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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
...stability and protein translation, as well as feeding back to the nucleus to affect chromatin states at target loci.Epigenetic mechanisms are especially critical in germ cells, which have the task of transmitting both genetic and epigenetic information from parent to progeny. In Caenorhabditis elegans...
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RESOURCE: Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
- Natalia J. Martinez,
- Maria C. Ow,
- John S. Reece-Hoyes,
- M. Inmaculada Barrasa,
- Victor R. Ambros,
- and Albertha J.M. Walhout
Genome Res. December 2008 18: 2005-2015; Published in Advance November 3, 2008, doi:10.1101/gr.083055.108
..., and disease. For instance, more than 30% of C. elegans TFs confer a detectable phenotype when knocked down by RNAi (291 out of 940 predicted TFs tested; data obtained from WormBase WS180) ( Vermeirssen et al. 2007b ). In contrast, with the exceptions of lin-4 ( Lee et al. 1993 ), let-7 ( Reinhart et al. 2000...
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Research: Trans-splicing enhances translational efficiency in C. elegans
- Yu-Fei Yang,
- Xiaoqing Zhang,
- Xuehua Ma,
- Taolan Zhao,
- Qiushi Sun,
- Qing Huan,
- Shaohuan Wu,
- Zhuo Du,
- and Wenfeng Qian
Genome Res. September 2017 27: 1525-1535; Published in Advance July 6, 2017, doi:10.1101/gr.202150.115
...-splicing Essential genes are defined as having lethal or sterile phenotypes upon gene perturbation or knockdown (Kamath et al. 2003). Interestingly, we found that essential genes also exhibited higher translational efficiencies than nonessential genes inC. elegans (P = 6 × 10−6, Mann-Whitney U test) (Fig. 5A...
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Research: Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels
- Arwen W. Gao,
- Mark G. Sterken,
- Jelmi uit de Bos,
- Jelle van Creij,
- Rashmi Kamble,
- Basten L. Snoek,
- Jan E. Kammenga,
- and Riekelt H. Houtkooper
Genome Res. September 2018 28: 1296-1308; Published in Advance August 14, 2018, doi:10.1101/gr.232322.117
...Table S9).E. coli OP50 was obtained from the Caenorhabditis Genetics Center (CGC), RNAi bacterial clones are E. coli HT115 strains, including those to knockdown acox-1.1, acox-1.3, acox-1.4, gpdh-1, T27F6.6, ech-7, lagr-1, Y87G2A.2, scrm-2, nhr-82, nhr-265, nhr-81, nhr-165, nhr-217, nhr-77, nhr-174, nhr...
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Research: Redundant and incoherent regulations of multiple phenotypes suggest microRNAs’ role in stability control
- Zhongqi Liufu,
- Yixin Zhao,
- Li Guo,
- Guangxia Miao,
- Juan Xiao,
- Yang Lyu,
- Yuxin Chen,
- Suhua Shi,
- Tian Tang,
- and Chung-I Wu
Genome Res. October 2017 27: 1665-1673; Published in Advance September 13, 2017, doi:10.1101/gr.222505.117
...R310s through the target sites shown in Figure 4A. Restoring wild-type expression by promoter-driven RNAi Expression of target genes increases in mir310s knockout lines. As noted before, the restoration of the expression of a major target gene to its wild-type pattern should fully rescue the phenotype...
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Resource: Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans
- Chuna Kim,
- Jun Kim,
- Sunghyun Kim,
- Daniel E. Cook,
- Kathryn S. Evans,
- Erik C. Andersen,
- and Junho Lee
Genome Res. June 2019 29: 1023-1035; Published in Advance May 23, 2019, doi:10.1101/gr.246082.118
..., 31 are reported to cause sterile or lethal phenotypes by RNAi, and six of them, including the incompatibility gene zeel-1, showed sterile or lethal phenotypes when deleted in the N2 background (Supplemental Fig. S9C–E; Supplemental Table S2; Seidel et al. 2008, 2011). High-impact SVs as defined...
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Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
- Cristel G. Thomas,
- Wei Wang,
- Richard Jovelin,
- Rajarshi Ghosh,
- Tatiana Lomasko,
- Quang Trinh,
- Leonid Kruglyak,
- Lincoln D. Stein,
- and Asher D. Cutter
Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
...rate lend it especially pronounced signatures of linked selection, with the effect on the C. elegans even more extreme (Andersen et al. 2012). Whether the corresponding genomic regions in obligatorily outbreeding, often hyperdiverse, species of Caenorhabditis will exhibit similar evolutionary...
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RESOURCE: Toward Improving Caenorhabditis elegans Phenome Mapping With an ORFeome-Based RNAi Library
- Jean-François Rual,
- Julian Ceron,
- John Koreth,
- Tong Hao,
- Anne-Sophie Nicot,
- Tomoko Hirozane-Kishikawa,
- Jean Vandenhaute,
- Stuart H. Orkin,
- David E. Hill,
- Sander van den Heuvel,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2162-2168; doi:10.1101/gr.2505604
.... The Human Genome Project: Lessons from large-scale biology. Science 300 : 286 -290. ↵ Cutter, A.D., Payseur, B.A., Salcedo, T., Estes, A.M., Good, J.M., Wood, E., Hartl, T., Maughan, H., Strempel, J., Wang, B., et al. 2003 . Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans...
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Research: Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans
- Deni Subasic,
- Anneke Brümmer,
- Yibo Wu,
- Sérgio Morgado Pinto,
- Jochen Imig,
- Martin Keller,
- Marko Jovanovic,
- Helen Louise Lightfoot,
- Sara Nasso,
- Sandra Goetze,
- Erich Brunner,
- Jonathan Hall,
- Ruedi Aebersold,
- Mihaela Zavolan,
- and Michael O. Hengartner
Genome Res. November 2015 25: 1680-1691; Published in Advance July 31, 2015, doi:10.1101/gr.183160.114
...-82 double mutant and the mir-80; mir-81-82 triple mutant showed an increase in IR-induced germ cell apoptosis (Fig. 5A). However, because the 6-kb deletion of mir-81-82 covers the T07D1.2 gene, whose RNAi resulted in increased levels of DNA damage–induced apoptosis (Fig. 5A), it is likely that the increase...
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Research: Profiling the RNA editomes of wild-type C. elegans and ADAR mutants
- Han-Qing Zhao,
- Pan Zhang,
- Hua Gao,
- Xiandong He,
- Yanmei Dou,
- August Y. Huang,
- Xi-Ming Liu,
- Adam Y. Ye,
- Meng-Qiu Dong,
- and Liping Wei
Genome Res. January 2015 25: 66-75; Published in Advance November 4, 2014, doi:10.1101/gr.176107.114
...channels (Higuchi et al. 1993; Burns et al. 1997), creating new splicing sites (Rueter et al. 1999), modifying miRNA seed sequences or their targeting sites (Kawahara et al. 2007a,b), and protecting pre-mRNA by competing with the RNAi pathway (Wu et al. 2011; Warf et al. 2012). RNA editing is a widespread...
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