Two main mechanisms help to specialize in a nocturnal or a diurnal niche ^[10][12]. In the mechanism called entrainment, light serves as a signal for the SCN, to match the period and the phase to the environmental oscillator, the light/dark regime. Adjusting the period is necessary, as the endogenous rhythm, persisting in constant darkness, is close to but not exact 24 h. The SCN in turn helps to anticipate the rhythmic changes in the environment and controls activity during the dark or the light phase. This is important, as many nocturnal mammals live in dark burrows and experience the environmental light conditions only when leaving the safe surrounding of the nest. Entrainment is adaptive, as the lengths of the light and dark phase change according to the seasons, depending on the latitude. In the mechanism called masking, light directly affects behavior obscuring the control from the circadian clock ^[11][13]. Masking is especially prominent in nocturnal species, and, here, light can have two opposite effects on activity depending on irradiance levels. In dim light, activity is increased compared to complete darkness. This enhancing effect of dim light, which is presumably due to increased confidence based on visual input ^[12][14], is called positive masking ^[10][12]. However, in complete darkness, activity is higher, despite the absence of visual cues, than under standard (bright) light conditions. This suppressive effect of bright light on activity is called negative masking ^[10][12]. Similarly, nocturnal animals prefer dark or dimly illuminated areas over brightly illuminated areas. This light aversion is strong enough to counteract the natural tendency to explore a novel environment, as shown by the light–dark test ^[13][15], a paradigm extensively used for tests on classic anxiolytics (benzodiazepines) ^[13][15], as well as anxiolytic-like compounds, such as serotonergic drugs or drugs acting on neuropeptide receptors (reviewed in ^[14][16]). In both diurnal and nocturnal mammals, light at night also elicits acute effects on physiological parameters, such as core body temperature and heart rate, as well as hormone secretion (see below). Importantly, the detection of visual information in the mammalian retina is conveyed by two parallel pathways, the rod–cone system for image-forming-vision and the melanopsin-based system of the ipRGCs for non-image-forming irradiance detection. Although ipRGCs are essential for the adaptive physiological responses to light, such as the pupillary light reflex ^[15][17], as well as circadian entrainment ^[16][17][18,19], and contribute to scotopic vision ^[18][20], both the rod–cone system and the ipRGCs seem to contribute to masking and light aversion ^[19][21]. Importantly, many commonly used laboratory mouse strains carry mutations that affect visual and/or non-visual physiology (reviewed in ^[20][22]).

Under natural conditions, entrainment and masking work in a complementary fashion ^[21][23]. However, in the laboratory, the two mechanisms can be segregated. As mentioned above, entrainment is highly adaptive to different photoperiods. In most animal facilities, the standard photoperiod is 12 h light and 12 h dark (LD 12:12), although some animal facilities have opted for different light conditions (e.g., LD 16:8), as the photoperiod has a high impact on reproduction in some species. The circadian clock also rapidly entrains to a phase shift one experiences when travelling across time zones or if the LD cycle is inverted. The re-entrainment capacity after jet lag is dependent on intrinsic factors, such as the robustness of the circadian clock or the signaling of hormones, such as melatonin ^[22][24]. Furthermore, the speed of re-entrainment to a phase shift depends on the direction; entrainment is usually faster in response to a phase delay than a phase advance ^[23][25]. Interestingly, this is the same in the diurnal human ^[24][26]. However, in nocturnal animals, brief light pulses during the early and late night are strong resetting cues for phase delays and advances of the circadian clock, respectively ^[25][27]. At the cellular level, photic resetting of the SCN molecular clockwork involves activation of the p44/42 mitogen-activated protein kinase (MAPK) signaling cascade, phosphorylation/activation of the transcription factor cAMP-response-element-binding protein (CREB) ^[26][28], the induction of the marker of neuronal activity c-Fos ^[27][29], inhibitors of DNA binding proteins ^[28][30], and expression of the clock gene Per1 ^[29][31]. In order to study entrainment in the absence of the interfering masking effects of light, nocturnal animals can be housed under a so-called skeleton photoperiod, consisting of two discrete pulses of light during the early (dawn) and the late (dusk) light phase ^[30][32]. For entrainment to this lighting schedule, the intergeniculate leaflet is essential, which receives direct photic information from the ipRGCs ^[31][33].

2.3. The Brain Molecular Clockwork

Various brain functions, such as sleep, wake, foraging, food intake, alertness, emotion, motivation, and cognitive performance, controlled by different brain regions, show circadian rhythms. Moreover, any information is processed in a temporal context. Consistently, many brain regions harbour circadian oscillators, which are governed by the SCN ^[32][34]. At the cellular level, these oscillators are composed of single cells each harbouring a molecular clockwork composed of transcriptional/translational feedback loops of clock genes. The clock genes encode for activators of transcription, such as CLOCK and its forebrain-specific analog NPAS2 ^[33][35], BMAL1, and ROR, as well as the repressors of transcription PER1 and PER2, CRY1, CRY2, and REV-ERBα ^[3][5].

