Searching journal content for articles similar to Furey et al. 14 (10b): 2034.

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  1. Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
    • Yuange Duan,
    • Min Huang,
    • Lin Ye,
    • Ling Ma,
    • Yashuai Wu,
    • Yating Du,
    • Jiyao Liu,
    • Fan Song,
    • Li Tian,
    • Wanzhi Cai,
    • Hu Li,
    • Xin Zhou,
    • and Shiqi Luo
    Genome Res. March 4, 2026 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
    ...and RNA editing 16 17 18 Abstract 19 ADAR-mediated adenosine-to-inosine (A-to-I) mRNA editing contributes to the proteomic 20 diversity and behavioral complexity of animals. While recent studies indicate that the gut 21 microbiome influences various aspects of animal behavior, the potential involvement...
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  2. Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
    • Zohar Rosenwasser,
    • Roni Cohen-Fultheim,
    • Ofir Shliefer,
    • Erez Y. Levanon,
    • and Eli Eisenberg
    Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
    ...-to-I editing occurs frequently in repetitive elements that fold into stable secondary structures(Wren et al. 1977; Porath et al. 2017). For example, the vast majority of mRNA editing in humans occurs within Alu repetitive elements. These ~300bp long elements are abundant and make up approximately 10...
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  3. 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
    ...derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier...
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  4. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...-methyladenosine (m6A) modifications in native mRNA. We used human and mouse cells with known genetic variants to assign the allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses reveal the importance of sequences adjacent...
  5. Research: Genome-wide analysis of differential RNA editing in epilepsy
    • Prashant Kumar Srivastava,
    • Marta Bagnati,
    • Andree Delahaye-Duriez,
    • Jeong-Hun Ko,
    • Maxime Rotival,
    • Sarah R. Langley,
    • Kirill Shkura,
    • Manuela Mazzuferi,
    • Bénédicte Danis,
    • Jonathan van Eyll,
    • Patrik Foerch,
    • Jacques Behmoaras,
    • Rafal M. Kaminski,
    • Enrico Petretto,
    • and Michael R. Johnson
    Genome Res. March 2017 27: 440-450; doi:10.1101/gr.210740.116
    ...and for common susceptibility variants associated with generalized epilepsy. These analyses reveal a functional convergence between genes that are differentially RNA-edited in acquired symptomatic epilepsy and those that contribute risk for genetic epilepsy. Taken together, our results suggest a potential role...
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  6. Research: RNA editing in nascent RNA affects pre-mRNA splicing
    • Yun-Hua Esther Hsiao,
    • Jae Hoon Bahn,
    • Yun Yang,
    • Xianzhi Lin,
    • Stephen Tran,
    • Ei-Wen Yang,
    • Giovanni Quinones-Valdez,
    • and Xinshu Xiao
    Genome Res. June 2018 28: 812-823; Published in Advance May 3, 2018, doi:10.1101/gr.231209.117
    ..., revealed remarkable interplay between RNA editing and splicing and expanded the repertoire of functional RNA editing sites.The maturation of eukaryotic mRNAs involves an intricate series of molecular processes that modify newly synthesized RNA molecules, such as 5′ capping, splicing, RNA editing...
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  7. Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
    • Charles Plessy,
    • Michael J. Mansfield,
    • Aleksandra Bliznina,
    • Aki Masunaga,
    • Charlotte West,
    • Yongkai Tan,
    • Andrew W. Liu,
    • Jan Grašič,
    • María Sara del Río Pisula,
    • Gaspar Sánchez-Serna,
    • Marc Fabrega-Torrus,
    • Alfonso Ferrández-Roldán,
    • Vittoria Roncalli,
    • Pavla Navratilova,
    • Eric M. Thompson,
    • Takeshi Onuma,
    • Hiroki Nishida,
    • Cristian Cañestro,
    • and Nicholas M. Luscombe
    Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
    ...interaction between the arms of individual chromosomes or sex-specific regions, which corresponds with the “type-I” architecture reported by Hoencamp et al. (2021). In O. dioica, a significant fraction of genes is densely packed in a head-to-tail configuration and transcribed in polycistronic mRNAs, forming...
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  8. Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
    • Kathleen Zeglinski,
    • Christian Montellese,
    • Matthew E. Ritchie,
    • Monther Alhamdoosh,
    • Cédric Vonarburg,
    • Rory Bowden,
    • Monika Jordi,
    • Quentin Gouil,
    • Florian Aeschimann,
    • and Arthur Hsu
    Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
    ...correlate with internal poly(A) tracts in the vector reference sequence, indicating that the 5′ coverage bias is due to internal priming during the RT step leading to the formation of fragments not reflecting the state of the lentiviral RNA.Plotting of the reads’ 3′ ends revealed the intended poly(A) sites...
  9. Research: A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations
    • Te-Lun Mai and
    • Trees-Juen Chuang
    Genome Res. November 2019 29: 1766-1776; Published in Advance September 12, 2019, doi:10.1101/gr.246033.118
    ...Te-Lun Mai and Trees-Juen Chuang Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan Corresponding author: trees@gate.sinica.edu.twAbstractAdenosine-to-inosine (A-to-I) RNA editing is a very common co-/posttranscriptional modification that can lead to A-to-G changes at the RNA level...
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  10. Research: Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes
    • Huiquan Liu,
    • Qinhu Wang,
    • Yi He,
    • Lingfeng Chen,
    • Chaofeng Hao,
    • Cong Jiang,
    • Yang Li,
    • Yafeng Dai,
    • Zhensheng Kang,
    • and Jin-Rong Xu
    Genome Res. April 2016 26: 499-509; Published in Advance March 2, 2016, doi:10.1101/gr.199877.115
    ...Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes Huiquan Liu 1 , Qinhu Wang 1 , Yi He 2 , Lingfeng Chen 1 , Chaofeng Hao 1 , Cong Jiang 1 , Yang Li 3 , Yafeng Dai 1 , Zhensheng Kang 1...
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