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Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
- Marcus J. Viscardi,
- Enisha Sehgal,
- and Joshua A. Arribere
Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
...categorized the 5′ ends of RNA reads based on the proximity of their 5′ end to the trans-splicing site (TSS; as many C. elegans gene mRNAs are trans-spliced after transcription, the 5′-most nucleotide of the spliced mRNA differs from the transcription start site). Decapping leaves a 5′ monophosphate (Wang et...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...more peaks in introns than worms. The distribution of peaks in C. elegans is slightly farther upstream of the TSS than in Drosophila, perhaps reflecting the fact that for many C. elegans gene models the annotated TSS is the site of trans-splicing, with the start of transcription occurring further...
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Research: Distinctive regulatory architectures of germline-active and somatic genes in C. elegans
- Jacques Serizay,
- Yan Dong,
- Jürgen Jänes,
- Michael Chesney,
- Chiara Cerrato,
- and Julie Ahringer
Genome Res. December 2020 30: 1752-1765; Published in Advance October 22, 2020, doi:10.1101/gr.265934.120
...most genes in C. elegans are trans-spliced to a 22-nt leader RNA (Blumenthal 2012), leading to removal and degradation of the initial 5′ sequence between the promoter and the trans-splice site, the beginning of the mature mRNA does not usually correspond to the transcription initiation site. Therefore...
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Resource: The time-resolved transcriptome of C. elegans
- Max E. Boeck,
- Chau Huynh,
- Lou Gevirtzman,
- Owen A. Thompson,
- Guilin Wang,
- Dionna M. Kasper,
- Valerie Reinke,
- LaDeana W. Hillier,
- and Robert H. Waterston
Genome Res. October 2016 26: 1441-1450; Published in Advance August 16, 2016, doi:10.1101/gr.202663.115
...reveal many more. Operons About 70% of C. elegans transcripts are trans-spliced, with the SL1 splice leader used for genes with independent promoters and the Figure 2. The relative abundance of novel versus known junctions in alternatively spliced pairs within WormBase gene models. For each splice...
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ARTICLE: Extensive Exon Reshuffling Over Evolutionary Time Coupled to Trans-Splicing in Drosophila
- Mariano Labrador and
- Victor G. Corces
Genome Res. October 2003 13: 2220-2228; doi:10.1101/gr.1440703
...transcribed pre-mRNAs to form a single mature transcript, potentially increasing the putative combinations of exons able to generate novel proteins ( Tasic et al. 2002 ). The most common form of trans -splicing is found in trypanosomes and Caenorhabditis elegans ; in these organisms, trans -splicing results...
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Resource: Long noncoding RNAs in C. elegans
- Jin-Wu Nam and
- David P. Bartel
Genome Res. December 2012 22: 2529-2540; Published in Advance June 15, 2012, doi:10.1101/gr.140475.112
..., but for the few that are trans-spliced, the trans-splicing plays a role apart from separating polycistronic transcripts or enhancing translation initiation. lincRNAs antisense to endo-siRNA clusters When mapping published (Batista et al. 2008; Gu et al. 2009) and newly generated small-RNA sequencing data...
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Research: Core promoter T-blocks correlate with gene expression levels in C. elegans
- Vladislav Grishkevich,
- Tamar Hashimshony,
- and Itai Yanai
Genome Res. May 2011 21: 707-717; Published in Advance March 2, 2011, doi:10.1101/gr.113381.110
...-blocks as opposed to A-blocks is likely due to the involvement of a uracil-rich motif for transsplicing. Trans-splicing is important for the expression of most C. elegans genes. Previous work has shown that trans-splicing efficiency depends upon the presence of a uracil-rich (U-rich) element located upstream...
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Research: Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans
- Colin S. Maxwell,
- Igor Antoshechkin,
- Nicole Kurhanewicz,
- Jason A. Belsky,
- and L. Ryan Baugh
Genome Res. October 2012 22: 1920-1929; Published in Advance April 26, 2012, doi:10.1101/gr.133587.111
...contain operons that are transcribed to produce poly-cistronic pre-mRNA. Nematodes also use trans-splicing to add a short (22 nt) leader sequence to the 59 end of most (;70%) mRNA transcripts (Blumenthal 2005). There are twomajor types of spliced leader in C. elegans: SL1 and SL2. SL1 is most common...
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PERSPECTIVE: Genomics in C. elegans: So many genes, such a little worm
- LaDeana W. Hillier,
- Alan Coulson,
- John I. Murray,
- Zhirong Bao,
- John E. Sulston,
- and Robert H. Waterston
Genome Res. December 2005 15: 1651-1660; doi:10.1101/gr.3729105
...forms ( Spieth and Lawson 2005 ). Trans -splicing is common in the worm, with more than half of C. elegans premRNAs receiving an SL1 leader sequence and 20% an SL2 ( Blumenthal 2005 ). More than 90% of the genes are directly supported by experimental evidence. Text Box 1. Completing the C. elegans...
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LETTER: A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
- Anton Valouev,
- Jeffrey Ichikawa,
- Thaisan Tonthat,
- Jeremy Stuart,
- Swati Ranade,
- Heather Peckham,
- Kathy Zeng,
- Joel A. Malek,
- Gina Costa,
- Kevin McKernan,
- Arend Sidow,
- Andrew Fire,
- and Steven M. Johnson
Genome Res. July 2008 18: 1051-1063; Published in Advance May 13, 2008, doi:10.1101/gr.076463.108
...the relationship between these sites and promoter sequences, we first needed at least an approximation to the list of C. elegans transcription start sites. Note that only a handful of transcriptional start sites are known for C. elegans , since trans -splicing tends to mask true initiation sites ( Blumenthal 1995...

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