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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: Cotargeting among microRNAs in the brain
- Jennifer M. Cherone,
- Vjola Jorgji,
- and Christopher B. Burge
Genome Res. November 2019 29: 1791-1804; Published in Advance October 24, 2019, doi:10.1101/gr.249201.119
...Jennifer M. Cherone1, Vjola Jorgji2 and Christopher B. Burge1 1Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; 2Department of Biology, Wellesley College, Wellesley, Massachusetts 02481, USA Corresponding author: cburge@mit.eduAbstractMicroRNAs (mi...
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Research: Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development
- Patricia Gerdes,
- Dorothy Chan,
- Mischa Lundberg,
- Francisco J. Sanchez-Luque,
- Gabriela O. Bodea,
- Adam D. Ewing,
- Geoffrey J. Faulkner,
- and Sandra R. Richardson
Genome Res. September 2023 33: 1465-1481; Published in Advance October 5, 2023, doi:10.1101/gr.278003.123
...; de la Rica et al. 2016; Gerdes et al. 2022). During embryonic development, the epi undergoes reprogramming including phases of global DNA demethylation (Hajkova et al. 2002; Seki et al. 2005; Abe et al. 2011; Saitou et al. 2012; Seisenberger et al. 2012; Smith et al. 2012; Cantone and Fisher 2013...
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Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
- Ran Zhang,
- Chengxiang Qiu,
- Galina N. Filippova,
- Gang Li,
- Jay Shendure,
- Jean-Philippe Vert,
- Xinxian Deng,
- William Stafford Noble,
- and Christine M. Disteche
Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
...and multimodal profiles across time, and extrapolate single-cell profiles in a missing modality. We apply Sunbear to reveal sex-biased transcription during mouse embryonic development and predict dynamic relationships between epigenetic priming and transcription for cells in which multimodal profiles...
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Research: Delayed DNA replication in haploid human embryonic stem cells
- Matthew M. Edwards,
- Michael V. Zuccaro,
- Ido Sagi,
- Qiliang Ding,
- Dan Vershkov,
- Nissim Benvenisty,
- Dieter Egli,
- and Amnon Koren
Genome Res. December 2021 31: 2155-2169; Published in Advance November 22, 2021, doi:10.1101/gr.275953.121
...address: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA Corresponding author: koren@cornell.eduAbstractHaploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication...
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Research: MicroRNAs reinforce repression of PRC2 transcriptional targets independently and through a feed-forward regulatory network
- Haridha Shivram,
- Steven V. Le,
- and Vishwanath R. Iyer
Genome Res. February 2019 29: 184-192; Published in Advance January 16, 2019, doi:10.1101/gr.238311.118
...14: 310–319. doi:10.1016/j.celrep.2015.12.031 ↵Graham B, Marcais A, Dharmalingam G, Carroll T, Kanellopoulou C, Graumann J, Nesterova TB, Bermange A, Brazauskas P, Xella B, et al. 2016. MicroRNAs of the miR-290–295 family maintain bivalency in mouse embryonic stem cells. Stem Cell Rep 6: 635–642. doi...
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Research: Embryonic LTR retrotransposons supply promoter modules to somatic tissues
- Kosuke Hashimoto,
- Eeva-Mari Jouhilahti,
- Virpi Töhönen,
- Piero Carninci,
- Juha Kere,
- and Shintaro Katayama
Genome Res. November 2021 31: 1983-1993; Published in Advance October 21, 2021, doi:10.1101/gr.275354.121
...to subsequent generations (Belshaw et al. 2004). Human germline cells express multiple distinct LTR families, such as human endogenous retrovirus L and H (HERV-L and HERV-H) (Göke et al. 2015). During embryonic activation (EGA), HERV-L elements are activated by the homeobox transcription factor DUX4...
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Research: Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals
- Daniel W. Bellott and
- David C. Page
Genome Res. February 2021 31: 198-210; Published in Advance January 21, 2021, doi:10.1101/gr.268516.120
...of duplication (Fig. 2C). MicroRNAs (miRNAs) are short, noncoding RNAs that fine-tune gene dosage by pairing to the 3′ untranslated region and lowering target mRNA levels (Bartel 2009). Conserved targeting by miRNAs is a feature of genes sensitive to changes in gene dosage, particularly to overexpression (Naqvi...
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Method: Degradation dynamics of microRNAs revealed by a novel pulse-chase approach
- Matteo J. Marzi,
- Francesco Ghini,
- Benedetta Cerruti,
- Stefano de Pretis,
- Paola Bonetti,
- Chiara Giacomelli,
- Marcin M. Gorski,
- Theresia Kress,
- Mattia Pelizzola,
- Heiko Muller,
- Bruno Amati,
- and Francesco Nicassio
Genome Res. April 2016 26: 554-565; Published in Advance January 28, 2016, doi:10.1101/gr.198788.115
...Degradation dynamics of microRNAs revealed by a novel pulse-chase approach Matteo J. Marzi 1 , 3 , Francesco Ghini 1 , 3 , Benedetta Cerruti 1 , Stefano de Pretis 1 , Paola Bonetti 1 , Chiara Giacomelli 1 , Marcin M. Gorski...
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Research: A-to-I editing of microRNAs in the mammalian brain increases during development
- Ylva Ekdahl,
- Hossein Shahrabi Farahani,
- Mikaela Behm,
- Jens Lagergren,
- and Marie Öhman
Genome Res. August 2012 22: 1477-1487; Published in Advance May 29, 2012, doi:10.1101/gr.131912.111
...A-to-I editing of microRNAs in the mammalian brain increases during development Ylva Ekdahl 1 , 3 , Hossein Shahrabi Farahani 2 , 3 , Mikaela Behm 1 , Jens Lagergren 2 and Marie Öhman 1 , 4 1Department of Molecular...

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