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Open Access Highly Accessed Database

zTrap: zebrafish gene trap and enhancer trap database

Koichi Kawakami12*, Gembu Abe1, Tokuko Asada1, Kazuhide Asakawa12, Ryuichi Fukuda1, Aki Ito1, Pradeep Lal12, Naoko Mouri1, Akira Muto1, Maximilliano L Suster15, Hitomi Takakubo1, Akihiro Urasaki1, Hironori Wada3 and Mikio Yoshida4

Author Affiliations

1 Division of Molecular and Developmental Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan

2 Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), 1111 Yata, Mishima, Shizuoka 411-8540, Japan

3 PRESTO, Japan Science and Technology Agency (JST), Honcho 4-1-8, Kawaguchi, Saitama 322-0012, Japan

4 Intec Systems Institute Inc., 1-3-3 Shinsuna, Koto-ku, Tokyo 136-0075, Japan

5 Current Address: Sars International Centre for Marine Molecular Biology, Thormøhlensgate 55, N-5008 Bergen, Norway

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BMC Developmental Biology 2010, 10:105  doi:10.1186/1471-213X-10-105

Published: 18 October 2010

Abstract

Background

We have developed genetic methods in zebrafish by using the Tol2 transposable element; namely, transgenesis, gene trapping, enhancer trapping and the Gal4FF-UAS system. Gene trap constructs contain a splice acceptor and the GFP or Gal4FF (a modified version of the yeast Gal4 transcription activator) gene, and enhancer trap constructs contain the zebrafish hsp70l promoter and the GFP or Gal4FF gene. By performing genetic screens using these constructs, we have generated transgenic zebrafish that express GFP and Gal4FF in specific cells, tissues and organs. Gal4FF expression is visualized by creating double transgenic fish carrying a Gal4FF transgene and the GFP reporter gene placed downstream of the Gal4-recognition sequence (UAS). Further, the Gal4FF-expressing cells can be manipulated by mating with UAS effector fish. For instance, when fish expressing Gal4FF in specific neurons are crossed with the UAS:TeTxLC fish carrying the tetanus neurotoxin gene downstream of UAS, the neuronal activities are inhibited in the double transgenic fish. Thus, these transgenic fish are useful to study developmental biology and neurobiology.

Description

To increase the usefulness of the transgenic fish resource, we developed a web-based database named zTrap http://kawakami.lab.nig.ac.jp/ztrap/ webcite. The zTrap database contains images of GFP and Gal4FF expression patterns, and genomic DNA sequences surrounding the integration sites of the gene trap and enhancer trap constructs. The integration sites are mapped onto the Ensembl zebrafish genome by in-house Blat analysis and can be viewed on the zTrap and Ensembl genome browsers. Furthermore, zTrap is equipped with the functionality to search these data for expression patterns and genomic loci of interest. zTrap contains the information about transgenic fish including UAS reporter and effector fish.

Conclusion

zTrap is a useful resource to find gene trap and enhancer trap fish lines that express GFP and Gal4FF in desired patterns, and to find insertions of the gene trap and enhancer trap constructs that are located within or near genes of interest. These transgenic fish can be utilized to observe specific cell types during embryogenesis, to manipulate their functions, and to discover novel genes and cis-regulatory elements. Therefore, zTrap should facilitate studies on genomics, developmental biology and neurobiology utilizing the transgenic zebrafish resource.