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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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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
...(Supplemental Fig. S1D,E), of similar depth to published nanopore direct RNA-seq data sets (Legnini et al. 2019; Roach et al. 2020; Viscardi and Arribere 2022), and of lower depth than short-read RNA-seq (Supplemental Fig. S1E). Overall, reads with the 5′ adapter were low abundance (∼2%–5% of libraries...
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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...et al. 2013).Evolution of the spacer and satellite sequenceTo reconstruct the evolutionary history of the subterminal satellites, we performed an independent analysis of the two classes of repeats that define its composition: the pCht (∼32 bp) satellite that exists in millions of copies throughout...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...; Packer et al. 2019).The aggregate expression patterns of these non-HOT targets of blmp-1 and GATAe are like the patterns of the respective TFs. blmp-1 in worms is expressed in a variety of cell classes, including hypodermis, seam cells, glia, excretory cells, and rectal cells with the aggregate...
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Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...the entire MHC class II region in a relatively large panel of rhesus macaques. Adaptive sampling is a real-time selective sequencing approach featured in ONT's MinKNOW software (Loose et al. 2016). Originally released as the open-source Read Until software, this enrichment strategy enables users to target...
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Research: Genome-wide redistribution of 24-nt siRNAs in rice gametes
- Chenxin Li,
- Hengping Xu,
- Fang-Fang Fu,
- Scott D. Russell,
- Venkatesan Sundaresan,
- and Jonathan I. Gent
Genome Res. February 2020 30: 173-184; Published in Advance January 2, 2020, doi:10.1101/gr.253674.119
...RNAs, and investigated the relationship of 24-nt siRNAs to DNA methylation in the gametes.ResultsWe prepared and sequenced small RNA Illumina libraries from seedling shoots, isolated sperm cells, isolated egg cells, and whole ovaries (after manual removal of egg cells) of rice variety Kitaake. For each...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...(Supplemental Fig. S5F); however, overall, a wide variety of gene functions are found in the different chromatin states. Together, these observations point to diverse regulatory mechanisms beyond the chromatin state that combine to determine expression levels of genes in the oogenesis-enriched class.We also...
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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
...communication between cis-regulatory elements. Many organisms, including S. cerevisiae, C. elegans, and A. thaliana contain cohesin but lack CTCF. Here, we used C. elegans to investigate the function of cohesin in 3D organization in the absence of CTCF. Using Hi-C data, we observe cohesin-dependent features...
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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
...are tissue and developmentally regulated (Gerstberger et al. 2014).The nematode worm C. elegans possesses multiple tissue types, including a well-differentiated nervous system estimated to contain at least 118 distinct neuronal subtypes, including the major neurotransmitter-releasing classes found...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...embryos.These findings highlight that stable and unstable transcripts are enriched for distinct sequence features, consistent with multiple mechanisms regulating mRNA stability. Codon optimality appears to be the single strongest predictor of mRNA stability in the C. elegans embryo. Additional complexity...

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