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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: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...MPRA (Fig. 4). In these MPRA experiments, a specific sequence is mutated, and the effect of these numerous mutations is tested in parallel using MPRA. As it measures variant effects across the same sequence, we provide the ability to select the different promoters/enhancers that were tested using...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...organisms. For model training, we mainly focused on six species: Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli, Geobacillus subterraneus, Geobacter pickeringii. The respective positive sample counts for these species are 125,628, 68,917, 109,289, 2068, 14...
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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
...targeted mRNAs and mitigate truncated protein production. The presence of independent degradation pathways conflicts with genetic evidence supporting the requirement of all of SMG-1 through SMG-7 in Caenorhabditis elegans’ NMD (Hodgkin et al. 1989; Cali et al. 1999; Anders et al. 2003).A contemporary SMG-5...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...development of multiomicmethods provided tools for the assessment of cell identity and cell-to-cell heterogeneity. Multiomic, single-cell methods also inform on distinct aspects of the epi in parallel with gene expression (Cao et al. 2018; Zhu et al. 2019; Flynn et al. 2023). Approaches that map features of 3...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...) or husbandry programs that utilize ART to rederive strains at regular intervals to curtail genetic drift (Taft et al. 2006). Assuming that ∼0.5% of new single-nucleotide mutations are strongly deleterious (Dukler et al. 2022), a baseline mouse mutation rate of μ = 0.5 × 10−9/bp/gen (Uchimura et al. 2015...
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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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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: Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
- Arne Sahm,
- Konstantin Riege,
- Marco Groth,
- Martin Bens,
- Johann Kraus,
- Martin Fischer,
- Hans Kestler,
- Christoph Englert,
- Ralf Schaible,
- Matthias Platzer,
- and Steve Hoffmann
Genome Res. December 2024 34: 2217-2228; Published in Advance December 4, 2024, doi:10.1101/gr.279025.124
...for this deviation from the prediction of the theory may lie in the adaptability offered by a higher mutation rate, as we were able to show that the of the widely studied Hydra magnipapillata strain 105 has undergone a process of strong positive selection since the strain's cultivation 50 years ago. This most likely...
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Method: Enhancing nanopore adaptive sampling for PromethION using readfish at scale
- Rory Munro,
- Alexander Payne,
- Nadine Holmes,
- Chris Moore,
- Inswasti Cahyani,
- and Matthew Loose
Genome Res. April 2025 35: 877-885; Published in Advance January 30, 2025, doi:10.1101/gr.279329.124
...These authors contributed equally to this work. Corresponding author: matt.loose@nottingham.ac.ukAbstractA unique feature of Oxford Nanopore Technologies sequencers, adaptive sampling, allows precise DNA molecule selection from sequencing libraries. Here, we present enhancements to our tool, readfish, enabling...
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