Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes of metabolic syndrome in rats

We developed a method to prioritise strain-specific haplotypes by integrating genomic variation and genomic regulatory data predicted to be involved in specific phenotypes. To identify genomic regions associated with metabolic syndrome (MetS), a disorder of energy utilization and storage affecting several organ systems, we compared two Lyon rat strains, LH/Mav which is susceptible to MetS, and LL/Mav, which is susceptible to obesity as an intermediate MetS phenotype, with a third strain (LN/Mav) that is resistant to both MetS and obesity. Applying a novel metric, we ranked the identified strain-specific haplotypes using evolutionary conservation of the occupancy three liver-specific transcription factors (HNF4A, CEBPA, and FOXA1) in five rodents including rat. We generated RNA-seq expression data from liver of LL rats and from kidney of all three Lyon strains (5 biological replicates) and integrated these with relevant existing data including the level of regulatory conservation for three liver-specific transcription factors (CEBPA, FOXA1 and HNF4A between rat and five related mouse species and strains. We also used RNA-seq expression data from liver of LH and LN rats previously generated (GSE50027). Our results show that the use of functional regulatory conservation is a potentially effective approach to select strain-specific genomic regions associated with phenotypic differences among Lyon rats and could be extended to other systems.

本研究开发了一种品系特异性单倍型优先排序方法，通过整合与特定表型相关的基因组变异及基因组调控数据。为鉴定与代谢综合征（metabolic syndrome, MetS）——一种影响多器官系统的能量利用与储存紊乱——相关的基因组区域，本研究选取两种里昂大鼠品系：LH/Mav（代谢综合征易感品系）与LL/Mav（以肥胖作为代谢综合征中间表型的易感品系），并将其与同时抵抗代谢综合征与肥胖的第三种品系LN/Mav进行对比。本研究引入一种全新量化指标，基于包括大鼠在内的5种啮齿类动物中3种肝脏特异性转录因子（HNF4A、CEBPA与FOXA1）的结合位点进化保守性，对鉴定得到的品系特异性单倍型进行排序。本研究生成了LL大鼠肝脏及全部3种里昂大鼠品系肾脏的RNA测序（RNA-seq）表达数据（每组设置5个生物学重复），并将其与现有相关数据进行整合，其中包括大鼠与5种近缘小鼠物种及品系间3种肝脏特异性转录因子（CEBPA、FOXA1与HNF4A）的调控保守水平。此外，本研究还使用了此前已公开的LH与LN大鼠肝脏的RNA-seq表达数据（数据集编号：GSE50027）。研究结果表明，利用功能调控保守性可有效筛选与里昂大鼠表型差异相关的品系特异性基因组区域，且该方法可推广至其他研究体系。