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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...target expression variation and covariation, but these observations have been limited to a few microRNAs. Here we systematically study microRNA alternative functions in mouse embryonic stem cells (mESCs) by genetically deleting Drosha, leading to global loss of microRNAs. We apply complementary single...
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Method: Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives
- Hyun-Hwan Jeong,
- Seon Young Kim,
- Maxime W.C. Rousseaux,
- Huda Y. Zoghbi,
- and Zhandong Liu
Genome Res. June 2019 29: 999-1008; Published in Advance April 23, 2019, doi:10.1101/gr.245571.118
...calculated recall (a recall value close to one indicates a prediction with a low false-negative rate), precision (a precision value close to one indicates a prediction with a low false-positive rate), and F-measure (the harmonic mean of PR) of all the methods at each FDR level. To allow each method...
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Research: The evolution of evolvability in microRNA target sites in vertebrates
- Jin Xu,
- Rui Zhang,
- Yang Shen,
- Guojing Liu,
- Xuemei Lu,
- and Chung-I Wu
Genome Res. November 2013 23: 1810-1816; Published in Advance September 27, 2013, doi:10.1101/gr.148916.112
...Y-L, Langenberger D, Gunsalus KC, Rajewsky N. 2005. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 1: e13. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp A-C, Munschauer M...
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Research: Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans
- Deni Subasic,
- Anneke Brümmer,
- Yibo Wu,
- Sérgio Morgado Pinto,
- Jochen Imig,
- Martin Keller,
- Marko Jovanovic,
- Helen Louise Lightfoot,
- Sara Nasso,
- Sandra Goetze,
- Erich Brunner,
- Jonathan Hall,
- Ruedi Aebersold,
- Mihaela Zavolan,
- and Michael O. Hengartner
Genome Res. November 2015 25: 1680-1691; Published in Advance July 31, 2015, doi:10.1101/gr.183160.114
...a framework for understanding how miRNA family members interact to regulate target mRNAs. [Supplemental material is available for this article.] MicroRNAs (miRNAs) are noncoding RNAmolecules of∼21 nucleotides in length that have an essential role in post-transcriptional regulation of gene expression...
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Method: Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
- Hua-Sheng Chiu,
- David Llobet-Navas,
- Xuerui Yang,
- Wei-Jen Chung,
- Alberto Ambesi-Impiombato,
- Archana Iyer,
- Hyunjae Ryan Kim,
- Elena G. Seviour,
- Zijun Luo,
- Vasudha Sehgal,
- Tyler Moss,
- Yiling Lu,
- Prahlad Ram,
- José Silva,
- Gordon B. Mills,
- Andrea Califano,
- and Pavel Sumazin
Genome Res. February 2015 25: 257-267; Published in Advance November 5, 2014, doi:10.1101/gr.178194.114
..., Leslie C. 2010. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 11: R90. Boissonneault V, Plante I, Rivest S, Provost P. 2009. MicroRNA-298 and microRNA-328 regulate expression of mouse beta-amyloid precursor protein-converting enzyme 1. J...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...RNA expression profiling in postmortem brains from individuals with ASD and controls and identified 60 circRNAs and three coregulated modules that were perturbed in ASD. By integrating circRNA, microRNA, and mRNA dysregulation data derived from the same cortex samples, we identified 8170 ASD-associated circRNA-microRNA...
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Resource: MicroRNA programs in normal and aberrant stem and progenitor cells
- Christopher P. Arnold,
- Ruoying Tan,
- Baiyu Zhou,
- Si-Biao Yue,
- Steven Schaffert,
- Joseph R. Biggs,
- Regis Doyonnas,
- Miao-Chia Lo,
- John M. Perry,
- Valérie M. Renault,
- Alessandra Sacco,
- Tim Somervaille,
- Patrick Viatour,
- Anne Brunet,
- Michael L. Cleary,
- Linheng Li,
- Julien Sage,
- Dong-Er Zhang,
- Helen M. Blau,
- Caifu Chen,
- and Chang-Zheng Chen
Genome Res. May 2011 21: 798-810; Published in Advance March 30, 2011, doi:10.1101/gr.111385.110
..., the microRNAs (miRNAs). miRNAs are;22-nucleotide (nt) regulatory RNAs that repress translation and/or initiate transcript degradation via imperfect base pairing with cognate target mRNAs (Bartel 2009). miRNAcoding genes represent;1%–5% of the predicted genes in worms, flies, mice, and humans. Each miRNA can...
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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
...reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution.MicroRNAs (miRNAs) are an extensive class of ∼22-nt RNAs that play important regulatory roles in diverse eukaryotic species (Flynt and Lai 2008; Axtell et al. 2011). In the canonical metazoan pathway...
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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
...revealed thousands of sex-biased genes in mammals and birds (Yang et al. 2006; Itoh et al. 2010; Harrison et al. 2015; Melé et al. 2015). Less attention has been given to the potential impact of sex-biased microRNAs (miRNAs)—short regulatory RNAs (∼21 nt) that enable expression fine-tuning of target m...
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Research: Signatures of RNA binding proteins globally coupled to effective microRNA target sites
- Anders Jacobsen,
- Jiayu Wen,
- Debora S. Marks,
- and Anders Krogh
Genome Res. August 2010 20: 1010-1019; Published in Advance May 27, 2010, doi:10.1101/gr.103259.109
...Signatures of RNA binding proteins globally coupled to effective microRNA target sites Anders Jacobsen 1 , 4 , Jiayu Wen 1 , Debora S. Marks 2 , 3 , 5 and Anders Krogh 1 , 3 , 5 1 The Bioinformatics Centre, Department...
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