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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
...a completely defined reference and corresponding isogenic wild-type strain for C. elegans, allowing unique opportunities for model and systems biology.The nematode Caenorhabditis elegans is a model for biology ranging from mechanistic functions of individual proteins and RNAs to multicellular interactions...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...; Brar and Weissman 2015), to uncover the complete transcriptome and translatome of S. pombe. Oxford Nanopore Technologies (ONT) direct RNA (dRNA) sequencing (dRNA-seq) offers several important advantages over previous RNA-seq approaches: (1) It provides an unbiased snapshot of the native polyadenylated...
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Research: Long-read sequencing of nascent RNA reveals coupling among RNA processing events
- Lydia Herzel,
- Korinna Straube,
- and Karla M. Neugebauer
Genome Res. July 2018 28: 1008-1019; Published in Advance June 14, 2018, doi:10.1101/gr.232025.117
.... The respective feature distribution is presented as a box plot below. Asterisks indicate significance of direct neighbors according to the Wilcoxon rank-sum test: (*) P < 0.05, (**) P < 0.01, (***) P < 0.001, (****) P < 0.0001 after Bonferroni-correction, in A, B, and D.Full-length nascent RNA sequencing...
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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
...to functional proteins. Splice site selection and tissue/developmental specificity are established by auxiliary trans-acting proteins and cis-acting sequence elements, which are primarily RNA-binding proteins (RBPs) and their cognate motifs, respectively (Lee and Rio 2015). Collectively, these elements direct...
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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
...the Drosophila melanogaster transcriptome. These included 17 known and six confident novel mirtrons among the top 51 candidates, and additional candidates had limited read evidence in available small RNA data. Our computational model also proved effective on Caenorhabditis elegans , for which...
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Research: Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
- Tim R. Mercer,
- Marcel E. Dinger,
- Cameron P. Bracken,
- Gabriel Kolle,
- Jan M. Szubert,
- Darren J. Korbie,
- Marjan E. Askarian-Amiri,
- Brooke B. Gardiner,
- Gregory J. Goodall,
- Sean M. Grimmond,
- and John S. Mattick
Genome Res. December 2010 20: 1639-1650; Published in Advance November 2, 2010, doi:10.1101/gr.112128.110
...al. 2008; Czech et al. 2008; Glazov et al. 2008). We also found that small RNAs derived from both nuclear and cytoplasmic preparations include spliced small RNAs (Supplemental Fig. S6; Taft et al. 2009). These EEJ-spanning small RNAs were orientated overwhelmingly in the sense direction, further...
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Research: Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles
- Jianbin Wang,
- Benjamin Czech,
- Amanda Crunk,
- Adam Wallace,
- Makedonka Mitreva,
- Gregory J. Hannon,
- and Richard E. Davis
Genome Res. September 2011 21: 1462-1477; Published in Advance June 17, 2011, doi:10.1101/gr.121426.111
.... 2009). Our data provide several lines of evidence that the piRNA pathway has been lost in Ascaris. First, our direct sequencing of discrete regions of both the male and female germlines did not reveal any small RNAs with characteristics of piRNAs (Fig. 3A,B; Supplemental Figs. S1–S4; Supplemental...
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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
...of the HSE and HSAS sites on the promoters of the two pairs of orthologous genes indicates that these elements are conserved across closely related species. This conservation can be more directly seen in a direct alignment of the C. elegans and C. briggsae upstream sequences (Fig. 3 D) using the GLASS...
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Research: Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
- Wei Niu,
- Zhi John Lu,
- Mei Zhong,
- Mihail Sarov,
- John I. Murray,
- Cathleen M. Brdlik,
- Judith Janette,
- Chao Chen,
- Pedro Alves,
- Elicia Preston,
- Cindie Slightham,
- Lixia Jiang,
- Anthony A. Hyman,
- Stuart K. Kim,
- Robert H. Waterston,
- Mark Gerstein,
- Michael Snyder,
- and Valerie Reinke
Genome Res. February 2011 21: 245-254; Published in Advance December 22, 2010, doi:10.1101/gr.114587.110
..., tRNAs, snRNAs, and snoRNAs. For this analysis, we did not count ncRNA genes located in introns and transcribed in the same direction as the parent gene as candidate targets, because such embedded genes are typically spliced from the parent transcript and are not independently regulated. However...
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LETTER: Tandem chimerism as a means to increase protein complexity in the human genome
- Genís Parra,
- Alexandre Reymond,
- Noura Dabbouseh,
- Emmanouil T. Dermitzakis,
- Robert Castelo,
- Timothy M. Thomson,
- Stylianos E. Antonarakis,
- and Roderic Guigó
Genome Res. January 2006 16: 37-44; Published in Advance December 12, 2005, doi:10.1101/gr.4145906
...two bona fide genes in tandem. First, RefSeq transcripts usually have a corresponding full-length cDNA clone. Such clones are obtained by reverse transcription of the messenger RNA by oligo(dT) priming—which targets poly(A) tails often associated with the transcription termination site. Also...

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