Searching journal content for articles similar to Kudoh et al. 11 (12): 1979.

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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
...genes expressed during embryogenesis. We identified 676 enrichment of terms related to the immune system and feeding behavior among 677 genes not expressed in the embryonic transcriptome, a result that aligns with 678 studies on zebrafish, where immune-like responses, such as phagocytic activity 679...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...maintaining key gene sequences and functions. 54 Indeed, though the last shared common ancestor of humans and zebrafish is estimated to 55 have inhabited the Earth 400 million years ago, 70% of human genes have at least one 56 obvious zebrafish orthologue (Howe et al. 2013). However, for conserved genes...
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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...2020). For example, genes such as btg2 and klf4, associated with the regulation of cell population proliferation, were clustered in shared module 1. btg2 is known for its antiproliferative roles during zebrafish early embryogenesis (Sakaguchi et al. 2001), and klf4 inhibits myoblast proliferation...
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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
...sets provided another dimension of information. With the expression dynamics of genes and accessibility dynamics of cis-regulatory elements, we investigated isoform switching, as well as regulatory logic between accessible elements and genes, during embryogenesis. We built a user-friendly medaka omics...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...for the study of vertebrate development, and over half of its consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...analysis of zebrafish TEs in the context of gene regulation is lacking. Here, we systematically investigate the epigenomic and transcriptomic landscape of TEs across 11 adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory...
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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...:0005905), which are a key avenue for endocytosis and were previously linked to developmental signaling (Seto et al. 2002; Robinson 2015) and heart defects (Arrigo and Lin 2021). Although few of these genes were discovered in screens of highly penetrant monogenic perturbations, our results suggest...
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Research: Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha
- James M. Davison,
- Colin R. Lickwar,
- Lingyun Song,
- Ghislain Breton,
- Gregory E. Crawford,
- and John F. Rawls
Genome Res. July 2017 27: 1195-1206; Published in Advance April 6, 2017, doi:10.1101/gr.220111.116
...nuclear factor 4 (HNF4) is the most ancient family of nuclear receptor transcription factors with important roles in human metabolic and inflammatory bowel diseases, but a role in host response to microbes is unknown. Using an unbiased screening strategy, we found that zebrafish Hnf4a specifically binds...
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Resource: Extensive alternative polyadenylation during zebrafish development
- Igor Ulitsky,
- Alena Shkumatava,
- Calvin H. Jan,
- Alexander O. Subtelny,
- David Koppstein,
- George W. Bell,
- Hazel Sive,
- and David P. Bartel
Genome Res. October 2012 22: 2054-2066; Published in Advance June 21, 2012, doi:10.1101/gr.139733.112
...numerous paralogous gene copies in the zebrafish , many of which have diverged in spatial and/or temporal expression during embryogenesis (Talbot et al. 2005; Semon and Wolfe 2007; Kassahn et al. 2009). Although the length of the coding sequence between paralogous pairs was highly consistent (Spearman r...
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Resource: Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
- Ozren Bogdanović,
- Ana Fernandez-Miñán,
- Juan J. Tena,
- Elisa de la Calle-Mustienes,
- Carmen Hidalgo,
- Ila van Kruysbergen,
- Simon J. van Heeringen,
- Gert Jan C. Veenstra,
- and José Luis Gómez-Skarmeta
Genome Res. October 2012 22: 2043-2053; Published in Advance May 16, 2012, doi:10.1101/gr.134833.111
...27ac at four developmental time-points of zebrafish embryogenesis and analyze embryonic enhancer activity. We find that (1) changes in H3K27ac enrichment at enhancers accompany the shift from pluripotency to tissue-specific gene expression, (2) in early embryos, the peaks of H3K27ac enrichment...

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