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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
...of concordantly up-regulated miRNAs across diapause conditions, which were further validated in embryos and ESCs (Supplemental Fig. S4B,C).Constructing the miRNA–target network of the paused pluripotent statemiRNAs act in a combinatorial fashion, cooperatively fine-tuning many genes at once. We thus...
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Research: Optical genome mapping identifies rare structural variants in neural tube defects
- Nikhil S. Sahajpal,
- Jane Dean,
- Benjamin Hilton,
- Timothy Fee,
- Cindy Skinner,
- Alex Hastie,
- Barbara R. DuPont,
- Alka Chaubey,
- Michael J. Friez,
- and Roger E. Stevenson
Genome Res. April 2025 35: 798-809; Published in Advance March 19, 2025, doi:10.1101/gr.279318.124
..., and FOXH1). FOXD4 (case 9, Fig. 2B; Table 1), is a forkhead transcription factor, that regulates the transition from pluripotent embryonic stem cells (ESCs) to neuroectodermal stem cell, and is necessary for neuronal differentiation (Neilson et al. 2012). McMohan et al. (2022) observed craniofacial...
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Research: Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis
- Paola Cornejo-Páramo,
- Kathrein Roper,
- Sandie M. Degnan,
- Bernard M. Degnan,
- and Emily S. Wong
Genome Res. March 2022 32: 474-487; Published in Advance January 19, 2022, doi:10.1101/gr.275864.121
...embryogenesis identifies three major developmental periods. As in bilaterian embryogenesis, early development in Amphimedon involves activating and repressive chromatin in regions both proximal and distal to transcription start sites. Transcriptionally repressive elements (“silencers”) are prominent during late...
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Research: Hormone-control regions mediate steroid receptor–dependent genome organization
- François Le Dily,
- Enrique Vidal,
- Yasmina Cuartero,
- Javier Quilez,
- A. Silvina Nacht,
- Guillermo P. Vicent,
- José Carbonell-Caballero,
- Priyanka Sharma,
- José Luis Villanueva-Cañas,
- Roberto Ferrari,
- Lara Isabel De Llobet,
- Gaetano Verde,
- Roni H.G. Wright,
- and Miguel Beato
Genome Res. January 2019 29: 29-39; Published in Advance December 14, 2018, doi:10.1101/gr.243824.118
...(expressed as normalized counts per million within the region depicted) using the 90-kb intergenic region (highlighted in blue) as bait. Panels below correspond to Genome Browser tracks of ChIP-seq reads per million (rpm) profiles obtained for the different factors and epigenetic marks listed in the absence...
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Research: Combinatorial DNA methylation codes at repetitive elements
- Christophe Papin,
- Abdulkhaleg Ibrahim,
- Stéphanie Le Gras,
- Amandine Velt,
- Isabelle Stoll,
- Bernard Jost,
- Hervé Menoni,
- Christian Bronner,
- Stefan Dimitrov,
- and Ali Hamiche
Genome Res. June 2017 27: 934-946; Published in Advance March 27, 2017, doi:10.1101/gr.213983.116
...(MEFs) and pluripotent ESCs. Our data decipher a dynamic combinatorial DNA methylation code at repetitive elements that could play a major role in cell differentiation and define novel DNA regulatory regions within the mouse . Results The available data showed that TDG could be implicated...
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Research: Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation
- Marina Veil,
- Lev Y. Yampolsky,
- Björn Grüning,
- and Daria Onichtchouk
Genome Res. March 2019 29: 383-395; Published in Advance January 23, 2019, doi:10.1101/gr.240572.118
...Figure 1. Nucleosomes cover all TFBSs pre-ZGA and are depleted from PSN triple-bound regions post-ZGA. Heat maps of six groups of genomic regions defined by combinatorial binding of Pou5f3, Nanog, and SoxB1 post-ZGA, as indicated at the left, and Ppre group bound by Pou5f3 only pre-ZGA. Three...
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Research: The role of insulators and transcription in 3D chromatin organization of flies
- Keerthi T. Chathoth,
- Liudmila A. Mikheeva,
- Gilles Crevel,
- Jareth C. Wolfe,
- Ioni Hunter,
- Saskia Beckett-Doyle,
- Sue Cotterill,
- Hongsheng Dai,
- Andrew Harrison,
- and Nicolae Radu Zabet
Genome Res. April 2022 32: 682-698; Published in Advance March 30, 2022, doi:10.1101/gr.275809.121
...knockdown). (E,F) Examples of a genomic region at DpnII restriction size resolution for: (E) BEAF-32; and (F) Cp190 and/or Chro knockdowns. Darker colors indicate more contacts retrieved by in situ Hi-C. Green arrow indicates maintained borders and red arrows lost borders. From top to bottom, we plot...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...that contain transcriptionally coregulated genes. We also uncovered the transcriptomic profiles of two previously molecularly uncharacterized cell types: isorhiza-type nematocytes and somatic gonad ectoderm. Finally, we identified novel candidate regulators of cell type–specific transcription, several of which...
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Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
- Yuning Zhang,
- Tiffany D. Ho,
- Nicolas E. Buchler,
- and Raluca Gordân
Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
...highlights the importance of direct TF-TF competition for genomic binding and gene regulation by TF paralogs, and proposes an approach for studying this competition in a quantitative and high-throughput manner.Transcription factor (TF) proteins recognize specific DNA targets across the to regulate gene...
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Research: Interactions between pluripotency factors specify cis-regulation in embryonic stem cells
- Chris Fiore and
- Barak A. Cohen
Genome Res. June 2016 26: 778-786; Published in Advance April 15, 2016, doi:10.1101/gr.200733.115
...Chris Fiore and Barak A. Cohen Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA Corresponding author: cohen@genetics.wustl.edu AbstractWe investigated how interactions between pluripotency transcription...

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