DOI: 10.5061/dryad.q03n7
title: Data from: Subfunctionalization of peroxisome proliferator response elements accounts for retention of duplicated fabp1 genes in zebrafish

description: Background: In the duplication-degeneration-complementation (DDC) model, a
 duplicated gene has three possible fates: it may lose functionality
 through the accumulation of mutations (non-functionalization), acquire a
 new function (neo-functionalization), or each duplicate gene may retain a
 subset of functions of the ancestral gene (sub-functionalization). The
 role that promoter evolution plays in retention of duplicated genes in
 eukaryotic genomes is not well understood. Fatty acid-binding proteins
 (Fabp) belong to a multigene family that are highly conserved in sequence
 and function, but differ in their gene regulation, suggesting selective
 pressure is exerted via regulatory elements in the promoter. A previous
 report showed that zebrafish fabp1b.1 and fabp1b.2 promoters underwent
 sub-functionalization of transcriptional control by peroxisome
 proliferator-activated receptors (PPAR). The fabp1b.1 promoter retained a
 functional PPAR response element (PPRE), while fabp1b.2 did not. Results:
 In this study, we describe the divergent PPAR regulation of zebrafish
 fabp1a, fabp1b.1, and fabp1b.2 promoters from the ancestral fabp1 gene.
 Promoter evolution was assessed by sequence analysis, and differential
 PPAR-agonist activation of fabp1 promoter activity in zebrafish liver and
 intestine ex vivo cells, and in HEK293 cells transiently transfected with
 wild-type and mutated fabp1promoter-reporter gene constructs. Spotted gar
 fabp1, representative of the ancestral fabp1, was responsive to both PPARα
 and PPARγ, and displayed a biphasic response to PPARα activation.
 Zebrafish fabp1a was PPARα-selective, fabp1b.1 was PPARγ-selective, while
 fabp1b.2 was not regulated by PPAR. Conclusions: The zebrafish fabp1
 promoters underwent two successive rounds of PPAR-selective
 subfunctionalization leading to retention of three zebrafish fabp1 genes
 that display stimuli-specific regulation.
description: Raw data package from:
 Subfunctionalization of Peroxisome Proliferator Response Elements Accounts
 for Retention of Duplicated fabp1 Genes in ZebrafishRaw data package
 contains the following: 1) File folder titled "ClustalOmega
 fabp1", this file folder contains: a) PHYLIP text files
 (fabp1_Aminoacids_Clustal_PHYLIP.rtf, fabp1_mRNA_Clustal_PHYLIP.rtf,
 fabp1_Promoter_Clustal_PHYLIP.rtf) containing raw data for the
 multiple-sequence alignments and their associated draw tree files, and b)
 a multi-fasta file containing the amino acid, mRNA, and promoter sequence
 files for Danio rerio (zebrafish) fabp1a, fabp1b.1, and fabp1b.2 and
 Lepisosteus oculatus (spotted gar) fabp1 genes. 2) A GraphPad Prism 6.0
 file containing the curve fitting and analyses of data presented in the
 associated manuscript (Laprairie et al 2016 BMC Evol Biol Analyses.pzfx).
 3) A Microsoft Excel files containing the raw data values for all data
 presented in the associated manuscript (Laprairie et al 2016 BMC Evol Biol
 Raw Data.xlsx). 4) The text output file for found peroxisome
 proliferator-activated receptor response elements (PPREs) in the isolated
 Danio rerio (zebrafish) fabp1a, fabp1b.1, and fabp1b.2 and Lepisosteus
 oculatus (spotted gar) fabp1 promoters described in the associated
 manuscript. 5) The multi-fasta file containing the sequenced pGL3 promoter
 constructs for Danio rerio (zebrafish) fabp1a, fabp1b.1, and fabp1b.2;
 fabp1a 5'flanking region mutant, fabp1a direct repeat 1 region
 mutant, fabp1b.1 5'flanking region mutant, fabp1b.1 direct repeat 1
 region mutant; Lepisosteus oculatus (spotted gar) fabp1; fabp1 PPRE-1
 mutant, fabp1 PPRE-2 mutant promoters sequences from the positive strand
 (RVprim3 primer) and negative strand (GLprim2 primer) of the pGL3 plasmid
 (Laprairie et al 2016 BMC Evol Biol Plasmid
 Sequencing.rtf).Data from Laprairie et al 2016
 BMC Evol Biol.zip