Data from: Subfunctionalization of peroxisome proliferator response elements accounts for retention of duplicated fabp1 genes in zebrafish

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.

背景：在重复-退化-互补（duplication-degeneration-complementation, DDC）模型中，重复基因存在三种潜在结局：通过突变积累丧失功能（non-functionalization，非功能化）、获得新功能（neo-functionalization，新功能化），或是每个重复基因保留祖先基因的部分功能（sub-functionalization，亚功能化）。目前，启动子进化在真核基因组重复基因保留过程中所发挥的作用尚未得到充分阐释。
脂肪酸结合蛋白（fatty acid-binding proteins, Fabp）属于多基因家族，其序列与功能高度保守，但基因调控模式存在差异，这提示选择压力通过启动子内的调控元件施加。既往研究显示，斑马鱼fabp1b.1与fabp1b.2启动子经历了过氧化物酶体增殖物激活受体（peroxisome proliferator-activated receptors, PPAR）介导的转录调控亚功能化：fabp1b.1启动子保留了具有功能的过氧化物酶体增殖物激活受体应答元件（PPAR response element, PPRE），而fabp1b.2则未保留该元件。
结果：本研究阐明了源自祖先fabp1基因的斑马鱼fabp1a、fabp1b.1与fabp1b.2启动子所呈现的差异化PPAR调控模式。本研究通过序列分析评估启动子进化情况，并分别在斑马鱼肝脏与肠道的离体培养细胞，以及转染了野生型与突变型fabp1启动子-报告基因重组载体的HEK293细胞中，检测了PPAR激动剂对fabp1启动子活性的差异化激活作用。作为祖先fabp1基因代表的斑点雀鳝fabp1，可同时响应PPARα与PPARγ的调控，并对PPARα激活呈现双相响应。斑马鱼fabp1a仅对PPARα具有选择性，fabp1b.1仅对PPARγ具有选择性，而fabp1b.2则不受PPAR的调控。
结论：斑马鱼fabp1启动子经历了两轮连续的PPAR选择性亚功能化过程，最终保留了三个呈现刺激特异性调控模式的斑马鱼fabp1基因。