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Research: A low-abundance class of Dicer-dependent siRNAs produced from a variety of features in C. elegans
- Thiago L. Knittel,
- Brooke E. Montgomery,
- Alex J. Tate,
- Ennis W. Deihl,
- Anastasia S. Nawrocki,
- Frederic J. Hoerndli,
- and Taiowa A. Montgomery
Genome Res. December 2024 34: 2203-2216; Published in Advance December 2, 2024, doi:10.1101/gr.279083.124
...editing by adenosine deaminases (ADARs) in C. elegans have identified numerous endogenous small RNAs with the hallmarks of canonical siRNA. For example, they appear to be processed from a dsRNA intermediate and are 22–24 nt long (Wu et al. 2011; Reich et al. 2018; Fischer and Ruvkun 2020). These siRNAs...
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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
...by the humanadenosine deaminases acting on RNA (ADAR) proteins was once regarded as rare events. Recently, hundreds of thousands of ADAR-mediated editing sites have been identified in human cells (Kawahara et al. 2004; Ju et al. 2011; Alon et al. 2012; Chen et al. 2012; Peng et al. 2012; Silberberg et al. 2012; Vesely...
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LETTER: Altered adenosine-to-inosine RNA editing in human cancer
- Nurit Paz,
- Erez Y. Levanon,
- Ninette Amariglio,
- Amy B. Heimberger,
- Zvi Ram,
- Shlomi Constantini,
- Zohar S. Barbash,
- Konstantin Adamsky,
- Michal Safran,
- Avi Hirschberg,
- Meir Krupsky,
- Issachar Ben-Dov,
- Simona Cazacu,
- Tom Mikkelsen,
- Chaya Brodie,
- Eli Eisenberg,
- and Gideon Rechavi
Genome Res. November 2007 17: 1586-1595; Published in Advance October 1, 2007, doi:10.1101/gr.6493107
...such as inhibition of the kinase activity of the dsRNA-activated protein kinase PKR, and suppression of eIF2a phosphorylation by ADAR through a mechanism independent of dsRNA editing ( Nie et al. 2006 ). Rather than acting as adenosine deaminase, ADARB2 could have other essential roles associated with its ssRNAs...
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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
.... Abstract Inosine is an abundant RNA modification in the human transcriptome and is essential for many biological processes in modulating gene expression at the post-transcriptional level. Adenosine deaminases acting on RNA (ADARs) catalyze the hydrolytic deamination of adenosines to inosines (A...
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Research: Effects of ADARs on small RNA processing pathways in C. elegans
- M. Bryan Warf,
- Brent A. Shepherd,
- W. Evan Johnson,
- and Brenda L. Bass
Genome Res. August 2012 22: 1488-1498; Published in Advance June 6, 2012, doi:10.1101/gr.134841.111
...and Brenda L. Bass1,4 1Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA; 2Department of Statistics, Brigham Young University, Provo, Utah 84602, USA; 3Department of Medicine, Boston University, Boston, Massachusetts 02118, USA Adenosine deaminases that act on RNA (ADARs...
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Methods: Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
- Ryan D. Morin,
- Michael D. O’Connor,
- Malachi Griffith,
- Florian Kuchenbauer,
- Allen Delaney,
- Anna-Liisa Prabhu,
- Yongjun Zhao,
- Helen McDonald,
- Thomas Zeng,
- Martin Hirst,
- Connie J. Eaves,
- and Marco A. Marra
Genome Res. April 2008 18: 610-621; Published in Advance February 19, 2008, doi:10.1101/gr.7179508
...for the other isomiRs. Enzymatic modification of microRNAs Although some reads were detected that may represent the result of pre-miRNA editing by adenosine deaminases (observed as A to G transitions) or cytidine deaminases (producing C to U transitions), examples of these were infrequent and few were...
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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
...utilize splicing to generate pre-miRNA hairpin mimics, termed mirtrons, which bypass DROSHA cleavage and are further processed by DICER1 (Westholm and Lai 2011).Adenosine deaminases acting on RNA (ADARs) are known to bind dsRNA regions of protein-coding genes and noncoding sequences, particularly pri-miRNAs...

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