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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
...421 developmental transitions and lineage specification 422 To identify the main TFs associated with chromatin accessibility dynamics in 423 candidate CREs regulated during embryogenesis, TFBM enrichment was 424 conducted for all DARs associated with promoters and putative enhancers. 425 Significant...
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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
...; Davis et al. 2018).A key issue within developmental biology involves how embryos transition from a totipotent to a lineage-committed state, and higher-order chromatin structures are known to influence enhancer–promoter interaction potential for developmental genes. To better understand, we sought...
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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 the wild type (Fig. 1C). Dgcr8 KO ESC colonies were lost within 2–3 d of MTORi (Fig. 1A,B). Therefore, a specific dependence on DGCR8 arises in ESCs during the dormancy transition. To corroborate this outcome within the setting of embryonic pluripotency, we generated chimeric embryos by aggregating diploid...
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Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
- Leandros Boukas,
- Teresa Romeo Luperchio,
- Afrooz Razi,
- Kasper D. Hansen,
- and Hans T. Bjornsson
Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
...the abnormalities in the different organs are driven by the same underlying chromatin disruption in the corresponding cell types. In other words, are the chromatin effects of variants in epigenetic regulators shared between different cell types or are they primarily cell type specific?There are two major reasons...
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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. They coincide with an increase in cis-regulatory regions harboring metazoan TF binding motifs, as well as an increase in the expression of metazoan-specific genes. Changes in chromatin state and gene expression in Amphimedon suggest the conservation of distal enhancers, dynamically silenced...
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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
...with the midblastula transition (MBT). Nanog was reported to contribute to the establishment of accessible chromatin and is involved in regulatory processes during ZGA (Lee et al. 2013; Liu et al. 2018; Veil et al. 2019; Pálfy et al. 2020). With the reliability of the FitCUT&RUN method demonstrated, in this study, we...
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Research: Decoding the function of bivalent chromatin in development and cancer
- Dhirendra Kumar,
- Senthilkumar Cinghu,
- Andrew J. Oldfield,
- Pengyi Yang,
- and Raja Jothi
Genome Res. December 2021 31: 2170-2184; Published in Advance October 19, 2021, doi:10.1101/gr.275736.121
...settings.ResultsBivalent chromatin does not poise genes for rapid activationTo assess whether bivalent chromatin represents a distinct epigenetic state and/or a regulatory mechanism, we investigated genes with bivalently marked promoters in pluripotent human embryonic stem cells (ESCs) (Supplemental Table...
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Research: Parental methylome reprogramming in human uniparental blastocysts reveals germline memory transition
- Jiawei Xu,
- Yimin Shu,
- Guidong Yao,
- Yu Zhang,
- Wenbin Niu,
- Yile Zhang,
- Xueshan Ma,
- Haixia Jin,
- Fuli Zhang,
- Senlin Shi,
- Yang Wang,
- Wenyan Song,
- Shanjun Dai,
- Luyao Cheng,
- Xiangyang Zhang,
- Wei Xie,
- Aaron J. Hsueh,
- and Yingpu Sun
Genome Res. September 2021 31: 1519-1530; Published in Advance July 30, 2021, doi:10.1101/gr.273318.120
...for analysis of genomic imprinting, gene function, and epigenetic dynamics (Dean et al. 2001a). However, species-specific epigenetic regulation does exist (Haaf 2006). Major epigenetic reprogramming during preimplantation development differs across mammalian species (Beaujean et al. 2004; Fulka et al. 2004...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...al. 2016; Wu and Knudson 2018). Some genes that emerge de novo not only provide new functions, but have even become essential to the species in which they emerged. For example, the human-specific de novo gene ESRG is required for the maintenance of pluripotency in human naive stem cells (Wang et al...
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Research: DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation
- Joseph C. Siefert,
- Constantin Georgescu,
- Jonathan D. Wren,
- Amnon Koren,
- and Christopher L. Sansam
Genome Res. August 2017 27: 1406-1416; Published in Advance May 16, 2017, doi:10.1101/gr.218602.116
...with the dynamic changes in transcription and epigenetic marks during early development is not fully understood (Schübeler et al. 2002; MacAlpine et al. 2004; Hiratani et al. 2009). Furthermore, the replication timing program correlates with chromatin conformation, as early and late replicating regions correspond...

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