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Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
..., there remains much to be understood about the splicing factors and the cis sequence elements controlling tissue and neuron subtype-specific splicing patterns. By using translating ribosome affinity purification coupled with deep-sequencing (TRAP-seq) in Caenorhabditis elegans, we have obtained high coverage...
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Resource: Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
- Aaron C. Daugherty,
- Robin W. Yeo,
- Jason D. Buenrostro,
- William J. Greenleaf,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. December 2017 27: 2096-2107; Published in Advance November 15, 2017, doi:10.1101/gr.226233.117
..., Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. 2015. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523: 486–490. ↵Byerly L, Cassada RC, Russell RL. 1976. The life cycle of the nematode Caenorhabditis elegans. I. Wild-type growth...
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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
..., Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, MacE D, et al. 2014. Regulatory analysis of the C. elegans with spatiotemporal resolution. Nature 512: 400–405. doi:10.1038/nature13497 ↵Baugh LR, Wen JC, Hill A, Slonim DK, Brown EL, Hunter CP. 2005. Synthetic lethal analysis of Caenorhabditis elegans...
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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 mutually exclusive alternative splicing in vivo. Genes Dev 22: 360–374. ↵Ohno G, Ono K, Togo M, Watanabe Y, Ono S, Hagiwara M, Kuroyanagi H. 2012. Muscle-specific splicing factors ASD-2 and SUP-12 cooperatively switch alternative pre-mRNA processing patterns of the ADF/cofilin gene in Caenorhabditis...
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LETTER: Novel transcription regulatory elements in Caenorhabditis elegans muscle genes
- Debraj GuhaThakurta,
- Lawrence A. Schriefer,
- Robert H. Waterston,
- and Gary D. Stormo
Genome Res. December 2004 14: 2457-2468; doi:10.1101/gr.2961104
...98195, USA Abstract We report the identification of three new transcription regulatory elements that are associated with muscle gene expression in the nematode Caenorhabditis elegans . Starting from a subset of well-characterized nematode muscle genes, we identified conserved DNA motifs...
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ARTICLE: Identification of a Novel cis-Regulatory Element Involved in the Heat Shock Response in Caenorhabditis elegans Using Microarray Gene Expression and Computational Methods
- Debraj GuhaThakurta,
- Lisanne Palomar,
- Gary D. Stormo,
- Pat Tedesco,
- Thomas E. Johnson,
- David W. Walker,
- Gordon Lithgow,
- Stuart Kim,
- and Christopher D. Link
Genome Res. May 1, 2002 12: 701-712; doi:10.1101/gr.228902
...Identification of a Novel cis -Regulatory Element Involved in the Heat Shock Response in Caenorhabditis elegans Using Microarray Gene Expression and Computational Methods Debraj GuhaThakurta 1 , 5 , Lisanne Palomar 1 , Gary D. Stormo 1 , Pat Tedesco 2...
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Method: Scaffolding a Caenorhabditis nematode genome with RNA-seq
- Ali Mortazavi,
- Erich M. Schwarz,
- Brian Williams,
- Lorian Schaeffer,
- Igor Antoshechkin,
- Barbara J. Wold,
- and Paul W. Sternberg
Genome Res. December 2010 20: 1740-1747; Published in Advance October 27, 2010, doi:10.1101/gr.111021.110
...of muscle-specific regulatory modules in Caenorhabditis elegans. Genome Res 17: 348–357. Received May 26, 2010; accepted in revised form August 24, 2010. RNA-seq-scaffolded nematode Genome Research 1747 www..org Scaffolding a Caenorhabditis nematode with RNA-seq Ali Mortazavi 1 , 2 , 3 , Erich M. Schwarz 1...
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Research: Evolutionary conservation of the eumetazoan gene regulatory landscape
- Michaela Schwaiger,
- Anna Schönauer,
- André F. Rendeiro,
- Carina Pribitzer,
- Alexandra Schauer,
- Anna F. Gilles,
- Johannes B. Schinko,
- Eduard Renfer,
- David Fredman,
- and Ulrich Technau
Genome Res. April 2014 24: 639-650; Published in Advance March 18, 2014, doi:10.1101/gr.162529.113
...methylation (Meissner et al. 2008; Suzuki and Bird 2008; Jones 2012; Long et al. 2012). While the invertebrate model organismsDrosophilamelanogaster andCaenorhabditis elegans lackDNA methylation, it has recently been shown that other invertebrates, including Nematostella vectensis, methylate CpGs throughout...
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Resource: A spatial and temporal map of C. elegans gene expression
- W. Clay Spencer,
- Georg Zeller,
- Joseph D. Watson,
- Stefan R. Henz,
- Kathie L. Watkins,
- Rebecca D. McWhirter,
- Sarah Petersen,
- Vipin T. Sreedharan,
- Christian Widmer,
- Jeanyoung Jo,
- Valerie Reinke,
- Lisa Petrella,
- Susan Strome,
- Stephen E. Von Stetina,
- Menachem Katz,
- Shai Shaham,
- Gunnar Rätsch,
- and David M. Miller III
Genome Res. February 2011 21: 325-341; Published in Advance December 22, 2010, doi:10.1101/gr.114595.110
....] The generation of specific cell types depends on spatial and temporal control of gene expression. The nematode Caenorhabditis elegans has been widely utilized to address this question because of its simple body plan and fully sequenced (Hillier et al. 2005). Although composed of fewer than 1000 somatic cells...
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Methods: Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
- Steven G. Kuntz,
- Erich M. Schwarz,
- John A. DeModena,
- Tristan De Buysscher,
- Diane Trout,
- Hiroaki Shizuya,
- Paul W. Sternberg,
- and Barbara J. Wold
Genome Res. December 2008 18: 1955-1968; Published in Advance November 3, 2008, doi:10.1101/gr.085472.108
...Abstract To learn how well ungapped sequence comparisons of multiple species can predict cis -regulatory elements in Caenorhabditis elegans , we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how prediction quality varied...

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