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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
..., such as Caenorhabditis elegans.C. elegans is a small nematode with an ∼100 Mb and ∼20,000 genes (Heger et al. 2009). Median gene length is ∼2 kb, and intergenic distances between genes (excluding operons encompassing ∼15% of genes) range from ∼2 to 10 kb (Nelson et al. 2004; Girard et al. 2007; Allen et al. 2011). Like...
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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
...Technologies to study the transcriptome complexity in Caenorhabditis elegans. We generated approximately six million reads using native poly(A)-tailed mRNAs from three developmental stages, with average read lengths ranging from 900 to 1100 nt. Around half of the reads represent full-length transcripts...
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Resource: Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis
- Rui Yokomori,
- Kotaro Shimai,
- Koki Nishitsuji,
- Yutaka Suzuki,
- Takehiro G. Kusakabe,
- and Kenta Nakai
Genome Res. January 2016 26: 140-150; Published in Advance December 14, 2015, doi:10.1101/gr.184648.114
...results in efficient trans-splicing in Caenorhabditis elegans (Conrad et al. 1995). The 2000-bp upper limit was derived from the report showing that most (>90%) of outrons are <2000 bp in C. elegans (Kruesi et al. 2013). In this study, the outron means discarded 5′ end regions of “non-operon-type” trans...
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Research: Extreme HOT regions are CpG-dense promoters in C. elegans and humans
- Ron A.-J. Chen,
- Przemyslaw Stempor,
- Thomas A. Down,
- Eva Zeiser,
- Sky K. Feuer,
- and Julie Ahringer
Genome Res. July 2014 24: 1138-1146; Published in Advance March 20, 2014, doi:10.1101/gr.161992.113
.... Cell 40: 91–99. Blumenthal T. 1995. Trans-splicing and polycistronic transcription in Caenorhabditis elegans. Trends Genet 11: 132–136. Blumenthal T. 2012. Trans-splicing and operons in C. elegans. InWormBook (ed. The C. elegans Research Community), pp. 1–11. http:// www.wormbook.org. Brenner S. 1974...
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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
.... elegans genes are organized in operons (Reinke and Cutter 2009), where two or more genes are initially transcribed into a single transcript that is separated by trans-splicing. Therefore, for analyses involving promoters, we only included nonoperon genes and first genes in operons. As reported previously...
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RESOURCE: Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
- Natalia J. Martinez,
- Maria C. Ow,
- John S. Reece-Hoyes,
- M. Inmaculada Barrasa,
- Victor R. Ambros,
- and Albertha J.M. Walhout
Genome Res. December 2008 18: 2005-2015; Published in Advance November 3, 2008, doi:10.1101/gr.083055.108
...and gene nomenclature . Nucleic Acids Res. 34 : D140 – D144 . ↵ Huang, P. , Pleasance, E.D. , Maydan, J.S. , Hunt-Newbury, R. , O’Neil, N.J. , Mah, A. , Baillie, D.L. , Marra, M.A. , Moerman, D.G. , Jones, S.J. ( 2007 ) Identification and analysis of internal promoters in Caenorhabditis elegans operons...
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Method: Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
- Wei-Jen Chung,
- Phaedra Agius,
- Jakub O. Westholm,
- Michael Chen,
- Katsutomo Okamura,
- Nicolas Robine,
- Christina S. Leslie,
- and Eric C. Lai
Genome Res. February 2011 21: 286-300; Published in Advance December 22, 2010, doi:10.1101/gr.113050.110
...Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans Wei-Jen Chung 1 , 3 , 4 , Phaedra Agius 2 , 3 , Jakub O. Westholm 1 , Michael Chen 1 , Katsutomo Okamura 1...
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Resource: The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution
- Adam D. Warner,
- Louis Gevirtzman,
- LaDeana W. Hillier,
- Brent Ewing,
- and Robert H. Waterston
Genome Res. June 2019 29: 1036-1045; Published in Advance May 23, 2019, doi:10.1101/gr.243394.118
...Adam D. Warner, Louis Gevirtzman, LaDeana W. Hillier, Brent Ewing and Robert H. Waterston Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA Corresponding author: watersto@uw.eduAbstractWe have used RNA-seq in Caenorhabditis elegans...
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Research: High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
- Sevinç Ercan,
- Yaniv Lubling,
- Eran Segal,
- and Jason D. Lieb
Genome Res. February 2011 21: 237-244; Published in Advance December 22, 2010, doi:10.1101/gr.115931.110
...was observed 20 to 30 bp from the dyad among nucleosomes in X-linked promoters, the significance of which is not clear (Supplemental Fig. 4C). Differences in operon usage or repeat frequency do not account for nucleosome occupancy differences between X and autosome promoters TheC. elegans contains over 1000...
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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
...of the complete Caenorhabditis elegans using transcriptome sequencing (RNA-seq) (Hillier et al. 2009; Ramani et al. 2011; Gerstein et al. 2014; Kuroyanagi et al. 2014; Ragle et al. 2015). Most of these analyses reported previously unannotated splice junctions, indicating that saturation has not yet been reached...

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