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J.M. Nickerson, R.A. Frey, V.T. Ciavatta, D. Stenkamp; The Two–Gene Teleost IRBP Locus: Evolutionary Origins and Differential Expression . Invest. Ophthalmol. Vis. Sci. 2006;47(13):3132.
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© ARVO (1962-2015); The Authors (2016-present)
A whole genome duplication just preceding the radiation of the teleosts provides the opportunity to detect diverse forms of IRBP gene loci and to discover IRBP genes with novel expression patterns, as fish genomes underwent subsequent evolution. The host of IRBP locus variants and their expression patterns offers the potential to discover the function of IRBP.
Bioinformatics was used to analyze recently completed genomes of several fish species, and their IRBP loci were obtained. Reverse transcriptase PCR (RT–PCR) and sequence analysis of zebrafish IRBP gene transcripts were conducted. In situ hybridizations with Gene 1– and Gene 2–specific probes in zebrafish were performed.
We report new IRBP locus structures for teleost fish. These loci includes a 2–gene locus arranged head to tail in which the first gene, Gene 1, is intronless and encodes 3 Repeats. It is followed by a second gene, Gene 2, which is the previously known IRBP gene consisting of 2 Repeats spread across 4 exons and 3 introns. RT–PCR and sequencing suggest that both genes are transcribed in zebrafish. Most, but not all, transcripts originate from the Gene 2 promoter. In situ hybridization studies with gene–specific probes indicated that Gene 2 is expressed in the photoreceptors (PhRs) and RPE. It is remarkable that Gene 1 is expressed in the ganglion cell layer and the inner nuclear layer but appears absent from RPE and PhRs.
In zebrafish and fugu, there are 2 IRBP genes in the IRBP locus. In Medaka there is only a single gene, corresponding to Gene 2. In Tetraodon there is a small Gene 1 remnant upstream of Gene 2. In zebrafish, in situ hybridizations demonstrated differential gene–specific expression supporting "subfunctionalization", with Gene 1 active in inner retinal cells, and Gene 2 active in PhRs and RPE. These results hint that IRBP has repeat–specific functions in different cell types. We suggest that the 2–gene locus in teleost fish arose as a consequence of whole genome duplication followed by a loss of repeats due to unequal crossing over.
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