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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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Method: Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- Michiel de Hoon,
- Alessandro Bonetti,
- Charles Plessy,
- Yoshinari Ando,
- Chung-Chau Hon,
- Yuri Ishizu,
- Masayoshi Itoh,
- Sachi Kato,
- Dongyan Lin,
- Sho Maekawa,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Jay W. Shin,
- Jens Stolte,
- Ana Maria Suzuki,
- Michihira Tagami,
- Hazuki Takahashi,
- Supat Thongjuea,
- Alistair R.R. Forrest,
- Yoshihide Hayashizaki,
- Juha Kere,
- and Piero Carninci
Genome Res. September 2022 32: 1727-1735; Published in Advance August 12, 2022, doi:10.1101/gr.276647.122
...Present address: AstraZeneca Discovery Sciences, Translational Genomics, 43183 Mölndal, Sweden Corresponding author: michiel.dehoon@riken.jpAbstractIn eukaryotes, capped RNAs include long transcripts such as messenger RNAs and long noncoding RNAs, as well as shorter transcripts such as spliceosomal RNAs...
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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
...from double-stranded RNA (dsRNA) by Dicer and associate with Argonautes to direct RNA silencing. In Caenorhabditis elegans, 22G-RNAs and 26G-RNAs are often referred to as siRNAs but display distinct characteristics. For example, 22G-RNAs do not originate from dsRNA and do not depend on Dicer, whereas...
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Research: Panoramic transcriptome analysis and functional screening of long noncoding RNAs in mouse spermatogenesis
- Kai Li,
- Jiayue Xu,
- Yanyun Luo,
- Dingfeng Zou,
- Ruiqin Han,
- Shunshun Zhong,
- Qing Zhao,
- Xinyu Mang,
- Mengzhen Li,
- Yanmin Si,
- Yan Lu,
- Pengyu Li,
- Cheng Jin,
- Zhipeng Wang,
- Fang Wang,
- Shiying Miao,
- Bo Wen,
- Linfang Wang,
- Yanni Ma,
- Jia Yu,
- and Wei Song
Genome Res. January 2021 31: 13-26; Published in Advance December 16, 2020, doi:10.1101/gr.264333.120
...; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China ↵3 These authors contributed equally to this work. Corresponding authors: songwei@ibms.pumc.edu.cn, j-yu@ibms.pumc.edu.cn, yanni_ma@126.comAbstractLong noncoding RNAs (lncRNAs) have...
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Research: Critical roles of long noncoding RNAs in Drosophila spermatogenesis
- Kejia Wen,
- Lijuan Yang,
- Tuanlin Xiong,
- Chao Di,
- Danhui Ma,
- Menghua Wu,
- Zhaoyu Xue,
- Xuedi Zhang,
- Li Long,
- Weimin Zhang,
- Jiaying Zhang,
- Xiaolin Bi,
- Junbiao Dai,
- Qiangfeng Zhang,
- Zhi John Lu,
- and Guanjun Gao
Genome Res. September 2016 26: 1233-1244; Published in Advance August 11, 2016, doi:10.1101/gr.199547.115
...Critical roles of long noncoding RNAs in Drosophila spermatogenesis Kejia Wen 1 , 6 , Lijuan Yang 1 , 2 , 6 , Tuanlin Xiong 1 , 6 , Chao Di 1 , Danhui Ma 1 , Menghua Wu 1 , Zhaoyu Xue 1 , Xuedi Zhang 1...
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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
...assays in IGN, such as transcriptome profiling (RNA-seq), histone modification profiling via chromatin immunoprecipitation (ChIP-seq), and chromatin accessibility profiling via assay for transposon-accessible chromatin (ATAC-seq) (Sanchez et al. 2023).In this study, we characterized C. elegans chromatin...
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Research: Widespread formation of double-stranded RNAs in testis
- Andreas Werner,
- James E. Clark,
- Calum Samaranayake,
- John Casement,
- Hany S. Zinad,
- Shaymaa Sadeq,
- Surar Al-Hashimi,
- Martin Smith,
- Noora Kotaja,
- and John S. Mattick
Genome Res. July 2021 31: 1174-1186; Published in Advance June 22, 2021, doi:10.1101/gr.265603.120
...including protein-coding and noncoding RNAs as well as antisense transcripts are overrepresented in testis. Many of even highly expressed protein-coding transcripts are not translated (Wang et al. 2019), suggesting that the RNA itself or the process of transcription fulfills a biological role.A family...
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Research: Systematic transcriptome analysis associated with physiological and chronological aging in Caenorhabditis elegans
- Seokjin Ham,
- Sieun S. Kim,
- Sangsoon Park,
- Eun Ji E. Kim,
- Sujeong Kwon,
- Hae-Eun H. Park,
- Yoonji Jung,
- and Seung-Jae V. Lee
Genome Res. November/December 2022 32: 2003-2014; Published in Advance November 9, 2022, doi:10.1101/gr.276515.121
..., such as noncoding RNAs and intron-derived transcripts, were up-regulated with chronological aging. In contrast, mRNAs with many biological functions, including RNA processing, were down-regulated with physiological aging. We also identified an age-dependent increase in the usage of distal 3′ splice sites in mRNA...
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Resource: Genome sequencing of C. elegans balancer strains reveals previously unappreciated complex genomic rearrangements
- Tatiana Maroilley,
- Stephane Flibotte,
- Francesca Jean,
- Victoria Rodrigues Alves Barbosa,
- Andrew Galbraith,
- Afiya Razia Chida,
- Filip Cotra,
- Xiao Li,
- Larisa Oncea,
- Mark Edgley,
- Don Moerman,
- and Maja Tarailo-Graovac
Genome Res. January 2023 33: 154-167; Published in Advance December 5, 2022, doi:10.1101/gr.276988.122
...-95 (Table 2), a long intervening noncoding RNA that may be important for fertility. In addition, the mIn1 inversion disrupts the essential gene tbc-17 (Table 2), which may explain why homozygous mIn1 animals do not survive freezing well (Edgley and Riddle 2001), although mIn1 also carries dpy-10(e128...
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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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