Effect of deletion of ERRalpha, ERRbeta and/or ERRgamma on gene expression in soleus and extensor digitorum longus (EDL) skeletal muscles

The three estrogen related receptors (ERRs) are regulators of oxidative metabolism in many cell types, yet their roles in skeletal muscle have not been elucidated. To address the roles and significance of ERRs for skeletal muscle mitochondria and muscle function, we generated mice lacking combinations of ERRs specifically in skeletal muscle. We then compared the impact of ERR loss on the transcriptomes of EDL and soleus, i.e., muscles rich in glycolytic or oxidative fibers, respectively. Our findings highlight an essential role of ERRs for skeletal muscle oxidative metabolism and identify broad classes of ERR-dependent gene programs in muscle. They also suggest a high degree of functional redundancy among muscle ERR isoforms for the protection of oxidative capacity, with ERR isoform-specific phenotypes being driven primarily, but not exclusively, by their relative levels in different muscles. To compare the relative contributions of ERRs for oxidative capacity in glycolytic and oxidative skeletal muscles, we generated mice lacking one or two ERRs specifically in skeletal muscle. We then performed gene expression profiling analysis using data obtained from RNA-seq of soleus and EDL muscles of WT and ERR KO mice . Comparative gene expression profiling analysis of RNA-seq data from skeletal muscles of ERR muscle-specific KO mice and their WT littermates. Three biological replicates of each KO class were compared to three WT replicates.三种雌激素相关受体（estrogen related receptors，ERRs）是多种细胞类型氧化代谢的调控因子，但其在骨骼肌中的作用尚未阐明。为探究ERRs在骨骼肌线粒体及肌肉功能中的作用与意义，我们构建了在骨骼肌中特异性缺失不同组合ERRs的小鼠模型。随后，我们对比了ERR缺失对趾长伸肌（extensor digitorum longus，EDL）与比目鱼肌（soleus）——前者为富含糖酵解纤维的肌肉，后者为富含氧化纤维的肌肉——转录组的影响。本研究结果揭示了ERRs在骨骼肌氧化代谢中的核心调控作用，并鉴定出肌肉中依赖ERRs的多类基因表达程序。同时发现，肌肉ERR亚型间在维持氧化代谢能力方面存在高度功能冗余；而ERR亚型特异性表型主要（但并非完全）由其在不同肌肉中的相对表达水平所决定。为比较ERRs在糖酵解型与氧化型骨骼肌中对氧化代谢能力的相对贡献，我们构建了在骨骼肌中特异性缺失单个或两个ERR亚型的小鼠模型。随后，我们利用野生型（wild type，WT）与ERR基因敲除（knockout，KO）小鼠的比目鱼肌与趾长伸肌的RNA-seq数据开展基因表达谱分析。本研究通过对比ERR骨骼肌特异性敲除小鼠与同窝野生型小鼠的骨骼肌RNA-seq数据，完成了比较基因表达谱分析。每一类敲除组均设置3个生物学重复，并与3个野生型重复样本进行比对。