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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
....vaquerizas@lms.mrc.ac.ukAbstractThere is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos and by the relative scarcity of active TEs in these organisms. The zebrafish is an outstanding model...
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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
...-order chromatin in mammalian sperm (Battulin et al. 2015; Jung et al. 2017; Wang et al. 2019), although structure is curiously lacking in human sperm (Chen et al. 2019), suggesting variation in mammals. Thus, an analysis of higher-order structure in zebrafish sperm (which lacks protamine) would complement those...
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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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Research: Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
- Aitor Serres-Armero,
- Brian W. Davis,
- Inna S. Povolotskaya,
- Carlos Morcillo-Suarez,
- Jocelyn Plassais,
- David Juan,
- Elaine A. Ostrander,
- and Tomas Marques-Bonet
Genome Res. May 2021 31: 762-774; Published in Advance April 16, 2021, doi:10.1101/gr.266049.120
....marques@upf.eduAbstractExtreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive -wide...
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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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Method: Detecting differential copy number variation between groups of samples
- Craig B. Lowe,
- Nicelio Sanchez-Luege,
- Timothy R. Howes,
- Shannon D. Brady,
- Rhea R. Daugherty,
- Felicity C. Jones,
- Michael A. Bell,
- and David M. Kingsley
Genome Res. February 2018 28: 256-265; Published in Advance December 11, 2017, doi:10.1101/gr.206938.116
...related vertebrate species, such as humans and chimpanzees, reveals that duplications and deletions are the classes of mutations that have affected the greatest number of base pairs (Cheng et al. 2005). Duplications and deletions underlie copy number variation, which occurs when a genomic segment appears...
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Method: High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9
- Gaurav K. Varshney,
- Wuhong Pei,
- Matthew C. LaFave,
- Jennifer Idol,
- Lisha Xu,
- Viviana Gallardo,
- Blake Carrington,
- Kevin Bishop,
- MaryPat Jones,
- Mingyu Li,
- Ursula Harper,
- Sunny C. Huang,
- Anupam Prakash,
- Wenbiao Chen,
- Raman Sood,
- Johan Ledin,
- and Shawn M. Burgess
Genome Res. July 2015 25: 1030-1042; Published in Advance June 5, 2015, doi:10.1101/gr.186379.114
...changed targeted mutagenesis. Here, we present a high-throughput targeted mutagenesis pipeline using CRISPR/Cas9 technology in zebrafish that will make possible both saturation mutagenesis of the and large-scale phenotyping efforts. We describe a cloningfree single-guide RNA (sgRNA) synthesis, coupled...
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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
...accessibility did not 26 affect promoters of differentially expressed genes, suggesting that their 27 accessibility precedes gene transcription changes. Comparative analyses with 28 zebrafish revealed a global transcriptomic correlation of single-copy orthologs at 29 matched stages. While conserved expression...
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Method: Targeted chromosomal deletions and inversions in zebrafish
- Ankit Gupta,
- Victoria L. Hall,
- Fatma O. Kok,
- Masahiro Shin,
- Joseph C. McNulty,
- Nathan D. Lawson,
- and Scot A. Wolfe
Genome Res. June 2013 23: 1008-1017; Published in Advance March 11, 2013, doi:10.1101/gr.154070.112
...Targeted chromosomal deletions and inversions in zebrafish Ankit Gupta 1 , Victoria L. Hall 1 , Fatma O. Kok 1 , Masahiro Shin 1 , Joseph C. McNulty 1 , Nathan D. Lawson 1 , 2 and Scot A. Wolfe 1 , 3 , 4...

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