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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: Recompleting the Caenorhabditis elegans genome
- Jun Yoshimura,
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Idan Gabdank,
- Lamia Wahba,
- Cheryl L. Smith,
- Mark L. Edgley,
- Ann E. Rougvie,
- Andrew Z. Fire,
- Shinichi Morishita,
- and Erich M. Schwarz
Genome Res. June 2019 29: 1009-1022; Published in Advance May 23, 2019, doi:10.1101/gr.244830.118
...Recompleting the Caenorhabditis elegans Jun Yoshimura1,7, Kazuki Ichikawa1,7, Massa J. Shoura2,7, Karen L. Artiles2,7, Idan Gabdank3, Lamia Wahba2, Cheryl L. Smith2,3, Mark L. Edgley4, Ann E. Rougvie5, Andrew Z. Fire2,3, Shinichi Morishita1 and Erich M. Schwarz6 1Department of Computational Biology...
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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
...and elements, we specifically focus on the ubiquitous-uniform class and for simplicity refer to them as “ubiquitous.”The data provide a comprehensive view of chromatin accessibility and transcriptional landscapes in the five major C. elegans tissues. To facilitate access and analyses of these new tissue...
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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, enriched in occurrences within core promoter forward strands in Caenorhabditis elegans. An increasing number of T-blocks on either strand is associated with increasing nucleosome eviction. Strikingly, only forward strand T-blocks are correlated with expression levels, whereby genes with$6 T-blocks have...
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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
...The transcription start site landscape of C. elegans Taro Leo Saito 1 , Shin-ichi Hashimoto 2 , Sam Guoping Gu 3 , 6 , J. Jason Morton 4 , 7 , Michael Stadler 3 , Thomas Blumenthal 4 , Andrew Fire 5 , 8...
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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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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
...nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans . These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our...
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LETTER: Nucleosome positioning in human HOX gene clusters
- Peter V. Kharchenko,
- Caroline J. Woo,
- Michael Y. Tolstorukov,
- Robert E. Kingston,
- and Peter J. Park
Genome Res. October 2008 18: 1554-1561; Published in Advance August 22, 2008, doi:10.1101/gr.075952.107
....P. , Albert, I. , Zanton, S.J. , Pugh, B.F. ( 2006 ) Nucleosome positions predicted through comparative genomics . Nat. Genet. 38 : 1210 – 1215 . ↵ Johnson, S.M. , Tan, F.J. , McCullough, H.L. , Riordan, D.P. , Fire, A.Z. ( 2006 ) Flexibility and constraint in the nucleosome core landscape of Caenorhabditis...
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LETTER: Nucleosome positioning signals in genomic DNA
- Heather E. Peckham,
- Robert E. Thurman,
- Yutao Fu,
- John A. Stamatoyannopoulos,
- William Stafford Noble,
- Kevin Struhl,
- and Zhiping Weng
Genome Res. August 2007 17: 1170-1177; Published in Advance July 9, 2007, doi:10.1101/gr.6101007
...its intrinsic DNA structure . EMBO J. 14 : 2570 – 2579 . ↵ Johnson, S.M. , Tan, F.J. , McCullough, H.L. , Riordan, D.P. , Fire, A.Z. ( 2006 ) Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin . Genome Res. 16 : 1505 – 1516 . ↵ Kiyama, R. , Trifonov, E...
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Letter: Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes
- Michael Y. Tolstorukov,
- Peter V. Kharchenko,
- Joseph A. Goldman,
- Robert E. Kingston,
- and Peter J. Park
Genome Res. June 2009 19: 967-977; Published in Advance February 26, 2009, doi:10.1101/gr.084830.108
...units of chromatin, the nucleosomes. The affinity of the histone core for DNA depends on the nucleotide sequence; however, it is unclear to what extent DNA sequence determines nucleosome positioning in vivo, and if the same rules of sequence-directed positioning apply to genomes of varying complexity...

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