The circadian regulator CLOCK is a histone acetyltransferase (HAT) that also acetylates a nonhistone substrate: its own partner, BMAL177. Both nonhistone acetyltransferase and HAT activities are essential to the circadian rhythmicity and activation of clock genes77. Sirt1 is a circadian deacetylase for core clock components78. The NAD(+)-dependent enzyme Sirt1, which functions as a histone deacetylase whose activity is also regulated by the redox states of NAD cofactors, counteracts the activity of CLOCK77. Additionally, Sirt1 binds to CLOCK-BMAL1 and Per2 in a circadian manner and supports the deacetylation and degradation of Per279. In the absence of Sirt1, constitutively high protein levels of Per2 may lead to the repression of Per1, Per2, Cry1, and retinoic acid-related orphan receptor γ (RORγ) mRNA expression79. On the other hand, Sirt1 may activate autophagy through the Sirt1-LKB1-AMPK pathway and by deacetylating ATG5, ATG7, LC3, and tuberous sclerosis complex 2 (TSC2), a component of the mTOR inhibitory complex upstream of mTORC180,81,82,83. Taken together, these findings suggest that Sirt1 serves as a link between autophagy and CR and between the redox state and the circadian clock.

Melatonin, an endocrine hormone synthesized and secreted by the pineal gland in the brain that helps to maintain CR, significantly enhances protective effects in different systems, including the central nervous, cardiovascular, gastrointestinal and endocrine systems, through the enhancement or inhibition of the autophagy process84. It is believed that oxidative stress can activate autophagy; for this reason, the antioxidant activity of melatonin could account for its inhibitory effects on autophagy85. If so, melatonin may affect mechanisms that stimulate autophagy, rather than affecting the process itself85. Melatonin seems to inhibit autophagy triggered by either mTOR activation or JNK/Bcl-2/Beclin1 pathway signaling86,87. Cyclosporine A is known to induce autophagy via ER stress88. Melatonin suppresses cyclosporine-induced autophagy in rat pituitary GH3 cells through the MAPK/ERK pathway, an effect that is due either totally or in part to the antioxidant properties of melatonin85,88. Deficiency of the nuclear melatonin receptor RORα aggravates autophagy dysfunction in diabetic hearts and myocardial ischemia/reperfusion injury in mice89,90,91. However, in regimen 1-treated N2a/APP cells, only a slight increase in cellular autophagy has been found using flow cytometry, and there is no significant alteration in the expression of the autophagy-associated markers Beclin-1 and LC3-I/II92. These results suggest that autophagy may play a negligible role in the beneficial effects of caffeine, melatonin, and coffee on AD92.

The circadian regulation of C/EBPβ and the autophagy disruption observed in mice lacking a functional liver clock suggest that C/EBPβ is a key factor that links autophagy to the biological clock and maintains nutrient homeostasis throughout light/dark cycles13. In zebrafish, a CLOCK-BMAL1 heterodimer binds to E-boxes to regulate the transcription of C/EBPβ, which in turn controls the transcription of autophagy-related genes indirectly50.

Fus1, a tumor suppressor protein residing in mitochondria, maintains mitochondrial homeostasis and is highly expressed in the brain93. One study revealed that KO mice showed sleep/wake disturbances compared to WT mice and that the autophagy marker LC3-II was decreased in both the olfactory bulbs and hippocampi, suggesting an early onset of autophagy dysregulation in Fus1 KO mice93. Heme oxygenase (Ho), whose silencing results in the downregulation of autophagy-related genes in both light and dark phases, is expressed in a circadian manner94. FoxOs are tightly controlled by fasting/feeding cycles and can upregulate the expression of ATG1474. Casein kinase 1α (CK1α) exhibits dual functions in autophagy regulation95. CK1α-mediated phosphorylation stimulates the degradation of Per1, suggesting a function in CR95.

The expression of the core clock genes Per2 and REV-ERBα is increased after weight loss96. Clock gene expression levels and their weight loss-induced changes are tightly correlated with each other and with the expression of genes involved in autophagy (LC3A and LC3B)96. Folic acid deprivation increases autophagic activity in hippocampal neuron cells, an effect that is associated with the activation of autophagy- and circadian-related genes97.

In the brain, acrylamide (ACR), a chronic neurotoxin, substantially attenuates spontaneous alternation. ACR dampens the oscillatory amplitudes of clock genes (BMAL1, Cry2 and REV-ERBβ) or causes a phase shift in clock genes (CLOCK, Per2 and REV-ERBα) and weakens the amplitude of Sirt1 oscillations. In addition, ACR increases the number of autophagic structures only in the night phase, which may cause nerve cell damage and apoptosis, ultimately leading to cognitive impairment (Fig. 3)98.