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Review
. 2007;8 Suppl 1(Suppl 1):S6.
doi: 10.1186/gb-2007-8-s1-s6.

Transposable elements in fish functional genomics: technical challenges and perspectives

Serguei Parinov  1 , Alexander Emelyanov
Affiliations
Review

Transposable elements in fish functional genomics: technical challenges and perspectives

Serguei Parinov et al. Genome Biol. 2007.

Abstract

The recent introduction of several transposable elements in zebrafish opens new frontiers for genetic manipulation in this important vertebrate model. This review discusses transposable elements as mutagenesis tools for fish functional genomics. We review various mutagenesis strategies that were previously applied in other genetic models, such as Drosophila, Arabidopsis, and mouse, that may be beneficial if applied in fish. We also discuss the forthcoming challenges of high-throughput functional genomics in fish.

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Figures

Figure 1
Figure 1
Strategies for mutagenesis of nearby genes by re-mobilization of genomic transposon inserts. (a) Regional mutagenesis using gene trap elements (for simplicity, only a 5' gene trap is illustrated). Here, the reporter gene at the donor site is silent. Transpositions can be detected when reporter gene expression is activated. (b) Regional mutagenesis from a 'launch pad'. A 'jumper' element carrying a selection marker 'A' (for example, green fluorescent protein under regulation of a constitutive promoter) is inserted between an open reading frame of a marker gene 'B' (for example, red fluorescent protein) and a suitable promoter. When the jumper element is excised, the expression of the 'B' is switched on. Animals carrying an empty donor site and retaining the jumper element can be analyzed by polymerase chain reaction (not shown). (c) Regional mutagenesis from a launch pad combined with site-specific recombination system (Cre/lox in this case). The system is a modification of the method shown in part b but the carrier and jumper elements both carry loxP sites. After local re-transposition of the jumper element the region between the loxP sites is deleted or inverted according to the orientation of loxP sites using Cre recombinase. (d) Selecting flanking deletions using flanking marker recombination (from the method of P induced male recombination in Drosophila; see text for references). This approach requires two closely linked markers (A and B) around the donor site. The transposon is usually retained at one side of the deletion. (e) Generating deletions by selecting for 'imprecise excision' events. (f) A compound element optimized for screening of flanking deletions. This approach can detect the same events as the methods shown in parts c and d but no additional markers are required. The animals that harbor deletion events can be identified by loss of one flanking marker, whereas retention of the other marker shows presence of the donor site.
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