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Resource: Epigenomics of embryogenesis in turbot
- Oscar Aramburu,
- Belen G Pardo,
- Ada Jimenez-Gonzalez,
- Andrés Blanco-Hortas,
- Daniel Macqueen,
- Carmen Bouza,
- and Paulino Martinez
Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
...Neuroscience, University of Sheffield, UK, S10 2TN 6 3The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of 7 Edinburgh, Easter Bush Campus, UK, EH25 9RG 8 ABSTRACT 9 Embryogenesis is the foundational step of ontogeny, where a complex organism 10 emerges from a single totipotent...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...during Drosophila embryogenesis. Using a combined haplotype test, we identified 9%–18% of TF-bound regions impacted by genetic variation even for essential regulators. By expanding WASP (a tool for allele-specific read mapping) to examine indels, we increased detection of allelically imbalanced peaks...
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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
...constructed the miRNA-mediated regulatory network of mouse early embryos specific to diapause. We find that individual miRNAs contribute to the combinatorial regulation by the network, and the perturbation of the network compromises embryo survival in diapause. We further identified the nutrient...
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Research: Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors
- James L. Shepherdson,
- Ryan Z. Friedman,
- Yiqiao Zheng,
- Chi Sun,
- Inez Y. Oh,
- David M. Granas,
- Barak A. Cohen,
- Shiming Chen,
- and Michael A. White
Genome Res. February 2024 34: 243-255; Published in Advance February 14, 2024, doi:10.1101/gr.278133.123
...corresponds with their phenotypic severity. The two variants affect similar sets of enhancers, and p.E168d2 has distinct effects on silencers. Cis-regulatory elements (CREs) near cone photoreceptor genes are enriched for silencers that are derepressed in the presence of p.E168d2. Chromatin environments of CRX...
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Research: Chromatin architecture transitions from zebrafish sperm through early embryogenesis
- Candice L. Wike,
- Yixuan Guo,
- Mengyao Tan,
- Ryohei Nakamura,
- Dana Klatt Shaw,
- Noelia Díaz,
- Aneasha F. Whittaker-Tademy,
- Neva C. Durand,
- Erez Lieberman Aiden,
- Juan M. Vaquerizas,
- David Grunwald,
- Hiroyuki Takeda,
- and Bradley R. Cairns
Genome Res. June 2021 31: 981-994; Published in Advance May 18, 2021, doi:10.1101/gr.269860.120
...boundaries emerging at 4 hpf, and that those established at 4 hpf are largely maintained at 5.3 and 24 hpf (Supplemental Fig. S2E,F). The clarity of TADs in 24 hpf embryos, which are diverse in cell types, shows that zebrafish share with other species a consistency in TAD organization between cell types...
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Method: ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome
- Tyler J. Hansen and
- Emily Hodges
Genome Res. August 2022 32: 1529-1541; Published in Advance July 20, 2022, doi:10.1101/gr.276766.122
...ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human Tyler J. Hansen1 and Emily Hodges1,2 1Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA; 2Vanderbilt Genetics Institute...
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Method: Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing
- Brendan L. O'Connell,
- Ruth V. Nichols,
- Dmitry Pokholok,
- Jerushah Thomas,
- Sonia N. Acharya,
- Andrew Nishida,
- Casey A. Thornton,
- Marissa Co,
- Andrew J. Fields,
- Frank J. Steemers,
- and Andrew C. Adey
Genome Res. February 2023 33: 208-217; Published in Advance February 15, 2023, doi:10.1101/gr.276655.122
...University, Knight Cardiovascular Institute, Portland, Oregon 97239, USA Corresponding author: adey@ohsu.eduAbstractHere we present advancements in single-cell combinatorial indexed Assay for Transposase Accessible Chromatin (sciATAC) to measure chromatin accessibility that leverage nanowell chips to achieve...
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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
...methylation pattern of repeat elements in differentiated mammalian cells. The biological significance of repetitive element methylation/oxidation remains elusive. Whereas the hypomethylation of repetitive elements appears to be a hallmark of cancer cells (Howard et al. 2008; Ehrlich 2009; Baba et al. 2010...
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Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...The of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals Christine E. Schnitzler1,2, E. Sally Chang3,4, Justin Waletich1,2, Gonzalo Quiroga-Artigas1,2,5, Wai Yee Wong6, Anh-Dao Nguyen3, Sofia N. Barreira3, Liam B. Doonan7...
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Method: Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN
- Xiangxiu Wang,
- Wen Wang,
- Yiman Wang,
- Jia Chen,
- Guifen Liu,
- and Yong Zhang
Genome Res. February 2022 32: 378-388; Published in Advance December 29, 2021, doi:10.1101/gr.275837.121
...Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN Xiangxiu Wang1, Wen Wang1, Yiman Wang, Jia Chen, Guifen Liu1 and Yong Zhang Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research...

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