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

PGC-1a 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-1a 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-1a 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-1a. Primary hepatocytes were used to perform seCLIP experiments with glucagon-induced endogenous PGC-1a. RNA sequencing reveals that a large fraction of the RNAs bound to PGC-1a 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-1a, such as OXPHOS or gluconeogenic genes. Validation of this analysis confirmed that among the top scoring RNA sequences bound to PGC-1a were Sik1, Camk1d, Ppard, Klf15, Gfra1 and Slc25a25. PGC-1a 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-1a-regulated metabolic pathway. These studies show that PGC-1a largely binds to intronic RNA sequences, some of them controlling transcript levels associated with glucagon action. Overall design: Transcriptome-Wide Analysis of PGC-1a-Binding RNAs