-length transcriptome of C. elegans using direct RNA sequencing
Nathan P. Roach, Norah Sadowski, Amelia F. Alessi, Winston Timp, James Taylor, John K. Kim
bioRxiv 598763; doi: https://doi.org/10.1101/598763

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