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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 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cisregulatory modules acting during vertebrate organogenesis Daniela M. Riley,1,7 Randa Elsayed,1,7 Mark D. Walsh,2,7 Simaran Johal,2 Ying Lin,3,4 Harry Walton,1 Till Bretschneider,5 Sascha Ott,1...
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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
...Corresponding authors: twang@wustl.edu, gzhao@wustl.eduAbstractFollowing amputation, zebrafish regenerate their injured caudal fin through lineage-restricted reprogramming. Although previous studies have charted various genetic and epigenetic dimensions of this process, the intricate gene regulatory programs...
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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
...of the zebrafish reference since its initial publication (Howe et al. 2013; Howe 2020). Among retroelements, the proportion of LTRs, LINEs, and SINEs is 6.0%, 4.1%, and 3.1%, respectively, whereas tyrosine recombinase–mediated retroelements (DIRS and Ngaro superfamilies) account for 2.1%. DNA transposons...
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Resource: A single-cell transcriptome atlas of the maturing zebrafish telencephalon
- Shristi Pandey,
- Anna J. Moyer,
- and Summer B. Thyme
Genome Res. April 2023 33: 658-671; Published in Advance April 18, 2023, doi:10.1101/gr.277278.122
..., dlx5a, dlx6a, tbr1b, and neurod1 distinguish between the zebrafish pallium and subpallium. Among the neuronal clusters, we also found one cluster belonging to the olfactory bulb (Supplemental Fig. S4), two clusters belonging to the habenula (Pandey et al. 2018), and two belonging to the preoptic area...
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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
...chromatin shows extensive remodeling during embryonic development, and although the cleavage-stage embryos of most species lack structure before zygotic activation (pre-ZGA), zebrafish has been reported to have structure. Here, we aimed to determine the chromosomal architecture in paternal/sperm zebrafish...
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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
...in the evolution of gene regulation previously observed in mammalian s (Pehrsson et al. 2019) to the zebrafish . We found that various TE subfamilies belonging to different classes are enriched for different categories of tissue-specific active regulatory elements (Fig. 3). This suggests that TEs have been able...
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Resource: High resolution annotation of zebrafish transcriptome using long-read sequencing
- German Nudelman,
- Antonio Frasca,
- Brandon Kent,
- Kirsten C. Sadler,
- Stuart C. Sealfon,
- Martin J. Walsh,
- and Elena Zaslavsky
Genome Res. September 2018 28: 1415-1425; Published in Advance July 30, 2018, doi:10.1101/gr.223586.117
...York 10029, USA ↵8 These authors are joint first authors and contributed equally to this work. Corresponding authors: elena.zaslavsky@gmail.com, martin.walsh@mssm.eduAbstractWith the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome...
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Research: Epigenetic suppression of the TGF-beta pathway revealed by transcriptome profiling in ovarian cancer
- Noriomi Matsumura,
- Zhiqing Huang,
- Seiichi Mori,
- Tsukasa Baba,
- Shingo Fujii,
- Ikuo Konishi,
- Edwin S. Iversen,
- Andrew Berchuck,
- and Susan K. Murphy
Genome Res. January 2011 21: 74-82; Published in Advance December 14, 2010, doi:10.1101/gr.108803.110
...of development (Suzuki and Bird 2008). Other representative GO terms that were enriched in this gene set included ‘‘adhesion,’’ ‘‘cell migration,’’ ‘‘angiogenesis,’’ and ‘‘immune response.’’ These GO terms, which are relevant to the functions of the TGF-beta superfamily pathway (Massague 2008), are suggestive...
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Research: Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition
- Vladimir Despic,
- Mario Dejung,
- Mengting Gu,
- Jayanth Krishnan,
- Jing Zhang,
- Lydia Herzel,
- Korinna Straube,
- Mark B. Gerstein,
- Falk Butter,
- and Karla M. Neugebauer
Genome Res. July 2017 27: 1184-1194; Published in Advance April 5, 2017, doi:10.1101/gr.215954.116
...). RNA-binding proteins (RBPs) are important regulators of posttranscriptional RNA processing events, yet their identities and functions during developmental transitions in vertebrates remain largely unexplored. Using mRNA interactome capture, we identified 227 RBPs in zebrafish embryos before and during...
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Resource: Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9
- Yonghua Sun,
- Bo Zhang,
- Lingfei Luo,
- De-Li Shi,
- Han Wang,
- Zongbin Cui,
- Honghui Huang,
- Ying Cao,
- Xiaodong Shu,
- Wenqing Zhang,
- Jianfeng Zhou,
- Yun Li,
- Jiulin Du,
- Qingshun Zhao,
- Jun Chen,
- Hanbing Zhong,
- Tao P. Zhong,
- Li Li,
- Jing-Wei Xiong,
- Jinrong Peng,
- Wuhan Xiao,
- Jian Zhang,
- Jihua Yao,
- Zhan Yin,
- Xianming Mo,
- Gang Peng,
- Jun Zhu,
- Yan Chen,
- Yong Zhou,
- Dong Liu,
- Weijun Pan,
- Yiyue Zhang,
- Hua Ruan,
- Feng Liu,
- Zuoyan Zhu,
- Anming Meng,
- and The ZAKOC Consortium
Genome Res. January 2020 30: 118-126; Published in Advance December 12, 2019, doi:10.1101/gr.248559.119
...Systematic editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9 Yonghua Sun1, Bo Zhang2, Lingfei Luo3, De-Li Shi4, Han Wang5, Zongbin Cui1, Honghui Huang3, Ying Cao6, Xiaodong Shu7, Wenqing Zhang8, Jianfeng Zhou9, Yun Li9, Jiulin Du10, Qingshun Zhao11, Jun Chen12, Hanbing Zhong13, Tao P...
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