At least 10% of the genes in any given cell are expressed in a cyclic manner under circadian control mediated by cyclic chromatin modifications at the promoters of clock-controlled genes. Here we show a schematic representation of the histone H3 tail, the relevant post-translational modifications and the chromatin remodelers involved in circadian control. Phosphorylation (serine 10 or S10), acetylation (lysine 9/14 or K9/14) and methylation (K4 and K27) are associated with circadian transcription. Some chromatin modifiers may be directly or indirectly modulated by the circadian system (). Methylation at K4 is consistently associated with gene activation and might be crucial for circadian gene transcription and recruitment of circadian chromatin remodeling complexes . Non-histone proteins can also undergo clock-dependent acetylation, as is the case for BMAL1 (). Several chromatin remodelers can be considered metabolic sensors, as they use metabolites for their enzymatic function; for example, the NAD⁺-dependent deacetylase SIRT1, whose role in circadian control and physical interaction with CLOCK revealed a link between the circadian clock and cellular metabolism. For enzymatic functions of these chromatin modifiers, references, and abbreviations, see . MSK1: mitogen- and stress-activated protein kinase (MSK1), RSK2: ribosomal S6 kinase 2 (see references ^, ).

The central clock in the SCN controls a variety of endocrine and metabolic functions. Neurons of the SCN undergo oscillations in depolarization, activation of the ERK/MAPK cascade and CREB activity, as well as oscillations in gene expression. In addition, several small molecules oscillate, including cAMP and calcium. While the SCN indirectly controls oscillations of humoral factors coming from other tissues such as the pineal and adrenal cortex, continuity within the SCN is mediated by loops within VIP and AVP-expressing neurons. Other tissues also maintain circadian output via positive and negative feedback loops within cells that make up different compartments of the tissue. Oscillations in humoral factors control the circadian release of factors from the periphery, such as ghrelin, leptin, insulin, and glucose and these in turn regulate CNS function. Melatonin, which is released in a circadian fashion from the pineal gland, is involved in feedback regulation of the SCN where melatonin receptors are abundantly expressed. Peripheral tissues provide positive and negative feedback to the brain by releasing soluble factors such as hormones and adipokines, including ghrelin (stomach), leptin (adipose tissue), insulin (pancreas), and glucose (liver and other tissues). Thus, the periphery may influence brain functions, and specifically SCN neurons, through a feedback mechanism.

The central role of the SCN as light-entrainable oscillator is well documented. The light signal, through the retinohypothalamic tract (RHT), exerts critical control over SCN neurons. Accumulating findings indicate the presence of a food-entrainable oscillator (FEO), probably in either the dorsomedial hypothalamus (DMH) or the ventromedial hypothalamus(VMH), as well as a methamphetamine-sensitive oscillator, which could be localized in the ventral tegmental area (VTA). The functional relationships and circuitry interplay among these centers remains unexplored.

The circadian clock controls the expression of nicotinamidephosphoribosyltransferase (Nampt), the rate limiting enzyme in mammalian NAD⁺ biosynthesis from nicotinamide (NAM), via the NAD⁺ salvage pathway. Oscillating levels of NAMPT result in cyclic variations in NAD⁺, which determine the circadian activity of SIRT1 and possibly other NAD⁺-dependent enzymes. Consequently, SIRT1 determines the oscillatory levels of its own co-enzyme, NAD⁺. In addition, Liver kinase B1 (LKB1)-activated AMPK has been shown to control the phosphorylation of CRY proteins as well as the activity of NAMPT. Thus, an enzymatic network that depends on cellular metabolism is intimately associated with the circadian clock machinery. This may constitute a critical link between sleep control and the circadian clock, as AMPK activity is coupled to sleep state.