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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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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
...editing by adenosine deaminases (ADARs) in C. elegans have identified numerous endogenous small RNAs with the hallmarks of canonical siRNA. For example, they appear to be processed from a dsRNA intermediate and are 22–24 nt long (Wu et al. 2011; Reich et al. 2018; Fischer and Ruvkun 2020). These siRNAs...
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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
...Technologies to study the transcriptome complexity in Caenorhabditis elegans. We generated approximately six million reads using native poly(A)-tailed mRNAs from three developmental stages, with average read lengths ranging from 900 to 1100 nt. Around half of the reads represent full-length transcripts...
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Resource: The full-length transcriptome of C. elegans using direct RNA sequencing
- Nathan P. Roach,
- Norah Sadowski,
- Amelia F. Alessi,
- Winston Timp,
- James Taylor,
- and John K. Kim
Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
...nanopore-based direct RNA sequencing to characterize the developmental polyadenylated transcriptome of C. elegans. Taking advantage of long reads spanning the full length of mRNA transcripts, we provide support for 23,865 splice isoforms across 14,611 genes, without the need for computational...
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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
...sites (Morse et al. 2002; Blow et al. 2004; Levanon et al. 2004; Mazloomian and Meyer 2015). In general, ADAR and splicing machineries may act on the same dsRNA substrates, leading to the interplay between these two processes (Reenan et al. 2000; Rieder et al. 2013). However, structure-mediated splicing...
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Research: Profiling neural editomes reveals a molecular mechanism to regulate RNA editing during development
- Suba Rajendren,
- Alfa Dhakal,
- Pranathi Vadlamani,
- Jack Townsend,
- Sarah N. Deffit,
- and Heather A. Hundley
Genome Res. January 2021 31: 27-39; Published in Advance December 18, 2020, doi:10.1101/gr.267575.120
...encodes two proteins with homology with the ADAR family, an editing-deficient family member, ADR-1, and the A-to-I editing enzyme, ADR-2. Previous C. elegans studies identified a few global mechanisms of regulating RNA editing. For example, C. elegans ADBP-1 positively regulates editing by promoting ADR-2...
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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
...editing in higher eukaryotes. Caenorhabditis elegans has two ADARs, ADR-1 and ADR-2, but their functions remain unclear. Here, we profiled the RNA editomes of C. elegans at different developmental stages of wild-type and ADAR mutants. We developed a new computational pipeline with a ‘‘bisulfite...
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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...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...to individual nucleotides, including processes such as methylation and editing. These marks contribute to a wide range of biological processes, many of which are related to host immune system defense. The functions of immune-related RNA modifications can be categorized into three main groups: regulation...
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Research: A-to-I RNA editing promotes developmental stage–specific gene and lncRNA expression
- Boaz Goldstein,
- Lily Agranat-Tamir,
- Dean Light,
- Orna Ben-Naim Zgayer,
- Alla Fishman,
- and Ayelet T. Lamm
Genome Res. March 2017 27: 462-470; Published in Advance December 28, 2016, doi:10.1101/gr.211169.116
...to this work. AbstractA-to-I RNA editing is a conserved widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions, mainly noncoding. Mutations in ADAR enzymes in Caenorhabditis elegans cause defects in normal development...

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