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Background  In the Duplication-Degeneration-Complementation (DDC) model, subfunctionalization and neofunctionalization have been proposed as important processes driving the retention of duplicated genes in the genome. These processes are thought to occur by gain or loss of regulatory elements in the promoters of duplicated genes. We tested the DDC model by determining the transcriptional induction of fatty acid-binding proteins (Fabps) genes by dietary fatty acids (FAs) in zebrafish. We chose zebrafish for this study for two reasons: extensive bioinformatics resources are available for zebrafish at zfin.org and zebrafish contains many duplicated genes owing to a whole genome duplication event that occurred early in the ray-finned fish lineage approximately 230-400 million years ago. Adult zebrafish were fed diets containing either fish oil (12% lipid, rich in highly unsaturated fatty acid), sunflower oil (12% lipid, rich in linoleic acid), linseed oil (12% lipid, rich in linolenic acid), or low fat (4% lipid, low fat diet) for 10 weeks. FA profiles and the steady-state levels of  fabp  mRNA and heterogeneous nuclear RNA in intestine, liver, muscle and brain of zebrafish were determined.    Result  FA profiles assayed by gas chromatography differed in the intestine, brain, muscle and liver depending on diet. The steady-state level of mRNA for three sets of duplicated genes,  fabp1a/fabp1b.1/fabp1b.2 ,  fabp7a/fabp7b , and  fabp11a / fabp11b , was determined by reverse transcription, quantitative polymerase chain reaction (RT-qPCR). In brain, the steady-state level of  fabp7b  mRNAs was induced in fish fed the linoleic acid-rich diet; in intestine, the transcript level of  fabp1b.1  and  fabp7b  were elevated in fish fed the linolenic acid-rich diet; in liver, the level of  fabp7a  mRNAs was elevated in fish fed the low fat diet; and in muscle, the level of  fabp7a  and  fabp11a  mRNAs were elevated in fish fed the linolenic acid-rich or the low fat diets. In all cases, induction of the steady-state level of  fabp  mRNAs by dietary FAs correlated with induced levels of hnRNA for a given  fabp  gene. As such, up-regulation of the steady-state level of  fabp  mRNAs by FAs occurred at the level of initiation of transcription. None of the sister duplicates of these  fabp  genes exhibited an increase in their steady-state transcript levels in a specific tissue following feeding zebrafish any of the four experimental diets.    Conclusion  Differential induction of only one of the sister pair of duplicated  fabp  genes by FAs provides evidence to support the DDC model for retention of duplicated genes in the zebrafish genome by either subfunctionalization or neofunctionalization.

bmc evolutionary biology

Differential transcriptional modulation of duplicated fatty acid-binding protein genes by dietary fatty acids in zebrafish (Danio rerio): evidence for subfunctionalization or neofunctionalization of duplicated genes