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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
...of 22 RNA editing in gut-brain interactions remains unexplored. Comparative transcriptomic 23 analyses were performed between heads of germ-free (GF) versus conventional (CV) 24 honey bees. A total of 1,528 A-to-I editing sites are identified in honey bee heads, among 25 which nonsynonymous editing...
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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
...the RNA products and the corresponding genomic sequences. A-to-I editing is also known as A-to-G editing because inosine is subsequently recognized as guanosine (G) by the cellular translation machinery. Since nonsynonymous A-to-G RNA editing events can result in amino acid changes at the RNA level (even...
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Research: A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing
- Konstantin Licht,
- Utkarsh Kapoor,
- Fabian Amman,
- Ernesto Picardi,
- David Martin,
- Prajakta Bajad,
- and Michael F. Jantsch
Genome Res. September 2019 29: 1453-1463; Published in Advance August 19, 2019, doi:10.1101/gr.242636.118
...authors: Michael.Jantsch@meduniwien.ac.at, Konstantin.Licht@meduniwien.ac.atAbstractPre-mRNA-splicing and adenosine to inosine (A-to-I) RNA-editing occur mostly cotranscriptionally. During A-to-I editing, a genomically encoded adenosine is deaminated to inosine by adenosine deaminases acting on RNA (ADARs...
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Research: Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers
- Yumeng Wang,
- Xiaoyan Xu,
- Shuangxing Yu,
- Kang Jin Jeong,
- Zhicheng Zhou,
- Leng Han,
- Yiu Huen Tsang,
- Jun Li,
- Hu Chen,
- Lingegowda S. Mangala,
- Yuan Yuan,
- A. Karina Eterovic,
- Yiling Lu,
- Anil K. Sood,
- Kenneth L. Scott,
- Gordon B. Mills,
- and Han Liang
Genome Res. July 2017 27: 1112-1125; Published in Advance April 14, 2017, doi:10.1101/gr.219741.116
...from miRNA sequencing data of The Cancer Genome Atlas and identified 19 adenosine-to-inosine (A-to-I) RNA editing hotspots. We independently validated 15 of them by perturbation experiments in several cancer cell lines. These miRNA editing events show extensive correlations with key clinical variables...
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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
...in the noncoding regions. By RNA-seq analyses, a large number of A-to-I RNA editing events have been identified in the transcriptomes of humans (Li et al. 2009; Bahn et al. 2012; Peng et al. 2012; Ramaswami et al. 2013; Sakurai et al. 2014) and other animals (Danecek et al. 2012; St Laurent et al. 2013; Chen et al...
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Research: Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models
- Gregor Diensthuber,
- Leszek P. Pryszcz,
- Laia Llovera,
- Morghan C. Lucas,
- Anna Delgado-Tejedor,
- Sonia Cruciani,
- Jean-Yves Roignant,
- Oguzhan Begik,
- and Eva Maria Novoa
Genome Res. November 2024 34: 1865-1877; Published in Advance September 13, 2024, doi:10.1101/gr.278849.123
...RNA modification types, such as m6A, yield relatively modest basecalling “error” signatures (Begik et al. 2021), leading to a relatively high number of false positives and false negatives when predicting them in a transcriptome-wide fashion (Liu et al. 2019).Basecalling “errors” in nanopore sequencing...
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Resource: A biochemical landscape of A-to-I RNA editing in the human brain transcriptome
- Masayuki Sakurai,
- Hiroki Ueda,
- Takanori Yano,
- Shunpei Okada,
- Hideki Terajima,
- Toutai Mitsuyama,
- Atsushi Toyoda,
- Asao Fujiyama,
- Hitomi Kawabata,
- and Tsutomu Suzuki
Genome Res. March 2014 24: 522-534; Published in Advance January 9, 2014, doi:10.1101/gr.162537.113
...-to-Gmismatches generated by inevitablemapping errors, unidentified SNPs, and sequencing noise. Combined with the sites identified by the conventional ICE method, we report here the identification of 19,791 novel editing sites in the human transcriptome and 1258 mRNAs in which A-to-I editing had not previously been...
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Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
- Uditi Bhatt,
- Anne Cucchiarini,
- Yu Luo,
- Cameron W. Evans,
- Jean-Louis Mergny,
- K. Swaminathan Iyer,
- and Nicole M. Smith
Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
...and Kawahara 2021). Notably, Z-RNA structures influence the adenine-to-inosine (A-to-I) editing ability of ADAR with downstream effects on autoimmune diseases and encephalopathy (Koeris et al. 2005; de Reuver et al. 2021; Nakahama et al. 2021; Tang et al. 2021; Zillinger and Bartok 2021; Jiao et al. 2022...
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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
...) RNA editing and its impact on alternative splicing. We observed that >95% A-to-I RNA editing events occurred in the chromatin-associated RNA prior to polyadenylation. We report about 500 editing sites in the 3′ acceptor sequences that can alter splicing of the associated exons. These exons are highly...
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Research: A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes
- Lily Bazak,
- Ami Haviv,
- Michal Barak,
- Jasmine Jacob-Hirsch,
- Patricia Deng,
- Rui Zhang,
- Farren J. Isaacs,
- Gideon Rechavi,
- Jin Billy Li,
- Eli Eisenberg,
- and Erez Y. Levanon
Genome Res. March 2014 24: 365-376; Published in Advance December 17, 2013, doi:10.1101/gr.164749.113
...content. Adenosine-to-inosine (A-to-I) RNA editing by ADAR proteins converts a genomically encoded adenosine into inosine. It is known that most RNA editing in human takes place in the primate-specific Alu sequences, but the extent of this phenomenon and its effect on transcriptome diversity are not yet...
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