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

Genome Research
Nicolas J TourasseDenis Dupuy

Abstract

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...Continue Reading

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Citations

May 28, 2019·Genome Research·Adam D WarnerRobert H Waterston
Jan 18, 2020·ELife·Vahan SerobyanDidier Yr Stainier
Feb 7, 2020·Genome Research·Nathan P RoachJohn K Kim
Jul 8, 2020·Genetics·Joshua A ArribereHeather A Hundley
Aug 29, 2019·Quantitative Biology·Wei Vivian Li, Jingyi Jessica Li
Aug 4, 2019·Ecotoxicology and Environmental Safety·Congting YeQingshun Quinn Li
Jul 9, 2021·Cell·Seth R TaylorDavid M Miller
Aug 17, 2021·Development·Dimitris KatsanosMichalis Barkoulas
Jan 15, 2022·Proceedings of the National Academy of Sciences of the United States of America·Justin M Shaffer, Iva Greenwald

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