Searching journal content for articles similar to Kingston and Bartel 29 (11): 1777.

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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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Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
- Dhanur P. Iyer,
- Lambert Moyon,
- Lars Wittler,
- Chieh-Yu Cheng,
- Francisca R. Ringeling,
- Stefan Canzar,
- Annalisa Marsico,
- and Aydan Bulut-Karslioğlu
Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
...these processes are coordinated to successfully transition cells to the resting dormant state remains unclear. Here we show that microRNA activity, which is otherwise dispensable for preimplantation development, is essential for the adaptation of early mouse embryos to the dormant state of diapause. In particular...
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Research: Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation
- Geng Chen,
- John Paul Schell,
- Julio Aguila Benitez,
- Sophie Petropoulos,
- Marlene Yilmaz,
- Björn Reinius,
- Zhanna Alekseenko,
- Leming Shi,
- Eva Hedlund,
- Fredrik Lanner,
- Rickard Sandberg,
- and Qiaolin Deng
Genome Res. October 2016 26: 1342-1354; Published in Advance August 2, 2016, doi:10.1101/gr.201954.115
...at the single-cell level, although these processes were globally correlated. In addition, highly expressed genes, including core pluripotency factors, were in general biallelically expressed. Taken together, our study sheds light on the dynamics of XCI progression and the asynchronicity between pluripotency...
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Research: Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes
- Mohamed Belhocine,
- Mathieu Simonin,
- José David Abad Flores,
- Agata Cieslak,
- Iris Manosalva,
- Lydie Pradel,
- Charlotte Smith,
- Eve-Lyne Mathieu,
- Guillaume Charbonnier,
- Joost H.A. Martens,
- Hendrik G. Stunnenberg,
- Muhammad Ahmad Maqbool,
- Aneta Mikulasova,
- Lisa J. Russell,
- Daniel Rico,
- Denis Puthier,
- Pierre Ferrier,
- Vahid Asnafi,
- and Salvatore Spicuglia
Genome Res. July 2022 32: 1328-1342; Published in Advance June 23, 2021, doi:10.1101/gr.266924.120
...lines Loucy and DND41 and primary T-ALL samples 864 and 845) of broad H3K4me3 domains, pointing out to potential global deregulation of epigenetic complexes affecting H3K4me3 spreading. Moreover, the Loucy and DND41 cell lines have broad H3K4me3 domains of a larger size compared with thymocytes...
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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
...RNAs in human oocytes and early embryos using an RNA-sequencing (RNA-seq) method suitable for low inputs of material. We show that OET in humans is temporally coupled with the transition from predominant expression of oocyte short piRNAs (os-piRNAs) in oocytes, to activation of microRNA (miRNA) expression...
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Research: A compendium of conserved cleavage and polyadenylation events in mammalian genes
- Ruijia Wang,
- Dinghai Zheng,
- Ghassan Yehia,
- and Bin Tian
Genome Res. October 2018 28: 1427-1441; Published in Advance August 24, 2018, doi:10.1101/gr.237826.118
...; Sanfilippo et al. 2017). In addition, APA can be globally regulated in cell proliferation, differentiation, and development, as well as in response to various environmental cues (Tian and Manley 2017). Both sequence motifs and protein factors have been shown to impact APA under different conditions (Zheng...
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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
...in gene expression and orchestrate production, function, and turnover of mRNAs. The accuracy and dynamics of RNA–protein interactions within these molecular machines are essential for their function and are mediated by RNA-binding proteins (RBPs). Here, we show that fission yeast whole-cell poly(A)+ RNA...
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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
...activation of zygotic transcription. Subsequently, the correlation of microRNA expression is the highest between neighboring stages, and similarity decreases with increasing developmental distance. Thus, developmental transitions in T. castaneum are accompanied by shifts in the global microRNA profiles...
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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
...Institute of Pharmaceutical Chemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland; 8Faculty of Science, University of Zurich, 8057 Zurich, Switzerland In animals, microRNAs frequently form families with related sequences. The functional relevance ofmiRNA families and the relative...
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Method: Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
- Mattia Furlan,
- Eugenia Galeota,
- Nunzio Del Gaudio,
- Erik Dassi,
- Michele Caselle,
- Stefano de Pretis,
- and Mattia Pelizzola
Genome Res. October 2020 30: 1492-1507; Published in Advance September 25, 2020, doi:10.1101/gr.260984.120
...in each sample and compared with the global trend depicted in C. Each gene is either not expressed (blue), is not differential (white; ratio between the dashed lines in C), or is differentially post-transcriptional regulated (red; ratio above the dashed lines). Above the heatmaps, two color bars indicate...
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