Searching journal content for articles similar to Tan et al. 25 (9): 1410.1.

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  1. 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
    ...data from human embryonic stem cells, we found that RNA variation is a relatively poor predictor of protein variation for the same gene, in single cells (Fig. 6C, above; Reimegård et al. 2021). We found that proteins that are less variable than their cognate mRNAs tend to have high protein-to-mRNA...
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  2. Research: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells
    • Jennifer Y. Tan,
    • Tamara Sirey,
    • Frantisek Honti,
    • Bryony Graham,
    • Allison Piovesan,
    • Matthias Merkenschlager,
    • Caleb Webber,
    • Chris P. Ponting,
    • and Ana C. Marques
    Genome Res. May 2015 25: 655-666; Published in Advance March 19, 2015, doi:10.1101/gr.181974.114
    ...Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells Jennifer Y. Tan 1 , 2 , 3 , Tamara Sirey 1 , 2 , Frantisek Honti 1 , 2 , 3 , Bryony Graham 4 , 5 , Allison Piovesan 6 , Matthias...
  3. Method: A versatile type VI CRISPR-based approach for targeted m6A demethylation in mRNAs
    • Panagiotis G. Adamopoulos,
    • Konstantina Athanasopoulou,
    • and Andreas Scorilas
    Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
    ..., and abundance are not yet fully disclosed (Nachtergaele and He 2017). Studies in mammalian cells have already characterized more than 170 RNA modifications, highlighting the presence of modified bases in many RNA classes, including mRNAs, long noncoding RNAs (lncRNAs), tRNAs, and rRNAs (Nombela et al. 2021...
  4. 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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  5. Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
    • Jennifer A. Urban,
    • Daniel Ringwalt,
    • John M. Urban,
    • Wingel Xue,
    • Ryan Gleason,
    • Keji Zhao,
    • and Xin Chen
    Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
    ...SC-like enriched gene sets contained expected markers, supporting cluster identity and the robustness of our analysis (Fig. 2B; Supplemental Table S2). First, the long noncoding RNAs (lncRNAs), long non-coding RNA on the X 1 (lncRNA:roX1) and lncRNA:roX2, components of the male dosage compensation complex found...
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  6. Method: Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs
    • Ziyan Rao,
    • Min Zhang,
    • Shaodong Huang,
    • Chenyang Wu,
    • Yuheng Zhou,
    • Weijie Zhang,
    • Xia Lin,
    • and Dongyu Zhao
    Genome Res. August 2025 35: 1842-1858; Published in Advance May 27, 2025, doi:10.1101/gr.280235.124
    ...-values are determined by one-tailed Wilcoxon test. (K) GSEA analysis shows enrichment of the I-CRLs and O-CRLs in hub lncRNAs in a cancer-related lncRNA-mRNA network. (L) Box plot to indicate the difference in centrality score between I-CRLs and O-CRLs. P-value is determined by one-tailed Wilcoxon test...
  7. Research: ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development
    • Charlie Y. Shi,
    • Lara E. Elcavage,
    • Raghu R. Chivukula,
    • Joanna Stefano,
    • Benjamin Kleaveland,
    • and David P. Bartel
    Genome Res. September 2023 33: 1482-1496; Published in Advance August 2, 2023, doi:10.1101/gr.278073.123
    ...degradation of endogenous miRNAs have been discovered. In a founding example of this endogenous TDMD, a site within the mouse Nrep mRNA directs degradation of miR-29b, which shapes the behavior of the animal, as does a site in an orthologous long noncoding RNA (lncRNA) in zebrafish (Bitetti et al. 2018...
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  8. Research: H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells
    • Haifen Chen,
    • Bo Hu,
    • Cynthia Horth,
    • Eric Bareke,
    • Phillip Rosenbaum,
    • Sin Young Kwon,
    • Jacinthe Sirois,
    • Daniel N. Weinberg,
    • Faith M. Robison,
    • Benjamin A. Garcia,
    • Chao Lu,
    • William A. Pastor,
    • and Jacek Majewski
    Genome Res. May 2022 32: 825-837; Published in Advance April 8, 2022, doi:10.1101/gr.276383.121
    ...interactions. Here, we use the mouse embryonic stem cell (mESC) model to describe in detail the relationships within the H3K27-H3K36-DNA methylation subnetwork. In particular, we focus on the major epigenetic reorganization caused by deletion of the histone 3 lysine 36 methyltransferase NSD1, which in m...
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  9. Corrigendum: Corrigendum: TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation
    • Wenli Xu,
    • Chang Liu,
    • Bing Deng,
    • Penghui Lin,
    • Zhenghua Sun,
    • Anrui Liu,
    • Jiajia Xuan,
    • Yuying Li,
    • Keren Zhou,
    • Xiaoqin Zhang,
    • Qiaojuan Huang,
    • Hui Zhou,
    • Qingyu He,
    • Bin Li,
    • Lianghu Qu,
    • and Jianhua Yang
    Genome Res. April 2026 36: 885; doi:10.1101/gr.282041.126
    ....126 Published by Cold Spring Harbor Laboratory Press Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.282041.126 ;36/4/885 ;gr.282041.126 885 gr.282041.126 Corrigendum Corrigendum Corrigenda Corrigendum Corrigendum Xu Wenli Liu...
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  10. Research: The predicted RNA-binding protein regulome of axonal mRNAs
    • Raphaëlle Luisier,
    • Catia Andreassi,
    • Lisa Fournier,
    • and Antonella Riccio
    Genome Res. September 2023 33: 1497-1512; Published in Advance August 15, 2023, doi:10.1101/gr.277804.123
    ...). Most RBPs are multifunctional, and the complexes undergo extensive remodeling in the cytoplasm (Hentze et al. 2018). RBP interaction with elements in the 3′ UTR mediates mRNA targeting to dendrites and axons, and this event is necessary for the establishment of synapses, axon growth, and nerve repair...
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