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

Abstract

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.

Dysregulation of PGC-1α-Dependent Transcriptional Programs in Neurological and Developmental Disorders: Therapeutic Challenges and Opportunities

“…Though relatively unexplored, recent studies indicate that PGC-1α itself is capable of directly binding mRNA. For example, a recent study performed with primary hepatocytes demonstrated that PGC-1α binds directly to mRNA of proteins involved in glucagon and fasting responses, transcripts that are not direct transcriptional targets of PGC-1α, to influence gene expression and/or specify isoform specific expression [ 39 ]. Additional mechanisms by which PGC-1α can coordinate transcription and splicing are discussed in [ 20 ].…”

RNA-bound PGC-1α controls gene expression in liquid-like nuclear condensates

“…3e). While the small overlap between RNA binding and differential gene expression was also observed in the liver 13 , our results indicate that RNA processing is not the main function of RNA binding to the CTD. Chromatin-bound RBPs have recently emerged as key regulators of gene transcription at active promoters and enhancers 12,14 .…”

“…3d). Such a diversity of RNA motifs has recently been found to be a common characteristic of a large number of RNA binding proteins (RBPs) 5,12 , including PGC-1α FL in primary hepatocytes 13 . Overall, our results now demonstrate that PGC-1α is a bona fide RBP, with a large promiscuity for binding several types of RNAs harbouring different recognition motifs.…”

“…Previous studies have linked PGC-1α CTD function to RNA processing 8 , e.g. for the stabilization of hepatic metabolic transcripts 13 . Integration of our RNA-seq and in vitro uvAP-seq datasets however revealed that over 90% of protein-coding RNAs bound by PGC-1α were neither DEG nor alternative spliced, while 97% of DEG were neither alternative spliced nor bound by PGC-1α (Fig.…”

The master energy homeostasis regulator PGC-1α couples transcriptional co-activation and mRNA nuclear export

“…This subsequently leads to the remodeling of NXF1 into a high RNA-affinity mode 40, 41 , which mediates transport through the channel of nuclear pores via transient interactions with protruding FG-repeats of nucleoporins 42, 43 . In 2020, PGC-1α was reported to differentially bind transcripts expressed from over a thousand genes in response to glucagon-induced fasting in mouse hepatocytes 44 . Although its role remains unknown, this study highlighted for the first time that the RNA-binding activity of PGC-1α is physiologically regulated.…”