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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
...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
...and sequence motif data. A-to-I microRNA editing hotspots in cancer Genome Research 1119 www..org from variants at the DNA level. The vast majority of RNA editing events identified are canonical A-to-I or C-to-U RNA editing, but there are still considerable numbers of other editing types. Since miRNAs...
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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
...channels and the Raw repeat protein OLRN-1 in C. elegans. Neural Dev 2: 24. ↵Bazak L, Haviv A, Barak M, Jacob-Hirsch J, Deng P, Zhang R, Isaacs FJ, Rechavi G, Li JB, Eisenberg E, et al. 2014. A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes. Genome Res...
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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
.... 2014; Alon et al. 2015). In general, RNA editing occurs more frequently in noncoding than in coding regions. In humans, more than 1.4 million A-to-I editing sites have been identified (Pinto et al. 2014). The vast majority (∼97%) of them target repetitive sequences located within introns and 5′- or 3...
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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
...Methods). (B) Number and percentage of A-to-I RNA editing sites in each editing kinetics group. (C) The editing ratios (ER) of each editing site in the four groups. The genomic location of an editing site is shown in color codes. All editing sites included in this analysis were required to have at least...
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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
...region (UTR) of target transcripts, thereby affecting gene function through changes in transcript stability and/or translational efficiency (Liu et al. 2014).The A-to-I type of RE has been reported as the most abundant conversion, with over 16,000 RNA-edited sites in whole brain tissue described (Lee et...
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Research: RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system
- Dan Bar-Yaacov,
- Ernest Mordret,
- Ruth Towers,
- Tammy Biniashvili,
- Clara Soyris,
- Schraga Schwartz,
- Orna Dahan,
- and Yitzhak Pilpel
Genome Res. October 2017 27: 1696-1703; Published in Advance September 1, 2017, doi:10.1101/gr.222760.117
...methyltransferase TRMT61B in all vertebrates. PLoS Biol 14: e1002557. Bazak L, Haviv A, Barak M, Jacob-Hirsch J, Deng P, Zhang R, Isaacs FJ, Rechavi G, Li JB, Eisenberg E, et al. 2014. A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes. Genome Res 24: 365...
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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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Research: RNA–DNA sequence differences in Saccharomyces cerevisiae
- Isabel X. Wang,
- Christopher Grunseich,
- Youree G. Chung,
- Hojoong Kwak,
- Girish Ramrattan,
- Zhengwei Zhu,
- and Vivian G. Cheung
Genome Res. November 2016 26: 1544-1554; Published in Advance September 16, 2016, doi:10.1101/gr.207878.116
...identification of edited microRNAs in the human brain. Genome Res 22: 1533–1540. Avesson L, Barry G. 2014. The emerging role of RNA and DNA editing in cancer. Biochim Biophys Acta 1845: 308–316. Bahn JH, Lee JH, LiG, Greer C, PengG, XiaoX. 2012. Accurate identification of A-to-I RNA editing in human...
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