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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
...Y, Mali P. 2022. Efficient in vitro and in vivo RNA editing via recruitment of endogenous ADARs using circular guide RNAs. Nat Biotechnol 40: 938–945. Kim DDY, Kim TTY, Walsh T, Kobayashi Y, Matise TC, Buyske S, Gabriel A. 2004. Widespread RNA Editing of Embedded Alu Elements in the Human...
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Resource: Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser
- Jiawei Shen,
- Siyuan Cheng,
- Deepak Purushotham,
- Xiaoyu Zhuo,
- Alan Y Du,
- Wenjin Zhang,
- Daofeng Li,
- and Ting Wang
Genome Res. February 21, 2025 gr.279764.124; Published in Advance February 21, 2025, doi:10.1101/gr.279764.124
..., Batut P, Chaisson M, Gingeras TR. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29: 15-21. Dominguez AA, Lim WA, Qi LS. 2016. Beyond editing: repurposing CRISPR–Cas9 for precision regulation and interrogation. Nature reviews Molecular cell biology 17: 5-15. Du AY, Chobirko JD, Zhuo X...
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Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
- Christopher J. Playfoot,
- Julien Duc,
- Shaoline Sheppard,
- Sagane Dind,
- Alexandre Coudray,
- Evarist Planet,
- and Didier Trono
Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
..., which identified widespread isoform diversity in human neurodevelopment (Jeffries et al. 2020). Advances in long-read sequencing technologies now enable de novo full-transcript assembly and isoform expression quantification, analyses challenging to perform with short-read RNA-seq approaches...
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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
.... 2001. A gene expression map for Caenorhabditis elegans. Science 293: 2087–2092. ↵Kim DD, Kim TT, Walsh T, Kobayashi Y, Matise TC, Buyske S, Gabriel A. 2004. Widespread RNA editing of embedded Alu elements in the human transcriptome. Genome Res 14: 1719–1725. ↵Kim Dh, Grün D, van Oudenaarden A. 2013...
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Method: The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells
- Mireia Jordà,
- Anna Díez-Villanueva,
- Izaskun Mallona,
- Berta Martín,
- Sergi Lois,
- Víctor Barrera,
- Manel Esteller,
- Tanya Vavouri,
- and Miguel A. Peinado
Genome Res. January 2017 27: 118-132; Published in Advance December 20, 2016, doi:10.1101/gr.207522.116
...Fig. S22C ). LINE density did not appear to affect the degree of hypomethylation ( Fig. 4 B). View larger version: In this window In a new window Figure 4. ( A ) Density of genomic elements (genes, Alu repeats, CpG islands, and small nuclear RNAs) in genomic segments according to the Alu...
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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
...or predicted bioinformatically in coding regions, introns, and untranslated regions of mRNAs in the human transcriptome (Wulff et al. 2011). Most A-to-I editing sites reside in Alu repeat elements in the untranslated regions and introns, andA-to-I editing is frequent and prominent in the transcriptomes...
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Method: Accurate identification of A-to-I RNA editing in human by transcriptome sequencing
- Jae Hoon Bahn,
- Jae-Hyung Lee,
- Gang Li,
- Christopher Greer,
- Guangdun Peng,
- and Xinshu Xiao
Genome Res. January 2012 22: 142-150; Published in Advance September 29, 2011, doi:10.1101/gr.124107.111
...evaluated whether the motif is specifically relevant to RNA editing or it is an artifact due to the prevalence of Alus near editing sites. For the motif occurring in Alu sequences in coding exons without A-to-I editing in the vicinity, the structural conservation is much less than those near editing sites...
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Research: RNA editing in the human ENCODE RNA-seq data
- Eddie Park,
- Brian Williams,
- Barbara J. Wold,
- and Ali Mortazavi
Genome Res. September 2012 22: 1626-1633; doi:10.1101/gr.134957.111
...for nuclear RNA editing. Proc Natl Acad Sci 91: 11457–11461. Kim DD, Kim TT, Walsh T, Kobayashi Y, Matise TC, Buyske S, Gabriel A. 2004.Widespread RNA editing of embeddedAlu elements in the human transcriptome. Genome Res 14: 1719–1725. Kiran A, Baranov PV. 2010. DARNED: A DAtabase of RNa EDiting in humans...
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Method: Identification of bona fide B2 SINE retrotransposon transcription through single-nucleus RNA-seq of the mouse hippocampus
- Sara B. Linker,
- Lynne Randolph-Moore,
- Kalyani Kottilil,
- Fan Qiu,
- Baptiste N. Jaeger,
- Jerika Barron,
- and Fred H. Gage
Genome Res. November 2020 30: 1643-1654; Published in Advance October 29, 2020, doi:10.1101/gr.262196.120
...trafficking and RNA editing (Athanasiadis et al. 2004; Buckley et al. 2011). These functional distinctions underscore the importance of accurately quantifying bona fide, versus passenger, TE transcription.The most promising methods to distinguish bona fide TE elements directly assess RNA through modifications...
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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
..., but the extent of this phenomenon and its effect on transcriptome diversity are not yet clear. Here, we analyzed large-scale RNA-seq data and detected ∼1.6 million editing sites. As detection sensitivity increases with sequencing coverage, we performed ultradeep sequencing of selected Alu sequences and showed...
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