Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1a in the regulation of the hypoxic gene program [ChIP-Seq]

Skeletal muscle tissue shows an extraordinary cellular plasticity, but the underlying molecular mechanisms are still poorly understood. Here we use a combination of experimental and computational approaches to unravel the complex transcriptional network of muscle cell plasticity centered on the peroxisome proliferator-activated receptor ? coactivator 1a (PGC-1a), a regulatory nexus in endurance training adaptation. By integrating data on genome-wide binding of PGC-1a and gene expression upon PGC-1a over-expression with comprehensive computational prediction of transcription factor binding sites (TFBSs), we uncover a hitherto underestimated number of transcription factor partners involved in mediating PGC-1a action. In particular, principal component analysis of TFBSs at PGC-1a binding regions predicts that, besides the well-known role of the estrogen-related receptor a (ERRa), the activator protein-1 complex (AP-1) plays a major role in regulating the PGC-1a-controlled gene program of hypoxia response. Our findings thus reveal the complex transcriptional network of muscle cell plasticity controlled by PGC-1a. Overall design: We performed ChIP-Seq experiments to identify all DNA recruitment sites for PGC-1alpha in C2C12 cells on genome-wide scale. The experiment was performed in duplicate and the Whole Cell Extract (WCE; =input DNA) was used as background condition.

骨骼肌组织展现出极强的细胞可塑性，但其背后的分子机制仍未得到充分阐明。本研究结合实验与计算手段，解析以过氧化物酶体增殖物激活受体γ辅激活因子1α（PGC-1α）为核心的肌细胞可塑性复杂转录调控网络——该因子是耐力训练适应过程中的关键调控枢纽。本研究整合PGC-1α全基因组结合数据、PGC-1α过表达后的基因表达数据，以及转录因子结合位点（TFBS）的全面计算预测结果，揭示了此前被低估的、参与介导PGC-1α调控功能的转录因子搭档数量。尤为关键的是，对PGC-1α结合区域内TFBS的主成分分析预测显示，除了已知的雌激素相关受体α（ERRα）的调控作用外，激活蛋白1复合物（AP-1）在PGC-1α介导的低氧应答基因程序调控中发挥核心作用。综上，本研究的发现揭示了PGC-1α调控的肌细胞可塑性复杂转录网络。实验整体设计：本研究通过染色质免疫共沉淀测序（ChIP-Seq）实验，在全基因组范围内鉴定C2C12细胞中PGC-1α的所有DNA招募结合位点。实验设置重复两组，并以全细胞提取物（WCE，即输入DNA样品）作为背景对照条件。