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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
...establish a more 411 comprehensive functional landscape of A-to-I RNA editing in the light of adaptive 412 evolution, and complete the complex connectome of gut-brain interaction. 413 Taken together, using honey bees as a model, we delicately demonstrate the complex 414 and dynamic transcriptomic diversity...
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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
...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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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
...different brain tissues. We therefore demonstrate that splicing efficiency is a major factor controlling tissue-specific differences in editing levels.Adenosine to inosine editing (A-to-I editing) deaminates adenosines in double-stranded RNAs leading to nucleotide differences between RNA and DNA (Licht...
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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
...of individual missense A-to-I RNA editing events in cancer development (Chen et al. 2013; Galeano et al. 2013; Han et al. 2014). More recently, we and other groups have systematically characterized the RNA-editing genomic landscape in various cancer types using mRNA-seq data from The Cancer Genome Atlas (TCGA...
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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
...-stranded RNA (dsRNA) (Bass 2006). A-to-I RNA editing is widespread, with modifications occurring in more than half of the human transcriptome (Bazak et al. 2014). As inosine (I) and guanosine (G) base pair similarly, RNA editing in coding regions of genes can alter the amino acid sequence of proteins...
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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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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
...Corresponding author: hahundle@indiana.eduAbstractAdenosine (A) to inosine (I) RNA editing contributes to transcript diversity and modulates gene expression in a dynamic, cell type–specific manner. During mammalian brain development, editing of specific adenosines increases, whereas the expression of A-to-I...
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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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Resource: The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting
- Lishi Li,
- Yulong Song,
- Xinrui Shi,
- Jianheng Liu,
- Shaolei Xiong,
- Wanying Chen,
- Qiang Fu,
- Zichao Huang,
- Nannan Gu,
- and Rui Zhang
Genome Res. January 2018 28: 132-143; Published in Advance December 12, 2017, doi:10.1101/gr.224386.117
..., Guangzhou 510275, PR China ↵2 Co-first authors, listed alphabetically Corresponding authors: zhangrui3@mail.sysu.edu.cn, gnannan3@mail.sysu.edu.cnAbstractAdenosine-to-inosine (A-to-I) RNA editing regulates miRNA biogenesis and function. To date, fewer than 160 miRNA editing sites have been identified. Here...

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