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Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans

Almost 20 years after the completion of the C. elegans genome sequence, gene structure annotation is still an ongoing process with new evidence for gene variants still being regularly uncovered by additional in-depth transcriptome studies. While alternative splice forms can allow a single gene to en...

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Autores principales: Tourasse, Nicolas J., Millet, Jonathan R.M., Dupuy, Denis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741048/
https://www.ncbi.nlm.nih.gov/pubmed/29089372
http://dx.doi.org/10.1101/gr.224626.117
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author Tourasse, Nicolas J.
Millet, Jonathan R.M.
Dupuy, Denis
author_facet Tourasse, Nicolas J.
Millet, Jonathan R.M.
Dupuy, Denis
author_sort Tourasse, Nicolas J.
collection PubMed
description Almost 20 years after the completion of the C. elegans genome sequence, gene structure annotation is still an ongoing process with new evidence for gene variants still being regularly uncovered by additional in-depth transcriptome studies. While alternative splice forms can allow a single gene to encode several functional isoforms, the question of how much spurious splicing is tolerated is still heavily debated. Here we gathered a compendium of 1682 publicly available C. elegans RNA-seq data sets to increase the dynamic range of detection of RNA isoforms, and obtained robust measurements of the relative abundance of each splicing event. While most of the splicing reads come from reproducibly detected splicing events, a large fraction of purported junctions is only supported by a very low number of reads. We devised an automated curation method that takes into account the expression level of each gene to discriminate robust splicing events from potential biological noise. We found that rarely used splice sites disproportionately come from highly expressed genes and are significantly less conserved in other nematode genomes than splice sites with a higher usage frequency. Our increased detection power confirmed trans-splicing for at least 84% of C. elegans protein coding genes. The genes for which trans-splicing was not observed are overwhelmingly low expression genes, suggesting that the mechanism is pervasive but not fully captured by organism-wide RNA-seq. We generated annotated gene models including quantitative exon usage information for the entire C. elegans genome. This allows users to visualize at a glance the relative expression of each isoform for their gene of interest.
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spelling pubmed-57410482018-06-01 Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans Tourasse, Nicolas J. Millet, Jonathan R.M. Dupuy, Denis Genome Res Resource Almost 20 years after the completion of the C. elegans genome sequence, gene structure annotation is still an ongoing process with new evidence for gene variants still being regularly uncovered by additional in-depth transcriptome studies. While alternative splice forms can allow a single gene to encode several functional isoforms, the question of how much spurious splicing is tolerated is still heavily debated. Here we gathered a compendium of 1682 publicly available C. elegans RNA-seq data sets to increase the dynamic range of detection of RNA isoforms, and obtained robust measurements of the relative abundance of each splicing event. While most of the splicing reads come from reproducibly detected splicing events, a large fraction of purported junctions is only supported by a very low number of reads. We devised an automated curation method that takes into account the expression level of each gene to discriminate robust splicing events from potential biological noise. We found that rarely used splice sites disproportionately come from highly expressed genes and are significantly less conserved in other nematode genomes than splice sites with a higher usage frequency. Our increased detection power confirmed trans-splicing for at least 84% of C. elegans protein coding genes. The genes for which trans-splicing was not observed are overwhelmingly low expression genes, suggesting that the mechanism is pervasive but not fully captured by organism-wide RNA-seq. We generated annotated gene models including quantitative exon usage information for the entire C. elegans genome. This allows users to visualize at a glance the relative expression of each isoform for their gene of interest. Cold Spring Harbor Laboratory Press 2017-12 /pmc/articles/PMC5741048/ /pubmed/29089372 http://dx.doi.org/10.1101/gr.224626.117 Text en © 2017 Tourasse et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Resource
Tourasse, Nicolas J.
Millet, Jonathan R.M.
Dupuy, Denis
Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans
title Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans
title_full Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans
title_fullStr Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans
title_full_unstemmed Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans
title_short Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans
title_sort quantitative rna-seq meta-analysis of alternative exon usage in c. elegans
topic Resource
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5741048/
https://www.ncbi.nlm.nih.gov/pubmed/29089372
http://dx.doi.org/10.1101/gr.224626.117
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