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

Genome Research

Volumn 23, Issue 4, 2013, Pages 727-735

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

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b PEKING UNIVERSITY   (China)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e Peking University   (China)

^f HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; FERTILIZATION IN VITRO; GENE FUNCTION; GENE INACTIVATION; GENE INSERTION SEQUENCE; GENE MAPPING; GENOMICS; HIGH THROUGHPUT SEQUENCING; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; ZEBRA FISH;

ALLELES; ANIMALS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; GAMMARETROVIRUS; GENE KNOCKOUT TECHNIQUES; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; MOLECULAR SEQUENCE ANNOTATION; MUTAGENESIS, INSERTIONAL; MUTATION; PHENOTYPE; VIRUS INTEGRATION; ZEBRAFISH;

DANIO RERIO; VERTEBRATA;

EID: 84876010801     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.151464.112     Document Type: Article

References (25)

1. Amsterdam A, Hopkins N. 1999. Retrovirus-mediated insertional mutagenesis in zebrafish. Methods Cell Biol 60: 87-98.
2. Bahary N, Davidson A, Ransom D, Shepard J, Stern H, Trede N, Zhou Y, Barut B, Zon LI. 2004. The Zon laboratory guide to positional cloning in zebrafish. Methods Cell Biol 77: 305-329.
3. Bedell VM,Wang Y, Campbell JM, Poshusta TL, Starker CG, Krug Ii RG, Tan W, Penheiter SG, Ma AC, Leung AY, et al. 2012. In vivo genome editing using a high-efficiency TALEN system. Nature 491: 114-118.
4. Castruita M, Casero D, Karpowicz SJ, Kropat J, Vieler A, Hsieh SI, Yan W, Cokus S, Loo JA, Benning C, et al. 2011. Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps. Plant Cell 23: 1273-1292.
5. Ciuffi A, Ronen K, Brady T, Malani N,Wang G, Berry CC, Bushman FD. 2009. Methods for integration site distribution analyses in animal cell genomes. Methods 47: 261-268.
6. Devon RS, Porteous DJ, Brookes AJ. 1995. Splinkerettes-improved vectorettes for greater efficiency in PCR walking. Nucleic Acids Res 23: 1644-1645.
7. Friedel RH, Plump A, Lu X, Spilker K, Jolicoeur C, Wong K, Venkatesh TR, Yaron A, Hynes M, Chen B, et al. 2005. Gene targeting using a promoterless gene trap vector ("targeted trapping") is an efficient method to mutate a large fraction of genes. Proc Natl Acad Sci 102: 13188-13193.
8. Gaiano N, Amsterdam A, Kawakami K, Allende M, Becker T, Hopkins N. 1996. Insertional mutagenesis and rapid cloning of essential genes in zebrafish. Nature 383: 829-832.
9. Hu J, Renaud G, Gomes TJ, Ferris A, Hendrie PC, Donahue RE, Hughes SH, Wolfsberg TG, Russell DW, Dunbar CE. 2008. Reduced genotoxicity of avian sarcoma leukosis virus vectors in rhesus long-term repopulating cells compared to standard murine retrovirus vectors. Mol Ther 16: 1617-1623.
10. Huang P, Xiao A, Zhou M, Zhu Z, Lin S, Zhang B. 2011. Heritable gene targeting in zebrafish using customized TALENs. Nat Biotechnol 29: 699-700.
11. International Human Genome Sequencing Consortium. 2004. Finishing the euchromatic sequence of the human genome. Nature 431: 931-945.
12. Jao LE, Burgess SM. 2009. Production of pseudotyped retrovirus and the generation of proviral transgenic zebrafish. Methods Mol Biol 546: 13-30.
13. Jao LE, Maddison L, Chen W, Burgess SM. 2008. Using retroviruses as a mutagenesis tool to explore the zebrafish genome. Brief Funct Genomic Proteomic 7: 427-443.
14. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
15. Mooslehner K, Karls U, Harbers K. 1990. Retroviral integration sites in transgenic Mov mice frequently map in the vicinity of transcribed DNA regions. J Virol 64: 3056-3058.
16. Mullins MC, Hammerschmidt M, Haffter P, Nusslein-Volhard C. 1994. Large-scale mutagenesis in the zebrafish: In search of genes controlling development in a vertebrate. Curr Biol 4: 189-202.
17. Scherdin U, Rhodes K, Breindl M. 1990. Transcriptionally active genome regions are preferred targets for retrovirus integration. J Virol 64: 907-912.
18. Solnica-Krezel L, Schier AF, Driever W. 1994. Efficient recovery of ENUinducedmutations fromthe zebrafish germline. Genetics 136: 1401-1420.
19. Talbot WS, Schier AF. 1999. Positional cloning of mutated zebrafish genes. Methods Cell Biol 60: 259-286.
20. Varga ZM. 2011. Aquaculture and husbandry at the Zebrafish International Resource Center. Methods Cell Biol 104: 453-478.
21. Varshney GK, Huang H, Zhang S, Lu J, Gildea DE, Yang Z,Wolfsberg TG, Lin S, Burgess SM. 2013. The Zebrafish Insertion Collection (ZInC): A web based, searchable collection of zebrafish mutations generated by DNA insertion. Nucleic Acids Res 41: D861-D864.
22. Wang D, Jao LE, Zheng N, Dolan K, Ivey J, Zonies S, Wu X, Wu K, Yang H, Meng Q, et al. 2007. Efficient genome-wide mutagenesis of zebrafish genes by retroviral insertions. Proc Natl Acad Sci 104: 12428-12433.
23. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
24. Williams-Carrier R, Stiffler N, Belcher S, Kroeger T, Stern DB, Monde RA, Coalter R, Barkan A. 2010. Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize. Plant J 63: 167-177.
25. Wu X, Li Y, Crise B, Burgess SM. 2003. Transcription start regions in the human genome are favored targets for MLV integration. Science 300: 1749-1751.