zTrap: zebrafish gene trap and enhancer trap database

<p>Abstract</p> <p>Background</p> <p>We have developed genetic methods in zebrafish by using the <it>Tol2 </it>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 <it>hsp70l </it>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.</p> <p>Description</p> <p>To increase the usefulness of the transgenic fish resource, we developed a web-based database named <it>z</it>Trap <url>http://kawakami.lab.nig.ac.jp/ztrap/</url>. The <it>z</it>Trap 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 <it>Ensembl </it>zebrafish genome by in-house Blat analysis and can be viewed on the <it>z</it>Trap and <it>Ensembl </it>genome browsers. Furthermore, <it>z</it>Trap is equipped with the functionality to search these data for expression patterns and genomic loci of interest. <it>z</it>Trap contains the information about transgenic fish including UAS reporter and effector fish.</p> <p>Conclusion</p> <p><it>z</it>Trap 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 <it>cis</it>-regulatory elements. Therefore, <it>z</it>Trap should facilitate studies on genomics, developmental biology and neurobiology utilizing the transgenic zebrafish resource.</p