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Resource: Small RNA expression and miRNA modification dynamics in human oocytes and early embryos
- Pauliina Paloviita,
- Christel Hydén-Granskog,
- Dawit A. Yohannes,
- Priit Paluoja,
- Juha Kere,
- Juha S. Tapanainen,
- Kaarel Krjutškov,
- Timo Tuuri,
- Urmo Võsa,
- and Sanna Vuoristo
Genome Res. August 2021 31: 1474-1485; doi:10.1101/gr.268193.120
...Y, de Hoon MJL, Tomaru Y, Nishibu T, Ukekawa R, Funakoshi T, Kurokawa T, Suzuki H, Hayashizaki Y, et al. 2010. A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness. Genome Res 20: 1398–1410. doi:10.1101/gr...
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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
...and the editing position are conserved in human and mouse.Functional significance of edited mature miRNAs in mammalsTo reveal the possible functional significance of edited mature miRNAs, we compared the target genes of the unedited and edited versions of each miRNA with editing events at seed region in mammals...
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Research: Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity
- Stacia K. Wyman,
- Emily C. Knouf,
- Rachael K. Parkin,
- Brian R. Fritz,
- Daniel W. Lin,
- Lucas M. Dennis,
- Michael A. Krouse,
- Philippa J. Webster,
- and Muneesh Tewari
Genome Res. September 2011 21: 1450-1461; Published in Advance August 3, 2011, doi:10.1101/gr.118059.110
...and common post-transcriptional event that shows selectivity for specific miRNAs and is observed across species ranging from C. elegans to human. The modifications result predominantly from adenylation and uridylation and are seen across tissue types, disease states, and developmental stages...
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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
...biogenesis, AGO sorting, and post-transcriptional modification. In this study, we analyzed a diverse collection of small RNA libraries to provide the most comprehensive annotation of miRNAs in any species to date. In addition, the deep profiling of known miRNAs revealed alternative Drosha and/or Dicer-1...
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Research: Global analyses of the dynamics of mammalian microRNA metabolism
- Elena R. Kingston and
- David P. Bartel
Genome Res. November 2019 29: 1777-1790; Published in Advance September 13, 2019, doi:10.1101/gr.251421.119
...between cell types, implying the influence of cell-specific factors in dictating turnover rate. The apparent influence of miRNA regions most important for targeting, together with the effect of one target on miR-7 accumulation, suggest that targets fulfill this role. Analysis of the tailing and trimming...
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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
...RNAs 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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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
...Hoon MJL, Tomaru Y, Nishibu T, Ukekawa R, Funakoshi T, Kurokawa T, Suzuki H, Hayashizaki Y, et al. 2010. A comprehensive survey of 39 animal miRNA modification events and a possible role for 39 adenylation in modulating miRNA targeting effectiveness. Genome Res 20: 1398–1410. Cenci C, Barzotti R...
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Research: Birth and expression evolution of mammalian microRNA genes
- Julien Meunier,
- Frédéric Lemoine,
- Magali Soumillon,
- Angélica Liechti,
- Manuela Weier,
- Katerina Guschanski,
- Haiyang Hu,
- Philipp Khaitovich,
- and Henrik Kaessmann
Genome Res. January 2013 23: 34-45; Published in Advance October 3, 2012, doi:10.1101/gr.140269.112
...number of false positive predictions that may be obtained using these in silico methods, differences in target sites, which could be subtle, may not be easily detectable. We then traced the evolution of miRNA mature sequences and its effect onpotential target gene pools. Of 237miRNA families with two...
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Research: Discovery of hundreds of mirtrons in mouse and human small RNA data
- Erik Ladewig,
- Katsutomo Okamura,
- Alex S. Flynt,
- Jakub O. Westholm,
- and Eric C. Lai
Genome Res. September 2012 22: 1634-1645; doi:10.1101/gr.133553.111
...of the strands is preferentially stably incorporated as a singlestranded RNA in an Argonaute (Ago) complex, and guides it to target transcripts (Czech and Hannon 2010). Although bioinformatic strategies have been used to identify miRNA genes (Lai et al. 2003; Lim et al. 2003; Huang et al. 2007; van der Burgt et...
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Research: Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition
- Vladimir Despic,
- Mario Dejung,
- Mengting Gu,
- Jayanth Krishnan,
- Jing Zhang,
- Lydia Herzel,
- Korinna Straube,
- Mark B. Gerstein,
- Falk Butter,
- and Karla M. Neugebauer
Genome Res. July 2017 27: 1184-1194; Published in Advance April 5, 2017, doi:10.1101/gr.215954.116
...that the Hnrnpa1 AGGGA motif is necessary for proper Hnrnpa1 binding to RNA targets in vivo. 3′ UTRs are common targets of RBPs and miRNAs that regulate mRNA stability and translation (Matoulkova et al. 2012). In transcriptionally silent embryos, maternal mRNA translation is tightly controlled by regulation...

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