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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: 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
...developmental gene expression in metazoans. Yet, the ancestral regulatory landscape of metazoan embryogenesis is unknown. Here, we generate chromatin accessibility profiles for six embryonic, plus larval and adult stages in the sponge Amphimedon queenslandica. These profiles are reproducible within stages...
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Resource: Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
- Yingshu Li,
- Yongjie Liu,
- Hang Yang,
- Ting Zhang,
- Kiyoshi Naruse,
- and Qiang Tu
Genome Res. June 2020 30: 924-937; Published in Advance June 26, 2020, doi:10.1101/gr.258871.119
...-quality sequence and a variety of genetic tools are available for this model organism. However, existing annotation is still rudimentary, as it was mainly based on computational prediction and short-read RNA-seq data. Here we report a dynamic transcriptome landscape of medaka embryogenesis profiled by long...
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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
.... Additionally, the lack of structure before ZGA has been observed previously in Drosophila, another species with fast cycling cells during early embryogenesis (Hug et al. 2017). In mammals, chromatin architecture in early embryos is limited to focal regions and is not fully established -wide until after ZGA (Du...
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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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Resource: Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling
- Jian Ming Khor,
- Jennifer Guerrero-Santoro,
- William Douglas,
- and Charles A. Ettensohn
Genome Res. September 2021 31: 1680-1692; Published in Advance July 30, 2021, doi:10.1101/gr.275684.121
...-seq) to profile eRNA expression and enhancer activity during embryogenesis of a model echinoderm: the sea urchin, Strongylocentrotus purpuratus. We identified more than 18,000 enhancers that were active in mature oocytes and developing embryos and documented a burst of enhancer activation during cleavage...
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Research: Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period
- Juan J. Tena,
- Cristina González-Aguilera,
- Ana Fernández-Miñán,
- Javier Vázquez-Marín,
- Helena Parra-Acero,
- Joe W. Cross,
- Peter W.J. Rigby,
- Jaime J. Carvajal,
- Joachim Wittbrodt,
- José L. Gómez-Skarmeta,
- and Juan R. Martínez-Morales
Genome Res. July 2014 24: 1075-1085; Published in Advance April 7, 2014, doi:10.1101/gr.163915.113
...Comparative epigenomics in distantly related teleost species identifies conserved cis -regulatory nodes active during the vertebrate phylotypic period Juan J. Tena 1 , 4 , Cristina González-Aguilera 1 , 4 , Ana Fernández-Miñán 1 , Javier Vázquez...
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Research: The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection
- Jialin Liu,
- Rebecca R. Viales,
- Pierre Khoueiry,
- James P. Reddington,
- Charles Girardot,
- Eileen E.M. Furlong,
- and Marc Robinson-Rechavi
Genome Res. September 2021 31: 1573-1581; Published in Advance July 15, 2021, doi:10.1101/gr.275212.121
...authors: furlong@embl.de, marc.robinson-rechavi@unil.chAbstractInter-species comparisons of both morphology and gene expression within a phylum have revealed a period in the middle of embryogenesis with more similarity between species compared with earlier and later time points. This “developmental...
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Perspective: Epigenomics and the structure of the living genome
- Nir Friedman and
- Oliver J. Rando
Genome Res. October 2015 25: 1482-1490; doi:10.1101/gr.190165.115
...Epigenomics and the structure of the living genome Nir Friedman 1 , 2 and Oliver J. Rando 3 1School of Computer Science and Engineering, The Hebrew University, Jerusalem 9190401, Israel; 2Institute of Life Sciences, The Hebrew University...
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Research: Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis
- Catia Attanasio,
- Alex S. Nord,
- Yiwen Zhu,
- Matthew J. Blow,
- Simon C. Biddie,
- Eric M. Mendenhall,
- Jesse Dixon,
- Crystal Wright,
- Roya Hosseini,
- Jennifer A. Akiyama,
- Amy Holt,
- Ingrid Plajzer-Frick,
- Malak Shoukry,
- Veena Afzal,
- Bing Ren,
- Bradley E. Bernstein,
- Edward M. Rubin,
- Axel Visel,
- and Len A. Pennacchio
Genome Res. June 2014 24: 920-929; Published in Advance April 21, 2014, doi:10.1101/gr.168930.113
...Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis Catia Attanasio 1 , 6 , Alex S. Nord 1 , 6 , Yiwen Zhu 1 , Matthew J. Blow 2 , Simon C. Biddie 2 , 3 , Eric M. Mendenhall 4...

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