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Method: Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
- Wei-Jen Chung,
- Phaedra Agius,
- Jakub O. Westholm,
- Michael Chen,
- Katsutomo Okamura,
- Nicolas Robine,
- Christina S. Leslie,
- and Eric C. Lai
Genome Res. February 2011 21: 286-300; Published in Advance December 22, 2010, doi:10.1101/gr.113050.110
.... Unexpectedly, we uncovered examples of clustered mirtrons in both fly and worm genomes, including a &lt;8-kb region in C. elegans harboring eight distinct mirtrons. Altogether, we demonstrate that discovery of functional mirtrons, unlike canonical miRNAs, is amenable to computational methods independent...
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Research: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
- Jaaved Mohammed,
- Alex S. Flynt,
- Alexandra M. Panzarino,
- Md Mosharrof Hossain Mondal,
- Matthew DeCruz,
- Adam Siepel,
- and Eric C. Lai
Genome Res. January 2018 28: 52-65; Published in Advance December 12, 2017, doi:10.1101/gr.226068.117
...criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death...
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Method: LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq
- Danny A. Bitton,
- Charalampos Rallis,
- Daniel C. Jeffares,
- Graeme C. Smith,
- Yuan Y.C. Chen,
- Sandra Codlin,
- Samuel Marguerat,
- and Jürg Bähler
Genome Res. July 2014 24: 1169-1179; Published in Advance April 7, 2014, doi:10.1101/gr.166819.113
..., most notably global translation. These results are consistent with the reported high toxicity of lariat accumulation (Nam et al. 1997) and a role for Dbr1 in processing of snoRNAs (Ooi et al. 1998) and mirtrons (Flynt et al. 2010). These findingsmay reflect the tight coordination and integration...
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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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Resource: Dynamics of microRNA expression during mouse prenatal development
- Sorena Rahmanian,
- Rabi Murad,
- Alessandra Breschi,
- Weihua Zeng,
- Mark Mackiewicz,
- Brian Williams,
- Carrie A. Davis,
- Brian Roberts,
- Sarah Meadows,
- Dianna Moore,
- Diane Trout,
- Chris Zaleski,
- Alex Dobin,
- Lei-Hoon Sei,
- Jorg Drenkow,
- Alex Scavelli,
- Thomas R. Gingeras,
- Barbara J. Wold,
- Richard M. Myers,
- Roderic Guigó,
- and Ali Mortazavi
Genome Res. November 2019 29: 1900-1909; Published in Advance October 23, 2019, doi:10.1101/gr.248997.119
...RBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42(Database issue): D68–D73. doi:10.1093/nar/gkt1181 ↵Ladewig E, Okamura K, Flynt AS, Westholm JO, Lai EC. 2012. Discovery of hundreds of mirtrons in mouse and human small RNA data. Genome Res 22: 1634–1645. doi:10.1101/gr...
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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
...through transcript degradation or translational inhibition (Jonas and Izaurralde 2015). Because each miRNA can potentially target many hundred mRNAs (Baek et al. 2008; Selbach et al. 2008), it has been proposed that miRNAs might have widespread effects that contribute to shaping male and female...
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Resource: High resolution annotation of zebrafish transcriptome using long-read sequencing
- German Nudelman,
- Antonio Frasca,
- Brandon Kent,
- Kirsten C. Sadler,
- Stuart C. Sealfon,
- Martin J. Walsh,
- and Elena Zaslavsky
Genome Res. September 2018 28: 1415-1425; Published in Advance July 30, 2018, doi:10.1101/gr.223586.117
...validated novel protein coding RNAs, we found only a few hundred novel ncRNAs. The RNAs in the libraries utilized were poly(A) tail-enriched. As both long noncoding and short noncoding RNAs are less likely to be poly(A) tailed (Pauli et al. 2012; Chew et al. 2013), this selection bias may have contributed...
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RESOURCE: A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach
- Evgeny A. Glazov,
- Pauline A. Cottee,
- Wesley C. Barris,
- Robert J. Moore,
- Brian P. Dalrymple,
- and Mark L. Tizard
Genome Res. June 2008 18: 957-964; Published in Advance May 9, 2008, doi:10.1101/gr.074740.107
...of the human mirtron ortholog in chicken. View this table: In this window In a new window Table 3. List of chicken mirtrons Discussion The results presented here provide experimental and bioinformatic evidence supporting the discovery of 361 new miRNAs, 88 new miRNA candidates, 18 mirtrons (including six novel...
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Research: Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
- Eugene Berezikov,
- Nicolas Robine,
- Anastasia Samsonova,
- Jakub O. Westholm,
- Ammar Naqvi,
- Jui-Hung Hung,
- Katsutomo Okamura,
- Qi Dai,
- Diane Bortolamiol-Becet,
- Raquel Martin,
- Yongjun Zhao,
- Phillip D. Zamore,
- Gregory J. Hannon,
- Marco A. Marra,
- Zhiping Weng,
- Norbert Perrimon,
- and Eric C. Lai
Genome Res. February 2011 21: 203-215; Published in Advance December 22, 2010, doi:10.1101/gr.116657.110
...by the Ambros, Tuschl, and Bartel groups in 2001, more than a hundred studies have sought to identify additional miRNAs in various species. We report here a meta-analysis of short RNA data from Drosophila melanogaster , aggregating published libraries with 76 data sets that we generated for the mod...
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Resource: Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines
- Jiayu Wen,
- Jaaved Mohammed,
- Diane Bortolamiol-Becet,
- Harrison Tsai,
- Nicolas Robine,
- Jakub O. Westholm,
- Erik Ladewig,
- Qi Dai,
- Katsutomo Okamura,
- Alex S. Flynt,
- Dayu Zhang,
- Justen Andrews,
- Lucy Cherbas,
- Thomas C. Kaufman,
- Peter Cherbas,
- Adam Siepel,
- and Eric C. Lai
Genome Res. July 2014 24: 1236-1250; Published in Advance July 1, 2014, doi:10.1101/gr.161554.113
...piRNA configurations. One hundred forty-nine overlapped CDS and/or 59 UTR exons, (e.g., Nipped-A) (Fig. 6F), which may potentially reflect decreased translational status of thesemRNAs (Robine et al. 2009). Curiously, we also identified 81 loci that generated substantial piRNAs from the sense strand...
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