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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
...regulatory transitions 253 during early development 254 To gain a comprehensive view of the regulatory landscape during turbot 255 embryogenesis, -wide chromatin state predictions were obtained by 256 integrating the ChIP-seq and ATAC-seq datasets using ChromHMM (Figure 6A, 257 Supplemental table S8). A 10...
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Research: Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
- Gregor Jessberger,
- Csilla Várnai,
- Roman R. Stocsits,
- Wen Tang,
- Georg Stary,
- and Jan-Michael Peters
Genome Res. December 2023 33: 2094-2107; Published in Advance December 21, 2023, doi:10.1101/gr.277865.123
...formation of TADs. TADs can be detected in mouse sperm samples, as reported, but these structures might originate from somatic chromatin contaminations. We therefore discuss the possibility that the absence of TADs might be a general feature of vertebrate sperm. To analyze sperm remodeling upon...
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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
...chromatin marks. Our expression pattern data revealed several intriguing properties of zebrafish lncRNAs. Notably, lncRNAs are expressed in particularly narrow developmental windows and in specific cell types. Moreover, lncRNAs are particularly numerous in the very early embryo. Computational analysis...
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Research: Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm
- Shan-Fu Wu,
- Haiying Zhang,
- and Bradley R. Cairns
Genome Res. April 2011 21: 578-589; Published in Advance March 7, 2011, doi:10.1101/gr.113167.110
...Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm Shan-Fu Wu , Haiying Zhang and Bradley R. Cairns 1 Howard Hughes Medical Institute, Department of Oncological Sciences, Huntsman Cancer Institute...
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Research: Inherited DNA methylation primes the establishment of accessible chromatin during genome activation
- Guifen Liu,
- Wen Wang,
- Shengen Hu,
- Xiangxiu Wang,
- and Yong Zhang
Genome Res. July 2018 28: 998-1007; Published in Advance May 29, 2018, doi:10.1101/gr.228833.117
...can prime the global re-establishment of accessible chromatin during zebrafish embryogenesis, which is closely associated with the rebuilding of zygotic gene transcriptional regulation. The DNA methylation signatures in the promoters with enriched unmethylated CpGs in the sperm and oocyte are fully...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...other species, enhancers are distinguished from promoters based on enrichment of distinct and conserved histone modifications, including H3K27 acetylation and H3K4 methylation (Evans et al. 2016; Daugherty et al. 2017). Mapping enhancer chromatin features and analyses of individual genes suggest...
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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
...fraction of loops are known to be conserved among cell types (Rao et al. 2014), and thus our study describes the dynamics of most common loops.Our study showed that, before ZGA, chromatin does not have any domain structures both in medaka and zebrafish. However, this appears to conflict with the main...
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Resource: Long noncoding RNAs in C. elegans
- Jin-Wu Nam and
- David P. Bartel
Genome Res. December 2012 22: 2529-2540; Published in Advance June 15, 2012, doi:10.1101/gr.140475.112
...or during embryonic development (Goodrich and Kugel 2006; Mercer et al. 2009; Huarte and Rinn 2010; Koziol and Rinn 2011; Pauli et al. 2011a; Tsai et al. 2011). For example, HOTAIR is a 2.2-kb lincRNA that recruits the polycomb complex to modify the chromatin state of HOX genes to repress...
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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
...with previous studies in zebrafish and Xenopus (Akkers et al. 2009; Zhang et al. 2018a; Laue et al. 2019), but the two modifications exist at low levels before ZGA, so that they can be detected in compact mitotic chromosome in medaka. We speculated that chromatin compaction during the mitotic phase increased...
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Research: Coordination of zygotic genome activation entry and exit by H3K4me3 and H3K27me3 in porcine early embryos
- Guowei Bu,
- Wei Zhu,
- Xin Liu,
- Jingjing Zhang,
- Longtao Yu,
- Kai Zhou,
- Shangke Wang,
- Zhekun Li,
- Zhengang Fan,
- Tingting Wang,
- Taotao Hu,
- Ruifeng Hu,
- Zhiting Liu,
- Tao Wang,
- Linhui Wu,
- Xia Zhang,
- Shuhong Zhao,
- and Yi-Liang Miao
Genome Res. August 2022 32: 1487-1501; Published in Advance July 22, 2022, doi:10.1101/gr.276207.121
...marks to instruct the chromatin state associated with temporal and spatial gene expression during maternal-to-zygotic transition and cell fate commitments (Dahl et al. 2016; Liu et al. 2016; Zhang et al. 2016, 2018; Zheng et al. 2016; Wang et al. 2018; Xia et al. 2019; Zhu et al. 2019). Compared to DNA...

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