Data from: Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon

Atlantic salmon migrates from rivers to sea to feed, grow and develop gonads before returning to spawn in freshwater. The transition to marine habitats is associated with dramatic changes in the environment, including water salinity, exposure to pathogens, and shift in dietary lipid availability. Many anticipatory changes in physiology occur before migration to sea, but little is known about the molecular nature of these changes.
Here we use a long term feeding experiment to study transcriptional regulation of lipid metabolism in Atlantic salmon gut and liver in both fresh- and saltwater. We find that lipid metabolism is highly plastic in response to differences in dietary lipid composition in freshwater, but then undergoes a marked shift when salmon transitions to the marine life-stage. Expression of genes in liver relating to lipogenesis and lipid transport decrease overall and become less responsive to diet, while genes for lipid uptake in gut become more highly expressed. Finally, analyses of evolutionary consequences of the salmonid specific whole-genome duplication on lipid metabolism reveals several pathways with significantly different (p<0.05) duplicate retention or duplicate regulatory conservation. We also find a limited number of cases where the whole genome duplication has resulted in an increased gene dosage.
Our results demonstrate the presence of a life-stage associated remodeling of lipid metabolism at the gene regulatory level, suggesting an evolved preparatory optimization of lipid metabolism

大西洋鲑（Atlantic salmon）会从河流洄游至海洋，以觅食、生长并发育性腺，之后再返回淡水环境产卵。从淡水转向海洋生境的过程，伴随着环境的剧烈变化，包括水体盐度改变、病原体暴露风险升高，以及膳食脂质可获得性的转变。洄游入海前，机体便已出现诸多预适应性生理变化，但目前对这些变化的分子机制仍知之甚少。
本研究通过长期饲喂实验，探究大西洋鲑在淡水与咸水环境下，肠道与肝脏脂质代谢的转录调控（transcriptional regulation）机制。研究发现，淡水环境中，脂质代谢对膳食脂质组成的差异呈现高度可塑性；而当鲑鱼转变为海洋生活阶段时，其脂质代谢会发生显著重塑。肝脏中与脂肪生成、脂质转运相关的基因整体表达量下调，且对膳食信号的响应性降低；与此同时，肠道内脂质摄取相关基因的表达水平显著升高。此外，针对鲑科特异性全基因组复制（salmonid specific whole-genome duplication）事件对脂质代谢的进化影响分析显示，多条通路的重复基因保留（duplicate retention）率或重复基因调控保守性（regulatory conservation）存在显著差异（p<0.05）。本研究还发现，极少数案例中全基因组复制导致了基因剂量（gene dosage）的提升。
本研究结果证实，在基因调控层面存在与生活阶段相关的脂质代谢重塑现象，表明脂质代谢经过进化形成了预适应性的优化调控策略。