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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
...cell. This process is orchestrated by changes 11 in transcriptional regulation, influenced by chromatin accessibility and 12 epigenetic modifications, enabling transcription factor accessibility. Epigenomic 13 regulation of embryogenesis has been studied in model fish, but little attention 14 has been...
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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
...or architectural structural proteins might bind at these enhancer regions to help establish enhancer domains and/or enhancer–promoter loops in the developing embryo, possibly to help prime these loci for future transcription. To test for factor binding, we performed the Assay for Transposase-Accessible Chromatin...
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Research: Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
- Hiroto S. Fukushima,
- Hiroyuki Takeda,
- and Ryohei Nakamura
Genome Res. April 2023 33: 572-586; Published in Advance April 28, 2023, doi:10.1101/gr.277577.122
...In a new window Figure 5. H3K27ac premarking is associated with future gain of histone modifications and accessibility at later stages in medaka. (A) Heatmap showing histone modification enrichments (H3K27ac, H3K27me3, and H3K4me2) and chromatin accessibility (Nakamura et al. 2021) at H3K27ac...
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Research: CTCF looping is established during gastrulation in medaka embryos
- Ryohei Nakamura,
- Yuichi Motai,
- Masahiko Kumagai,
- Candice L. Wike,
- Haruyo Nishiyama,
- Yoichiro Nakatani,
- Neva C. Durand,
- Kaori Kondo,
- Takashi Kondo,
- Tatsuya Tsukahara,
- Atsuko Shimada,
- Bradley R. Cairns,
- Erez Lieberman Aiden,
- Shinichi Morishita,
- and Hiroyuki Takeda
Genome Res. June 2021 31: 968-980; Published in Advance May 18, 2021, doi:10.1101/gr.269951.120
...cell cycles proceed under the control of maternally provided factors (Jukam et al. 2017). During this process, epigenetic modifications and chromatin accessibility are globally reprogrammed (Lee et al. 2014). Next, zygotic activation (ZGA), simultaneous transcription of thousands of zygotic genes...
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Method: Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data
- Shuze Wang,
- Mary P. Lee,
- Scott Jones,
- Jie Liu,
- and Joerg Waldhaus
Genome Res. October 2021 31: 1885-1899; Published in Advance April 9, 2021, doi:10.1101/gr.271080.120
...'s delicate function during development and differentiation, spatiotemporal gene expression is strictly controlled by chromatin accessibility and cell type–specific transcription factors, jointly representing the regulatory landscape. Bulk sequencing technology and cellular heterogeneity obscured...
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Resource: Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
- Andrea Pauli,
- Eivind Valen,
- Michael F. Lin,
- Manuel Garber,
- Nadine L. Vastenhouw,
- Joshua Z. Levin,
- Lin Fan,
- Albin Sandelin,
- John L. Rinn,
- Aviv Regev,
- and Alexander F. Schier
Genome Res. March 2012 22: 577-591; Published in Advance November 22, 2011, doi:10.1101/gr.133009.111
...-confidence transcripts in 28,912 loci, recovering the vast majority of expressed RefSeq transcripts while identifying thousands of novel isoforms and expressed loci. We defined a stringent set of 1133 noncoding multi-exonic transcripts expressed during embryogenesis. These include long intergenic ncRNAs (linc...
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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
...regulatory regions (SPARRs), are simultaneously active in both species during the phylotypic period. Interestingly, genes associated with this small set of co-acetylated regions show a broader and more complex regulatory landscape. In fact, this collection of genes is highly enriched in transcription factors...

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