A large-scale zebrafish gene knockout resource for the genome-wide study of gene function

Gaurav K. Varshney, Jing Lu, Derek E. Gildea, Haigen Huang, Wuhong Pei, Zhongan Yang, Sunny C. Huang, David Schoenfeld, Nam H. Pho, David Casero, Takashi Hirase, Deborah Mosbrook-Davis, Suiyuan Zhang, Li-En Jao, Bo Zhang, Ian G. Woods, Steven Zimmerman, Alexander F. Schier, Tyra G. Wolfsberg, Matteo PellegriniShawn M. Burgess, Shuo Lin

Research output: Contribution to journalArticle

68 Citations (Scopus)

Abstract

With the completion of the zebrafish genome sequencing project, it becomes possible to analyze the function of zebrafish genes in a systematic way. The first step in such an analysis is to inactivate each protein-coding gene by targeted or random mutation. Here we describe a streamlined pipeline using proviral insertions coupled with high-throughput sequencing and mapping technologies to widely mutagenize genes in the zebrafish genome. We also report the first 6144 mutagenized and archived F1's predicted to carry up to 3776 mutations in annotated genes. Using in vitro fertilization, we have rescued and characterized ∼0.5% of the predicted mutations, showing mutation efficacy and a variety of phenotypes relevant to both developmental processes and human genetic diseases. Mutagenized fish lines are being made freely available to the public through the Zebrafish International Resource Center. These fish lines establish an important milestone for zebrafish genetics research and should greatly facilitate systematic functional studies of the vertebrate genome.

Original languageEnglish (US)
Pages (from-to)727-735
Number of pages9
JournalGenome Research
Volume23
Issue number4
DOIs
StatePublished - Apr 2013
Externally publishedYes

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Gene Knockout Techniques
Zebrafish
Genome
Mutation
Genes
Fishes
Genetic Research
Inborn Genetic Diseases
Medical Genetics
Fertilization in Vitro
Vertebrates
Technology
Phenotype
Proteins

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Varshney, G. K., Lu, J., Gildea, D. E., Huang, H., Pei, W., Yang, Z., ... Lin, S. (2013). A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Genome Research, 23(4), 727-735. https://doi.org/10.1101/gr.151464.112

A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. / Varshney, Gaurav K.; Lu, Jing; Gildea, Derek E.; Huang, Haigen; Pei, Wuhong; Yang, Zhongan; Huang, Sunny C.; Schoenfeld, David; Pho, Nam H.; Casero, David; Hirase, Takashi; Mosbrook-Davis, Deborah; Zhang, Suiyuan; Jao, Li-En; Zhang, Bo; Woods, Ian G.; Zimmerman, Steven; Schier, Alexander F.; Wolfsberg, Tyra G.; Pellegrini, Matteo; Burgess, Shawn M.; Lin, Shuo.

In: Genome Research, Vol. 23, No. 4, 04.2013, p. 727-735.

Research output: Contribution to journalArticle

Varshney, GK, Lu, J, Gildea, DE, Huang, H, Pei, W, Yang, Z, Huang, SC, Schoenfeld, D, Pho, NH, Casero, D, Hirase, T, Mosbrook-Davis, D, Zhang, S, Jao, L-E, Zhang, B, Woods, IG, Zimmerman, S, Schier, AF, Wolfsberg, TG, Pellegrini, M, Burgess, SM & Lin, S 2013, 'A large-scale zebrafish gene knockout resource for the genome-wide study of gene function', Genome Research, vol. 23, no. 4, pp. 727-735. https://doi.org/10.1101/gr.151464.112
Varshney, Gaurav K. ; Lu, Jing ; Gildea, Derek E. ; Huang, Haigen ; Pei, Wuhong ; Yang, Zhongan ; Huang, Sunny C. ; Schoenfeld, David ; Pho, Nam H. ; Casero, David ; Hirase, Takashi ; Mosbrook-Davis, Deborah ; Zhang, Suiyuan ; Jao, Li-En ; Zhang, Bo ; Woods, Ian G. ; Zimmerman, Steven ; Schier, Alexander F. ; Wolfsberg, Tyra G. ; Pellegrini, Matteo ; Burgess, Shawn M. ; Lin, Shuo. / A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. In: Genome Research. 2013 ; Vol. 23, No. 4. pp. 727-735.
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