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Research: Trans-splicing enhances translational efficiency in C. elegans
- Yu-Fei Yang,
- Xiaoqing Zhang,
- Xuehua Ma,
- Taolan Zhao,
- Qiushi Sun,
- Qing Huan,
- Shaohuan Wu,
- Zhuo Du,
- and Wenfeng Qian
Genome Res. September 2017 27: 1525-1535; Published in Advance July 6, 2017, doi:10.1101/gr.202150.115
..., the factors influencing such regulation are poorly understood. In Caenorhabditis elegans, 62% of genes are trans-spliced to a specific spliced leader (SL1), which replaces part of the native 5′ untranslated region (5′ UTR). Given the pivotal role the 5′ UTR plays in the regulation of translational efficiency...
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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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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...communication between cis-regulatory elements. Many organisms, including S. cerevisiae, C. elegans, and A. thaliana contain cohesin but lack CTCF. Here, we used C. elegans to investigate the function of cohesin in 3D organization in the absence of CTCF. Using Hi-C data, we observe cohesin-dependent features...
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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: Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency
- Chan-Shuo Wu,
- Chun-Ying Yu,
- Ching-Yu Chuang,
- Michael Hsiao,
- Cheng-Fu Kao,
- Hung-Chih Kuo,
- and Trees-Juen Chuang
Genome Res. January 2014 24: 25-36; Published in Advance October 16, 2013, doi:10.1101/gr.159483.113
...Integrative transcriptome sequencing identifies trans -splicing events with important roles in human embryonic stem cell pluripotency Chan-Shuo Wu 1 , 3 , Chun-Ying Yu 2 , 3 , Ching-Yu Chuang 2 , Michael Hsiao 1 , Cheng-Fu Kao 2...
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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 full-length transcriptome of C. elegans using direct RNA sequencing
- Nathan P. Roach,
- Norah Sadowski,
- Amelia F. Alessi,
- Winston Timp,
- James Taylor,
- and John K. Kim
Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
...of the 5′-most 10–15 bases prevented us from examining splice leader-based trans splicing, a common RNA modification in C. elegans (see discussion in Supplemental Material). The average length of unique splice isoforms identified in our sequencing libraries was 1596 nt (Fig. 1E,F and discussed below...
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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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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...stability, transcription initiation, transcription termination, and pre-mRNA splicing by measuring the propensity of sequences at TSSs, transcript end sites (TESs), and 5′ trans-splicing acceptor sites (TASs) to melt.ResultsAn efficient -wide method to map supercoilsTo map supercoils, we developed a method...
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Resource: Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans
- Nicolas J. Tourasse,
- Jonathan R.M. Millet,
- and Denis Dupuy
Genome Res. December 2017 27: 2120-2128; Published in Advance October 31, 2017, doi:10.1101/gr.224626.117
....0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.References ↵Allen MA, Hillier LW, Waterston RH, Blumenthal T. 2011. A global analysis of C. elegans trans-splicing. Genome Res 21: 255–264. ↵Amrane S, Rebora K, Zniber I, Dupuy D, Mackereth CD. 2014. Backbone-independent nucleic acid...

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