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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
...). Here, we performed a systematic analysis of miRNA editing events based on high-throughput TCGA small RNA sequencing data of 20 different cancer types. Results Systematic detection of RNA editing hotspots in miRNAs across cancer types To comprehensively characterize the profiles of miRNA editing events...
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Method: Barcoding bias in high-throughput multiplex sequencing of miRNA
- Shahar Alon,
- Francois Vigneault,
- Seda Eminaga,
- Danos C. Christodoulou,
- Jonathan G. Seidman,
- George M. Church,
- and Eli Eisenberg
Genome Res. September 2011 21: 1506-1511; Published in Advance July 12, 2011, doi:10.1101/gr.121715.111
...M, KishimaM, Lassmann T, Faulkner GJ, Mattick JS, et al. 2010. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res 20: 257–264. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. 2008. Substantial biases in ultra-short read data sets from...
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Method: Systematic identification of edited microRNAs in the human brain
- Shahar Alon,
- Eyal Mor,
- Francois Vigneault,
- George M. Church,
- Franco Locatelli,
- Federica Galeano,
- Angela Gallo,
- Noam Shomron,
- and Eli Eisenberg
Genome Res. August 2012 22: 1533-1540; Published in Advance April 12, 2012, doi:10.1101/gr.131573.111
...and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res 20: 257–264. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. 2008. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36: e105. Ebhardt HA, Tsang HH, Dai DC...
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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
...UrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrUrNrN), which remove the sequence-specific biases of RNA ligases (Jayaprakash et al. 2011). All libraries were sequenced on HiSeq 2500 or NextSeq 500 (Illumina) to produce single-end 67-bp reads.Identification of edited mature miRNAsCustom edited pre-miRNA databases were generated by replacing the A with G...
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Research: Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation
- Maria Warnefors,
- Katharina Mössinger,
- Jean Halbert,
- Tania Studer,
- John L. VandeBerg,
- Isa Lindgren,
- Amir Fallahshahroudi,
- Per Jensen,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1961-1973; Published in Advance October 27, 2017, doi:10.1101/gr.225391.117
..., Sweden Corresponding authors: maria.warnefors@gmail.com, h.kaessmann@zmbh.uni-heidelberg.deAbstractSexual dimorphism depends on sex-biased gene expression, but the contributions of microRNAs (miRNAs) have not been globally assessed. We therefore produced an extensive small RNA sequencing data set...
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Research: A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness
- A. Maxwell Burroughs,
- Yoshinari Ando,
- Michiel J.L. de Hoon,
- Yasuhiro Tomaru,
- Takahiro Nishibu,
- Ryo Ukekawa,
- Taku Funakoshi,
- Tsutomu Kurokawa,
- Harukazu Suzuki,
- Yoshihide Hayashizaki,
- and Carsten O. Daub
Genome Res. October 2010 20: 1398-1410; Published in Advance August 18, 2010, doi:10.1101/gr.106054.110
...These authors contributed equally to this work. Abstract Animal microRNA sequences are subject to 3′ nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation of miRNA is globally present and conserved across Drosophila and vertebrates...
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Resource: Structural and operational complexity of the Geobacter sulfurreducens genome
- Yu Qiu,
- Byung-Kwan Cho,
- Young Seoub Park,
- Derek Lovley,
- Bernhard Ø. Palsson,
- and Karsten Zengler
Genome Res. September 2010 20: 1304-1311; Published in Advance June 30, 2010, doi:10.1101/gr.107540.110
...Hoon MJL, Taft RJ, Hashimoto T, Kanamori-Katayama M, Kawaji H, KawanoM, KishimaM, Lassmann T, Faulkner GJ, Mattick JS, et al. 2010. Cross-mapping and identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res. doi: 10.1101/ gr.095273.095109. Feist AM...

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