Full-length transcriptomic analysis in murine and human heart reveals diversity of PGC-1α promoters and isoforms regulated distinctly in myocardial ischemia and obesity

Background: Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1 alpha) acts as a transcriptional coactivator and regulates mitochondrial function. Various isoforms are generated by alternative splicing and differentially regulated promoters. In the heart, total PGC-1 alpha deficiency knockout leads to dilatative cardiomyopathy, but knowledge on the complexity of cardiac isoform expression of PGC-1 alpha remains sparse. Thus, this study aims to generate a reliable dataset on cardiac isoform expression pattern by long-read mRNA sequencing, followed by investigation of differential regulation of PGC-1 alpha isoforms under metabolic and ischemic stress, using high-fat-high-sucrosediet-induced obesity and a murine model of myocardial infarction. Results: Murine (C57B1/6J) or human heart tissue (obtained during LVAD-surgery) was used for long-read mRNA sequencing, resulting in full-length transcriptomes including 58,000 mRNA isoforms with 99% sequence accuracy. Automatic bioinformatic analysis as well as manual similarity search against exonic sequences leads to identification of putative coding PGC-1 alpha isoforms, validated by PCR and Sanger sequencing. Thereby, 12 novel transcripts generated by hitherto unknown splicing events were detected. In addition, we postulate a novel promoter with homologous and strongly conserved sequence in human heart. High-fat diet as well as ischemia/reperfusion (I/R) injury transiently reduced cardiac expression of PGC-1 alpha isoforms, with the most pronounced effect in the infarcted area. Recovery of PGC-1 alpha-isoform expression was even more decelerated when I/R was performed in diet-induced obese mice. Conclusions: We deciphered for the first time a complete full-length transcriptome of the murine and human heart, identifying novel putative PGC-1 alpha coding transcripts including a novel promoter. These transcripts are differentially regulated in I/R and obesity suggesting transcriptional regulation and alternative splicing that may modulate PGC-1 alpha function in the injured and metabolically challenged heart.