Transcriptome-wide analysis of PGC-1α–binding RNAs identifies genes linked to glucagon metabolic action

• Published in: Proceedings of the National Academy of Sciences - PNAS 2020-09, Vol.117 (36), p.22204-22213
• Main Authors: Tavares, Clint D. J., Aigner, Stefan, Sharabi, Kfir, Sathe, Shashank, Mutlu, Beste, Yeo, Gene W., Puigserver, Pere
• Format: Article
• Language: English
• Subjects: Adaptation; Adenosine Triphosphate - metabolism; Animals; Arginine; Biological Sciences; Calcium-Binding Proteins - genetics; Calcium-Binding Proteins - metabolism; Cells, Cultured; Crosslinking; Depletion; Fasting; FOXO1 protein; Gene expression; Gene Expression Profiling; Gene Expression Regulation - drug effects; Gene Expression Regulation - physiology; Gene sequencing; Genes; Glucagon; Glucagon - metabolism; Glucagon - pharmacology; Gluconeogenesis - physiology; Glucose - metabolism; Guanosine Triphosphate - metabolism; Hepatocytes; Hepatocytes - metabolism; Immunoprecipitation; Laboratory testing; Liver - metabolism; Male; Metabolic pathways; Metabolism; Metabolomics; Mice; Mice, Inbred C57BL; Mitochondrial Membrane Transport Proteins - genetics; Mitochondrial Membrane Transport Proteins - metabolism; Period 1 protein; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha - genetics; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha - metabolism; Protein Binding; Ribonucleic acid; RNA; Serine; Transcription; Transcriptome
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2000643117

The peroxisome proliferator-activated receptor gamma coactivator 1-alpha (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 other coactivators, PGC-1α contains protein domains involved in RNA regulation such as serine/arginine (SR) and RNA recognition motifs (RRMs). However, the RNA targets of PGC-1α and how they pertain to metabolism are unknown. To address this, we performed enhanced ultraviolet (UV) cross-linking and immunoprecipitation followed by sequencing (eCLIP-seq) in primary hepatocytes induced with glucagon. A large fraction of RNAs bound to PGC-1α were intronic sequences of genes involved in transcriptional, signaling, or metabolic function linked to glucagon and fasting responses, but were not the canonical direct transcriptional PGC-1α targets such as OXPHOS or gluconeogenic genes. Among the top-scoring RNA sequences bound to PGC-1α were Foxo1, Camk1δ, Per1, Klf15, Pln4, Cluh, Trpc5, Gfra1, and Slc25a25. PGC-1α depletion decreased a fraction of these glucagon-induced messenger RNA (mRNA) transcript levels. Importantly, knockdown of several of these genes affected glucagon-dependent glucose production, a PGC-1α–regulated metabolic pathway. These studies show that PGC-1α binds to intronic RNA sequences, some of them controlling transcript levels associated with glucagon action.