Quantitative RNA-seq meta-analysis of alternative exon usage in <i>C. elegans</i>

Tourasse, Nicolas J.; Millet, Jonathan R.M.; Dupuy, Denis

doi:10.1101/gr.224626.117

Cited by 40 publications

(47 citation statements)

References 46 publications

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“…Despite years of study, our understanding of the C. elegans transcriptome remains incomplete. Although studies have been performed profiling transcription start sites, splicing in both cis and trans, 3 ′ -UTR isoforms, poly(A) tail lengths, RNA base modifications, and gene and isoform expression levels, the short read lengths intrinsic to the prevailing technologies have limited the examination to one or two of these features at a time (Hillier et al 2009;Mangone et al 2010;Jan et al 2011;Saito et al 2013;Zhao et al 2015;Lima et al 2017;Tourasse et al 2017;West et al 2018;Packer et al 2019). Even within these data sets, short read lengths and reliance on PCR amplification eliminate single-molecule resolution and make correlation of distant features within transcripts impossible.…”

Section: Discussionmentioning

confidence: 99%

“…The nematode Caenorhabditis elegans is an ideal experimental model organism due to its compact, well-annotated genome (The C. elegans Sequencing Consortium 1998;Wilson 1999;Hillier et al 2005;Gerstein et al 2010), invariant cell lineage (Sulston et al 1983), and wide array of molecular methods. Our current understanding of the C. elegans transcriptome has been determined with EST-and cDNA-based libraries, and Illumina-based cDNA and RNA sequencing (Walhout et al 2000;Reboul et al 2001;Lamesch et al 2004;Hillier et al 2009;Gerstein et al 2010;Spieth et al 2014;Tourasse et al 2017). Most coding sequences (CDSs) span more than 600 nt (excluding introns), and the typical C. elegans gene contains 6.4 coding exons on average (Spieth et al 2014).…”

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confidence: 99%

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

et al. 2020

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Current transcriptome annotations have largely relied on short read lengths intrinsic to the 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 23,865 splice isoforms across 14,611 genes, without the need for computational reconstruction of gene models. Of the isoforms identified, 3452 are novel splice isoforms not present in the WormBase WS265 annotation. Furthermore, we identified 16,342 isoforms in the 3 ′ untranslated region (3 ′ UTR), 2640 of which are novel and do not fall within 10 bp of existing 3 ′-UTR data sets and annotations. Combining 3 ′ UTRs and splice isoforms, we identified 28,858 fulllength transcript 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 publicly accessible track hub, enabling researchers to explore this data set easily in a genome browser.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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

et al. 2020

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“…In C. elegans, although earlier work suggested that 70% of mRNAs are trans-spliced to one of two spliced leaders, SL1 or SL2 (Allen et al 2011), more recent estimates suggest as many as 85% are trans-spliced (Tourasse et al, 2017). We identified a total of 8830 sites (6190 genes) where splice leaders are added to a transcript, with 5099 (58%) of sites SL1 only, 2064 (23%) of sites SL2 only, and 1667 (19%) of sites both an SL1 and an SL2 (Supplemental File S3; Supplemental Table S11).…”

Section: Dynamics Of Gene Expressionmentioning

confidence: 96%

The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution

et al. 2019

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We have used RNA-seq in Caenorhabditis elegans to produce transcription profiles for seven specific embryonic cell populations from gastrulation to the onset of terminal differentiation. The expression data for these seven cell populations, covering major cell lineages and tissues in the worm, reveal the complex and dynamic changes in gene expression, both spatially and temporally. Also, within genes, start sites and exon usage can be highly differential, producing transcripts that are specific to developmental periods or cell lineages. We have also found evidence of novel exons and introns, as well as differential usage of SL1 and SL2 splice leaders. By combining this data set with the modERN ChIP-seq resource, we are able to support and predict gene regulatory relationships. The detailed information on differences and similarities between gene expression in cell lineages and tissues should be of great value to the community and provides a framework for the investigation of expression in individual cells.

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“…S3). A similar approach was previously applied to study C. elegans transcriptomes in the past (Tourasse et al 2017).…”

Section: An Updated 3 ′ -End Mapping Strategymentioning

confidence: 99%

The C. elegans 3′ UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3′-UTR biology, and miRNA targeting

et al. 2019

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′ Untranslated regions (3 ′ UTRs) of mRNAs emerged as central regulators of cellular function because they contain important but poorly characterized cis-regulatory elements targeted by a multitude of regulatory factors. The model nematode Caenorhabditis elegans is ideal to study these interactions because it possesses a well-defined 3 ′ UTRome. To improve its annotation, we have used a genome-wide bioinformatics approach to download raw transcriptome data for 1088 transcriptome data sets corresponding to the entire collection of C. elegans trancriptomes from 2015 to 2018 from the Sequence Read Archive at the NCBI. We then extracted and mapped high-quality 3 ′-UTR data at ultradeep coverage. Here, we describe and release to the community the updated version of the worm 3 ′ UTRome, which we named 3 ′ UTRome v2. This resource contains high-quality 3 ′-UTR data mapped at single-base ultraresolution for 23,084 3 ′-UTR isoform variants corresponding to 14,788 protein-coding genes and is updated to the latest release of WormBase. We used this data set to study and probe principles of mRNA cleavage and polyadenylation in C. elegans. The worm 3 ′ UTRome v2 represents the most comprehensive and high-resolution 3 ′-UTR data set available in C. elegans and provides a novel resource to investigate the mRNA cleavage and polyadenylation reaction, 3 ′-UTR biology, and miRNA targeting in a living organism.

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

Cited by 40 publications

References 46 publications

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

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

The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution

The C. elegans 3′ UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3′-UTR biology, and miRNA targeting

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