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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...are highly abundant, the Spirodela TraPR profile displays very low levels of 24 nt siRNAs, and it is dominated by 21–22 nt sRNAs (Fig. 1B; Supplemental Fig. S3), predominantly contributed by regulatory microRNAs (miRNAs). The lack of 24 nt siRNAs in the Spirodela TraPR profile is more pronounced than...
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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
....111 ↵Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281–297. doi:10.1016/S0092-8674(04)00045-5 ↵Bartel DP. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136: 215–233. doi:10.1016/j.cell.2009.01.002 ↵Bernstein E, Kim SY, Carmell MA, Murchison EP...
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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
..., and post-transcriptional modifications of miRNAs. Beyond conserved loci, the trove of “young” miRNAs allows us to quantify distinct rates of miRNA flux according to biogenesis type, genomic locale, tissue restriction, and evolutionary clade. We identify patterns of structural change associated with flux...
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Method: NanoPARE: parallel analysis of RNA 5′ ends from low-input RNA
- Michael A. Schon,
- Max J. Kellner,
- Alexandra Plotnikova,
- Falko Hofmann,
- and Michael D. Nodine
Genome Res. December 2018 28: 1931-1942; Published in Advance October 24, 2018, doi:10.1101/gr.239202.118
...RNAs such as those involved in splicing (snoRNA) or translation (rRNAs, tRNAs) also generates diverse RNA 5′ ends (Wang et al. 1988; Filipowicz and Pogačić 2002; Granneman et al. 2011; Henras et al. 2015). Moreover, small regulatory RNAs such as microRNAs (miRNAs) and small interfering RNAs (siRNAs...
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Research: MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum
- Maria Ninova,
- Matthew Ronshaugen,
- and Sam Griffiths-Jones
Genome Res. January 2016 26: 85-96; Published in Advance October 30, 2015, doi:10.1101/gr.193367.115
...multiple paralogs from several Tribolium -specific microRNA families expressed during a narrow interval of time immediately after the activation of zygotic transcription. These novel microRNAs, together with several early expressed conserved microRNAs, target a significant number of maternally deposited...
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Perspective: Decrypting noncoding RNA interactions, structures, and functional networks
- Muller Fabbri,
- Leonard Girnita,
- Gabriele Varani,
- and George A. Calin
Genome Res. September 2019 29: 1377-1388; Published in Advance August 21, 2019, doi:10.1101/gr.247239.118
.... 2017). Over the last decade, advances in bioinformatics and deep sequencing technology have allowed the identification and annotation of tens of thousands of short and long ncRNAs (lncRNAs). These include endogenous microRNAs (miRNAs), small interfering RNAs (endo-siRNAs), PIWI-interacting RNAs (piRNAs...
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Method: System-wide analyses of the fission yeast poly(A)⁺ RNA interactome reveal insights into organization and function of RNA–protein complexes
- Cornelia Kilchert,
- Tea Kecman,
- Emily Priest,
- Svenja Hester,
- Ebru Aydin,
- Krzysztof Kus,
- Oliver Rossbach,
- Alfredo Castello,
- Shabaz Mohammed,
- and Lidia Vasiljeva
Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
...characterize RNA-binding activities of novel RBPs that have been recurrently detected in the RNA interactomes of multiple species. We find that many of these, including cyclophilins and thioredoxins, are substoichiometric RNA interactors in vivo. Because RBPomes show very good overall agreement between species...
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Research: Widespread context dependency of microRNA-mediated regulation
- Florian Erhard,
- Jürgen Haas,
- Diana Lieber,
- Georg Malterer,
- Lukasz Jaskiewicz,
- Mihaela Zavolan,
- Lars Dölken,
- and Ralf Zimmer
Genome Res. June 2014 24: 906-919; Published in Advance March 25, 2014, doi:10.1101/gr.166702.113
.... Expression of genes is not only regulated at the level of transcription but also post-transcriptionally in various ways, of which regulation mediated by microRNAs is one of the most prevalent (He andHannon 2004). MicroRNAs are 20- to 24-nt long noncoding RNAs that have been found in animals and plants...
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Research: Redundant and incoherent regulations of multiple phenotypes suggest microRNAs’ role in stability control
- Zhongqi Liufu,
- Yixin Zhao,
- Li Guo,
- Guangxia Miao,
- Juan Xiao,
- Yang Lyu,
- Yuxin Chen,
- Suhua Shi,
- Tian Tang,
- and Chung-I Wu
Genome Res. October 2017 27: 1665-1673; Published in Advance September 13, 2017, doi:10.1101/gr.222505.117
...of microRNAs on protein output. Nature 455: 64–71. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281–297. Bartel DP. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136: 215–233. Bejarano F, Smibert P, Lai EC. 2010. miR-9a prevents apoptosis during...
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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
.... Evolution of mammalian microRNA genes Genome Research 41 www..org strong regulatory effects. Our findings lend support to previous predictions (Chen and Rajewsky 2007) and are in line with patterns observed in insects and plants (Lu et al. 2008; Fahlgren et al. 2010). Our analyses also revealed that ;25...
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