Transcriptome-Wide Analysis of PGC-1α-Binding RNAs Identifies Genes Linked to Glucagon Metabolic Action

PGC-1α is a transcriptional coactivator that controls expression of metabolic/energetic genes programming cellular responses to nutrient and environmental adaptations such as fasting, cold or exercise. Unlike most other coactivators, PGC-1α contains protein domains involved in RNA binding and processing such as serine/arginine (SR) and RNA Recognition (RRM) motifs. However, little is known regarding the specific RNAs that bind PGC-1α to possibly control specific metabolic and energetic functions. To address this, we have performed single-end enhanced crosslinking and immunoprecipitation (seCLIP)-based transcriptome-wide analysis to identify specific RNA sequences that bind to PGC-1α. Primary hepatocytes were used to perform seCLIP experiments with glucagon-induced endogenous PGC-1α. RNA sequencing reveals that a large fraction of the RNAs bound to PGC-1α were intronic sequences related to genes involved in transcriptional, signaling or metabolic function linked to glucagon and fasting responses, but were not the canonical direct transcriptional targets of PGC-1α, such as OXPHOS or gluconeogenic genes. Validation of this analysis confirmed that among the top scoring RNA sequences bound to PGC-1α were Sik1, Camk1d, Ppard, Klf15, Gfra1 and Slc25a25. PGC-1α depletion decreased a fraction of mRNA transcript levels of these glucagon-induced genes. Importantly, knock-down of these genes affected glucagon-dependent glucose production, a PGC-1α-regulated metabolic pathway. These studies show that PGC-1α largely binds to intronic RNA sequences, some of them controlling transcript levels associated with glucagon action. Transcriptome-Wide Analysis of PGC-1α-Binding RNAs