A large-scale zebrafish gene knockout resource for the genome-wide study of gene function
- Gaurav K. Varshney1,8,
- Jing Lu2,3,8,
- Derek E. Gildea4,
- Haigen Huang3,
- Wuhong Pei1,
- Zhongan Yang3,
- Sunny C. Huang1,
- David Schoenfeld3,
- Nam H. Pho1,
- David Casero3,
- Takashi Hirase3,
- Deborah Mosbrook-Davis1,
- Suiyuan Zhang4,
- Li-En Jao5,
- Bo Zhang6,
- Ian G. Woods7,
- Steven Zimmerman7,
- Alexander F. Schier7,
- Tyra G. Wolfsberg4,
- Matteo Pellegrini3,
- Shawn M. Burgess1,9 and
- Shuo Lin2,3,9
- 1Developmental Genomics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
- 2Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, 100083 Shenzhen, China;
- 3Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA;
- 4Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
- 5Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37235, USA;
- 6Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, Center of Developmental Biology and Genetics, College of Life Sciences, Peking University, 100083 Beijing, China;
- 7Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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↵8 These authors contributed equally to this work.
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.
Footnotes
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↵9 Corresponding authors
Email shuolin{at}ucla.edu
Email burgess{at}mail.nih.gov
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.151464.112.
- Received October 31, 2012.
- Accepted January 23, 2013.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.
