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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...CGC1, a new reference for Caenorhabditis elegans Kazuki Ichikawa1, Massa J. Shoura2,8, Karen L. Artiles2, Dae-Eun Jeong2, Chie Owa1, Haruka Kobayashi1, Yoshihiko Suzuki1, Manami Kanamori3, Yu Toyoshima3, Yuichi Iino3, Ann E. Rougvie4, Lamia Wahba5, Andrew Z. Fire2,6, Erich M. Schwarz7 and Shinichi...
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Resource: The million mutation project: A new approach to genetics in Caenorhabditis elegans
- Owen Thompson,
- Mark Edgley,
- Pnina Strasbourger,
- Stephane Flibotte,
- Brent Ewing,
- Ryan Adair,
- Vinci Au,
- Iasha Chaudhry,
- Lisa Fernando,
- Harald Hutter,
- Armelle Kieffer,
- Joanne Lau,
- Norris Lee,
- Angela Miller,
- Greta Raymant,
- Bin Shen,
- Jay Shendure,
- Jon Taylor,
- Emily H. Turner,
- LaDeana W. Hillier,
- Donald G. Moerman,
- and Robert H. Waterston
Genome Res. October 2013 23: 1749-1762; Published in Advance June 25, 2013, doi:10.1101/gr.157651.113
...The million mutation project: A new approach to genetics in Caenorhabditis elegans Owen Thompson 1 , Mark Edgley 2 , Pnina Strasbourger 1 , Stephane Flibotte 2 , Brent Ewing 1 , Ryan Adair 2 , Vinci Au 2 , Iasha...
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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
...-AC), then the junction was considered as conserved between C. elegans and the other species (the junction need not to be identical between the two species to be considered present). Supplemental Table 3 contains the data pertaining to this conservation analysis.Trans-splice site identificationTrans-splice sites were...
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Research: Competition between virus-derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans
- Peter Sarkies,
- Alyson Ashe,
- Jérémie Le Pen,
- Mikel A. McKie,
- and Eric A. Miska
Genome Res. August 2013 23: 1258-1270; Published in Advance June 28, 2013, doi:10.1101/gr.153296.112
...Competition between virus-derived and endogenous small RNAs regulates gene expression in Caenorhabditis elegans Peter Sarkies 1 , 2 , 3 , 4 , Alyson Ashe 1 , 2 , 3 , Jérémie Le Pen 1 , 2 , Mikel A. McKie 1 , 2 and Eric A. Miska 1...
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ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- Adam Siepel,
- Gill Bejerano,
- Jakob S. Pedersen,
- Angie S. Hinrichs,
- Minmei Hou,
- Kate Rosenbloom,
- Hiram Clawson,
- John Spieth,
- LaDeana W. Hillier,
- Stephen Richards,
- George M. Weinstock,
- Richard K. Wilson,
- Richard A. Gibbs,
- W. James Kent,
- Webb Miller,
- and David Haussler
Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
...compact Drosophila melanogaster (37%–53%), Caenorhabditis elegans (18%–37%), and Saccharaomyces cerevisiae (47%–68%) s. From yeasts to vertebrates, in order of increasing size and general biological complexity, increasing fractions of conserved bases are found to lie outside of the exons of known protein...
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Method: Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome
- Ulrich Omasits,
- Maxime Quebatte,
- Daniel J. Stekhoven,
- Claudia Fortes,
- Bernd Roschitzki,
- Mark D. Robinson,
- Christoph Dehio,
- and Christian H. Ahrens
Genome Res. November 2013 23: 1916-1927; Published in Advance July 22, 2013, doi:10.1101/gr.151035.112
...of Zurich, 8057 Zurich, Switzerland Prokaryotes, due to their moderate complexity, are particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based...
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Research: Coordinated tissue-specific regulation of adjacent alternative 3′ splice sites in C. elegans
- James Matthew Ragle,
- Sol Katzman,
- Taylor F. Akers,
- Sergio Barberan-Soler,
- and Alan M. Zahler
Genome Res. July 2015 25: 982-994; Published in Advance April 28, 2015, doi:10.1101/gr.186783.114
...not exhibit proximal AG dinucleotide conservation in species related to C. elegans; 64% of the proximal AG dinucleotides from this class are only found in C. elegans, while only 15% are conserved across all four Caenorhabditis species. In contrast, introns with intermediate (20%–59%) and high (60%–100%) usage...
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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
..., a few of which have known biological roles. To better understand the genomics and features of lncRNAs in invertebrates, we used available RNA-seq, poly(A)-site, and ribosome-mapping data to identify lncRNAs of Caenorhabditis elegans. We found 170 long intervening ncRNAs (lincRNAs), which had single...
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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
.... briggsae (Stein et al. 2003); it encodes a full Caenorhabditis proteome, and 2672 highly conserved DNA elements that may be regulatory. Results Sequencing of the and RNA-seq-mediated scaffolding We sequenced and assembled 200-bp fragment libraries at 100-fold nominal combined coverage (assuming a 100-Mb...
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Resource: The transcription start site landscape of C. elegans
- Taro Leo Saito,
- Shin-ichi Hashimoto,
- Sam Guoping Gu,
- J. Jason Morton,
- Michael Stadler,
- Thomas Blumenthal,
- Andrew Fire,
- and Shinichi Morishita
Genome Res. August 2013 23: 1348-1361; Published in Advance May 1, 2013, doi:10.1101/gr.151571.112
..., CO 80045, USA. Abstract More than half of Caenorhabditis elegans pre-mRNAs lose their original 5′ ends in a process termed “ trans -splicing” in which the RNA extending from the transcription start site (TSS) to the site of trans -splicing of the primary transcript, termed the “outron...
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