Searching journal content for articles similar to Ramani et al. 21 (2): 342.

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  1. 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...
  2. Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
    • Kristina Krassovsky,
    • Rajarshi P. Ghosh,
    • and Barbara J. Meyer
    Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
    ...overwind or underwind DNA, creating DNA supercoils (Kouzine and Levens 2007). Supercoils can, in turn, induce formation of single-stranded DNA (ssDNA, hereafter SS DNA) or other non-B DNA structures.Genome-wide mapping of alternative DNA structures in cell lines and computational predictions in s suggested...
  3. 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...
  4. Resource: Genome-wide dynamics of alternative polyadenylation in rice
    • Haihui Fu,
    • Dewei Yang,
    • Wenyue Su,
    • Liuyin Ma,
    • Yingjia Shen,
    • Guoli Ji,
    • Xinfu Ye,
    • Xiaohui Wu,
    • and Qingshun Q. Li
    Genome Res. December 2016 26: 1753-1760; Published in Advance October 12, 2016, doi:10.1101/gr.210757.116
    ...Genome-wide dynamics of alternative polyadenylation in rice Haihui Fu 1 , 5 , Dewei Yang 2 , 5 , Wenyue Su 1 , Liuyin Ma 1 , Yingjia Shen 1 , Guoli Ji 3 , Xinfu Ye 2 , Xiaohui Wu 3 and Qingshun Q. Li 1...
  5. 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
    ..., a significant fraction of multiexon genes undergo alternative splicing, with higher frequencies reported across vertebrates (Pan et al. 2008; Wang et al. 2008; Barbosa-Morais et al. 2012; Merkin et al. 2012) in comparison to invertebrate model organisms such as the nematode Caenorhabditis elegans and the fruit...
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  6. 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
    ...organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites...
  7. Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
    • José Carlos Montañés,
    • Marta Huertas,
    • Simone G. Moro,
    • William R. Blevins,
    • Mercè Carmona,
    • José Ayté,
    • Elena Hidalgo,
    • and M. Mar Albà
    Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
    ...(fission yeast) retains many of the splicing features observed in humans and is thus an excellent model to study the basic mechanisms of splicing. Nearly half the genes contain introns, but the impact of alternative splicing in gene regulation and proteome diversification remains largely unexplored. Here...
  8. Resource: The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution
    • Adam D. Warner,
    • Louis Gevirtzman,
    • LaDeana W. Hillier,
    • Brent Ewing,
    • and Robert H. Waterston
    Genome Res. June 2019 29: 1036-1045; Published in Advance May 23, 2019, doi:10.1101/gr.243394.118
    ...Adam D. Warner, Louis Gevirtzman, LaDeana W. Hillier, Brent Ewing and Robert H. Waterston Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA Corresponding author: watersto@uw.eduAbstractWe have used RNA-seq in Caenorhabditis elegans...
    OPEN ACCESS ARTICLE
  9. Resource: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
    • Timothy J. Durham,
    • Riza M. Daza,
    • Louis Gevirtzman,
    • Darren A. Cusanovich,
    • Olubusayo Bolonduro,
    • William Stafford Noble,
    • Jay Shendure,
    • and Robert H. Waterston
    Genome Res. October 2021 31: 1952-1969; Published in Advance April 22, 2021, doi:10.1101/gr.271791.120
    ..., Cummings Life Science Center, Chicago, IL 60637, USA Corresponding author: watersto@uw.eduAbstractRecently developed single-cell technologies allow researchers to characterize cell states at ever greater resolution and scale. Caenorhabditis elegans is a particularly tractable system for studying...
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  10. 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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