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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: 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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Method: Highly efficient and scarless genome editing via essential gene-coupled homology-directed repair
- Joo Hye Yeo,
- Hyongbum Henry Kim,
- Sang Ho Oh,
- and Jinu Lee
Genome Res. April 15, 2026 gr.281194.125; Published in Advance April 15, 2026, doi:10.1101/gr.281194.125
...disrupt endogenous gene regulation and 106 compromise genomic stability. Thus, selection cassettes are sometimes placed in 107 intronic regions to mitigate this limitation (Wang et al. 2022); however, these can 108 interfere with splicing and generate aberrant transcripts. Meanwhile, “safe harbor” loci...
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Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
- Elina Abaev-Schneiderman,
- Linh Nguyen,
- Raz Shalev,
- Tzofit Elbaz Biton,
- Anand Chopra,
- Giritharan Jagadeesan,
- Daniel Sevilla-Sanchez,
- Nili Tickotsky Moskovitz,
- Liron Levin,
- Michal Feldman,
- Capucine Van Rechem,
- and Dan Levy
Genome Res. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
...show that the genomic distribution of ACTB is SETD3-dependent and that this regulation modulates the transcription of genes involved in cell adhesion and mRNA translation in colorectal cancer cells. Proteomic analyses reveal that ACTB and SETD3 interact with multiple large protein complexes, including...
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Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
- Marcus J. Viscardi,
- Enisha Sehgal,
- and Joshua A. Arribere
Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
...role in human health by degrading mRNAs containing PTCs, which drive diverse diseases (Mort et al. 2008). NMD also regulates the abundance of ∼5%–20% of endogenous transcripts in animals, making NMD broadly relevant for gene expression (Mendell et al. 2004; Rehwinkel et al. 2005; Wittmann et al. 2006...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...processes of selection on somatic mutations, driving tumor growth through aberrant regulation of the cell cycle. Somatic mutations caused by multiple endogenous and exogenous factors are mostly neutral passengers, with only a few drivers of clonal expansion under strong positive selection. Cancer genomic...
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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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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...that these ERVs also function as enhancers. To test this proposal, from the 1170 ERV loci potentially regulated by KZFPs, we first selected 286 ERV loci based on their transcripts and the adjacent gene transcripts being detected by RNA-seq either in KIT+ SGs or in PSs. Whereas expression of intergenic ERVs...
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Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
- Thiago L. Knittel,
- Brooke E. Montgomery,
- Alex J. Tate,
- Ennis W. Deihl,
- Anastasia S. Nawrocki,
- Frederic J. Hoerndli,
- and Taiowa A. Montgomery
Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
...). Nonetheless, even at low abundance, they could have important roles in gene regulation and thus their identification would be an important step toward a more complete understanding of the small RNA landscape of C. elegans. In this study, our aim was to identity and characterize these siRNAs in the context...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
..., referred to as tsRNAs, is emerging with a potential to exert a new layer in gene regulation. These RNAs are breakdown products of tRNAs, either through active processing or passive cleavage or both. Since tRNAs are part of the general machinery for translation, their expression levels and activities...

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