Mammalian circadian clock and metabolism - the epigenetic link

Abstract

Circadian rhythms regulate a wide variety of physiological and metabolic processes. The clock machinery comprises complex transcriptional-translational feedback loops that, through the action of specific transcription factors, modulate the expression of as many as 10% of cellular transcripts. This marked change in gene expression necessarily implicates a global regulation of chromatin remodeling. Indeed, various descriptive studies have indicated that histone modifications occur at promoters of clock-controlled genes (CCGs) in a circadian manner. The finding that CLOCK, a transcription factor crucial for circadian function, has intrinsic histone acetyl transferase (HAT) activity has paved the way to unraveling the molecular mechanisms that govern circadian chromatin remodeling. A search for the histone deacetylase (HDAC) that counterbalances CLOCK activity revealed that SIRT1, a nicotinamide adenin dinucleotide (NAD(+))-dependent HDAC, functions in a circadian manner. Importantly, SIRT1 is a regulator of aging, inflammation and metabolism. As many transcripts that oscillate in mammalian peripheral tissues encode proteins that have central roles in metabolic processes, these findings establish a functional and molecular link between energy balance, chromatin remodeling and circadian physiology. Here we review recent studies that support the existence of this link and discuss their implications for understanding mammalian physiology and pathology.

Fig. 1.

Schematic representation of the transcriptional–translational loops regulating circadian rhythms in mammals. The positive regulators CLOCK–BMAL1 activate genes with E-box elements in their promoters; these are commonly indicated as clock-controlled genes (CCGs). Among the CCGs are also the genes encoding the CRY and PER proteins that act as negative regulators of their own transcription. Most CCGs encode essential regulators of hormonal and metabolic control; here, vasopressin is shown as example. Additional loops of the circadian machinery involve other transcription factors, whose expression is primarily activated by CLOCK–BMAL1. These are DBP and REV-ERBα, which control the expression of genes with D-Box and RORE elements in their promoters (Reppert and Weaver, 2002).

Fig. 2.

Clock regulators undergo a large variety of post-translational modifications. Phosphorylation is common and elicited by a number of kinases activated by various signaling pathways (Hirayama and Sassone-Corsi, 2005). GSK3β has been shown to phosphorylate most clock proteins, thereby controlling their stability and subcellular localization. A direct link to protein destabilization was demonstrated for the AMPK-mediated phosphorylation of CRYs (Lamia et al., 2009). Other post-translational modifications include acetylation of BMAL1, a modification that is crucial for circadian rhythmicity (Hirayama et al., 2007). Ubiquitylation and sumoylation have also been described for a number of clock regulators (Akashy et al., 2002; Cardone et al., 2005; Gatfield and Schibler, 2007; Kwon et al., 2006; Lee et al., 2008; Sahar et al., 2010; Yin et al., 2006).

Fig. 3.

CLOCK is a HAT. The core circadian regulator CLOCK was identified to have intrinsic HAT activity (Doi et al., 2006) and to acetylate also non-histone proteins, in particular its own dimerization partner BMAL1 (Hirayama et al., 2007). It is tempting to speculate that, similarly to other HATs (Glozak et al., 2005), CLOCK also acetylates other cellular proteins, thereby establishing functional connections to a variety of metabolic pathways as shown here. A substantial proportion of nuclear receptors has been shown to be expressed in a circadian manner (Yang et al., 2006), suggesting that nuclear receptors are regulated by CLOCK-mediated acetylation. Likewise, a number of cell-cycle regulators could be targeted by CLOCK, as some of them are known to be acetylated, for example, p53 (Gu and Roeder, 1997). Also, as CLOCK is in a nuclear complex (see Fig. 4) and thus could associate with other nuclear regulators, it is possible that CLOCK also modifies chromatin remodelers. Finally, the conceptual link between the clock and the sleep-wake cycle could indicate a molecular connection between sleep-related peptides and signaling to CLOCK.

Fig. 4.

The CLOCK chromatin complex. CLOCK is associated in a nuclear complex with BMAL1 and SIRT1, an HDAC that is directly regulated by cellular metabolism. This complex is recruited to circadian gene promoters in a cyclic manner and is thought to be responsible for the circadian acetylation of histone H3 at K9 and K14. A balance between HAT and HDAC functions controls the opening and closing of chromatin loci at the level of circadian gene promoters through the modification of histone acetylation levels, thus leading to cyclic gene expression. It has been predicted that other chromatin remodelers and regulators participate in the CLOCK chromatin complex, possibly in a time-dependent and tissue-specific manner.

Fig. 5.

The metabolite NAD⁺ oscillates in a circadian manner. Recent studies (Nakahata et al., 2009; Ramsey et al., 2009) have shown that the circadian clock machinery controls the cyclic synthesis of NAD⁺ through control of the NAD⁺ salvage pathway. The gene encoding the enzyme NAMPT, whose transcription is the rate-limiting step in the NAD⁺ salvage pathway, contains E-boxes and is controlled by CLOCK–BMAL1. A crucial step in the NAD⁺ salvage pathway is controlled by SIRT1, which also contributes to the regulation of the Nampt promoter by associating with CLOCK–BMAL1 in the CLOCK chromatin complex (see Fig. 4). Thus, the feedback transcriptional loop of circadian regulation is closely linked to an enzymatic feedback loop. Through this regulation, SIRT1 controls the cellular levels of its own coenzyme NAD⁺. NAD⁺, nicotinamide adenin dinucleotide; NAM, nicotinamide; NMN, nicotinamide mononucleotide; ~, oscillation of CCGs (Nampt) and metabolites (NAD⁺).

Fig. 6.

Model of the circadian clock (pacemaker) and its most important input signal, light. Light signaling directly influences neurons in the central clock in the hypothalamic SCN, thereby modulating the self-sustained clock circadian regulation. The outputs of the circadian system include a large array of physiological, metabolic and neuronal functions. Disruption of clock function can cause dramatic pathophysiological effects, including neurodegeneration and cancer. Some metabolites appear to feed back to the central pacemaker and function as adjusting signals. An example for this is NAD⁺, which is used by SIRT1 as coenzyme (Nakahata et al., 2009).