Epigenetic Regulation of Mitochondrial Homeostasis and Energy Metabolism

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Mitochondria are powerhouses regulating cellular and systemic energy metabolism. Although mitochondria have their own DNA encoding 13 oxidative phosphorylation proteins, mitochondrial function is mainly regulated by more than 1,000 proteins encoded by the “mitochondrial genes” in the nuclear genome. While transcription factors have been the focus of research on mitochondrial gene regulation, major gaps exist in understanding how epigenetic factors are integrated into the transcriptional networks. Here the applicant proposes that lysine-specific demethylase-1 (LSD1) in liver serves as a novel housekeeping mechanism coordinating histone methylation and NAD+-modulated transcription factors to control mitochondrial gene expression and function and to regulate systemic energy metabolism. LSD1 catalyzes the removal of mono- and di-methylation of lysine 4 and 9 on histone 3 (H3K4/9). LSD1 also targets non-histone proteins to regulate their activity. Hepatic LSD1 was reduced in aged and obese mice. As LSD1 is essential to development, the applicant’s laboratory generated liver-specific LSD1 knockout in adult mice (LSD1-LKO). RNA-seq analysis revealed that LSD1 knockout in liver decreased approximately one-third of all known mitochondrial genes. Preliminary mechanistic studies showed that H3K9 methylation contributed to mitochondrial gene reduction. LSD1 did not directly target mitochondrial transcription factors, but rather targeted NAD+-synthetic enzyme NMNAT1 to regulate the activity of Sirt1 and Sirt7, which are positioned upstream of the mitochondrial transcription factors. Surprisingly, despite the reduced hepatic mitochondrial gene expression and function, LSD1-LKO mice showed improved metabolic phenotype including increased energy expenditure and reduced adiposity. We identified complement C1q like 4 (C1ql4), a member of adiponectin superfamily, as a potential novel mitochondrial stress-induced hepatic mitokine that regulates systemic energy expenditure. The applicant therefore hypothesizes that LSD1 modulates histone and NMNAT1 methylation to control mitochondrial gene expression and hepatic mitokine production for regulating systemic energy metabolism. Aim 1 is to determine the mechanisms for LSD1-regulated hepatic mitochondrial gene expression, focusing on 1) LSD1 demethylase activity and histone methylation; 2) NMNAT1 methylation and NAD+-mediated transcription factor activation. Aim 2 is to elucidate the mechanisms by which hepatic LSD1 regulates systemic energy metabolism. We will focus on C1ql4 and study 1) regulation of C1ql4 expression by mitochondrial stress and histone methylation; 2) effects of C1ql4 on obesity; 3) mechanism of C1ql4 action for increasing energy expenditure; 4) role of C1ql4 induction in the improved systemic energy metabolism in the LSD1-LKO mice. Overall, the proposal will provide molecular, cellular and physiological insights into the housekeeping roles of LSD1 in controlling mitochondrial gene expression and function. Furthermore, the identification of C1ql4 as a novel hepatic mitokine not only highlights the significance of mitokines in regulating systemic energy metabolism, but may also provide a novel target for obesity treatment.