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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
..., Stratton MR. 2004. A survey of RNA editing in human brain. Genome Res 14: 2379–87. Brisse M, Ly H. 2019. Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5. Front Immunol 10. Chen J. 2004. Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res...
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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
...splicing (AS) and alternative cleavage and polyadenylation (APA) in humans. Yet, these studies are generally performed with mature mRNA, so they report on the outcome rather than the processes of RNA maturation and thus may overlook how variants directly modulate pre-mRNA processing. The order in which...
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Method: Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated
- Sindri Emmanúel Antonsson and
- Páll Melsted
Genome Res. August 2025 35: 1832-1841; Published in Advance July 7, 2025, doi:10.1101/gr.279886.124
..., Burgin G, Delorey TM, Howitt MR, Katz Y, et al. 2017. A single-cell survey of the small intestinal epithelium. Nature 551: 333–339. doi:10.1038/nature24489 ↵Haghverdi L, Lun ATL, Morgan MD, Marioni JC. 2018. Batch effects in single-cell RNA sequencing data are corrected by matching mutual nearest...
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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
...Dayea Park and Can Cenik Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA Corresponding author: ccenik@austin.utexas.eduAbstractLong-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights...
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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
...an intricate series of RNA processing steps to achieve mRNA maturation. RNA editing and alternative splicing are two major RNA processing steps that can introduce significant modifications to the final gene products. By tackling these processes in isolation, recent studies have enabled substantial progress...
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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
...As have a relatively high fitness (Popitsch et al. 2017). Accumulating evidence indicates that RNA editing is crucial in the neuronal dynamic in the mammalian central nervous system (Gal-Mark et al. 2017). A handful of editing events have been demonstrated to be highly regulated during brain development...
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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
...with other RNA-binding proteins. The splicing factor SRSF9 was found to repress ADARB1-mediated editing of brain-specific sites (Huang et al. 2018; Shanmugam et al. 2018; Quinones-Valdez et al. 2019). Moreover, a recent survey for the impact of RNA-binding proteins on editing levels revealed that alternative...
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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
...in human cancers, we developed a computational pipeline that is similar to a previous analysis of miRNA editing in the human brain (Alon et al. 2012), but with some key improvements, and applied it to TCGA small RNA sequencing data (Fig. 1A; Methods; The Cancer Genome Atlas Research Network et al. 2013...
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Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
- Yongkang Long,
- Bin Zhang,
- Shuye Tian,
- Jia Jia Chan,
- Juexiao Zhou,
- Zhongxiao Li,
- Yisheng Li,
- Zheng An,
- Xingyu Liao,
- Yu Wang,
- Shiwei Sun,
- Ying Xu,
- Yvonne Tay,
- Wei Chen,
- and Xin Gao
Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
...editing.Accordingly, many tools have also been developed for the identification and quantification of APA based on RNA-seq data. Almost all of them are designed to detect the drops in RNA-seq read coverage along the gene body. However, due to high fluctuation of the sequencing coverage potentially caused...
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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
...24: 365–376. ↵Blow M, Futreal PA, Wooster R, Stratton MR. 2004. A survey of RNA editing in human brain. Genome Res 14: 2379–2387. ↵Brenner S. 1974. The genetics of Caenorhabditis elegans. Genetics 77: 71–94. ↵Burns CM, Chu H, Rueter SM, Hutchinson LK, Canton H, Sanders-Bush E, Emeson RB. 1997...

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