The molecular clockwork drives the rhythmic expression of clock controlled gene (see below) and posttranscriptional processes (reviewed in ^[34][36]) and modulates the chromatin landscape ^[35][37], thus regulating rhythmic cell function at multiple levels. The molecular clockwork in the SCN and subordinate extra-SCN brain circadian oscillators drives various rhythms in neuron and glia function including ATP concentration ^[36][38], neuronal electrical activity (reviewed in ^[37][39]), metabolism ^[38][40], redox homeostasis (reviewed in ^[39][41]), tyrosine hydroxylase expression in dopaminergic neurons ^[40][42], dopamine receptor signalling in the hippocampus ^[41][43], and extracellular glutamate homeostasis ^[42][44]. In addition, some rhythms in the SCN are time-of day-dependent and do not persist in constant darkness, such as rhythmic expression of connexion 30 ^[43][45], which contribute to astrocyte gap junctions and hemichannels (reviewed in ^[44][46]), as well as the stability of circadian rhythms and re-entrainment under challenging conditions ^[43][45]. Circadian clock gene expression in the SCN and the hippocampus persists with high robustness in vitro, indicating a strong coupling of single cell oscillators, while it damps rapidly in other brain regions, indicating a weak coupling ^[45][46][47][47,48,49]. Mice with a targeted deletion of the essential clock gene Bmal1 are arrhythmic under constant environmental conditions ^[48][50], so a loss of function in a single gene strongly affects circadian rhythmicity. In mouse models for compromised molecular clockwork function, such as Bmal1-deficient mice, Per1/2 double mutants, and Cry1/Cry2 double mutants, circadian rhythms are abolished, while various parameters of physiology and behaviour are rhythmic under the LD 12:12 conditions due to masking ^[48][49][50][50,51,52]. This emphasizes the strong impact of the environmental light/dark conditions on rhythmic brain function. In this context, it is important to note that Cry1/Cry2 double mutants and Bmal1-deficient mice show deficits in retinal visual physiology ^[51][53] and, consequently, impaired visual input into the circadian system ^[52][53][54,55]. Nevertheless, even under LD 12:12 conditions, many brain functions, such as spatial memory consolidation and contextual fear ^[54][55][56,57], adult neurogenesis ^[56][58], and sleep architecture ^[57][59] are affected in Bmal1-deficient mice, indicating the importance of this clock gene/transcription factor for general brain function.

2.4. Rhythmic Gene and Protein Expression in the Brain

About 43% of all coding genes and about 1000 noncoding RNAs show circadian rhythms in transcription somewhere in the body, largely in an organ/tissue-specific manner ^[58][59][60][60,61,62]. The rhythmic transcriptome in peripheral organs is dependent on the SCN ^[60][62] but continues to oscillate in vitro for a few cycles ^[61][63]. Only 22% of circadian rhythmic mRNA is driven by de novo transcription, indicating that the molecular clock drives transcription and posttranslational modification ^[35][37]. Moreover, the epigenetic landscape is modulated in a circadian manner ^[35][37]. A comparable number of transcripts show a circadian oscillation in the SCN and the liver, while only about 10% of them show an overlap ^[59][61]. The core clock genes Arntl (encoding for Bmal1), Dbp, Nr1d1 and Nr1d2 (encoding for Rev-Erb alpha and beta, respectively), Per1, Per2, and Per3, as well as the clock controlled genes Usp2, Tsc22d3, and Tspan4 oscillate in many organs and parts of the brain ^[58][60]. Importantly, many commonly used drugs target the products of the circadian genes, so the timed application of these drugs, chronotherapy, might maximize efficacy, and minimize side effects ^[58][60]. In accordance with the important role of the brain stem in the regulation of autonomous and vital functions, more than 30% of the drug-target circadian genes listed in the study by Zhang et al. (2014) are rhythmically expressed in this part of the brain. In the retina, about 277 genes show a circadian rhythm, implicated in a variety of functions, including synaptic transmission, photoreceptor signalling, intracellular communication, cytoskeleton reorganization, and chromatin remodelling ^[62][64]. Intriguingly, in LD 12:12, about 10 times as many genes oscillate, indicating that the LD cycle drives the rhythmic expression of a large number of genes in the retina ^[62][64]. In the forebrain synapses, a comparable amount of genes (2085, thus 67% of synaptic RNAs) show a time-of-day-dependent rhythm, and a high percentage of these genes remain rhythmic in constant darkness (circadian) ^[63][65]. Interestingly, the rhythmic genes in the forebrain synapses can be segregated into two temporal domains, predusk and predawn, relating to distinct functions; predusk mRNAs relate to synapse organization, synaptic transmission, cognition, and behaviour, while predawn mRNAs relate to metabolism, translation, and cell proliferation or development ^[63][65]. The oscillation of the synaptic proteome resembles those of the transcriptome ^[63][65] and a high percentage show an oscillation in the phosphorylation state ^[64][66].

2.5 Sleep Deprivation, Epilepsy, and Glucocorticoids Affect Gene and Protein Expression in the Brain

Sleep deprivation induced by gentle handling, cage tapping, and the introduction of novel objects during the light/inactive phase affects clock gene expression in the cerebral cortex ^[65][67] and leads to a reduction in transcript oscillation in the entire brain to about 20% ^[66][68]. This indicates that the sleep disruption itself, and/or the manipulation, as well as the associated additional light exposure, which mice usually do not experience while sleeping, strongly affects rhythmic transcription. On the other hand, it shows that only 20% of the rhythmic transcriptome in the brain is resilient to sleep deprivation, manipulation, and light exposure during the light/inactive phase. In forebrain synapses, sleep deprivation has a higher impact on the proteome and on rhythmic protein phosphorylation than on the transcriptome ^[63][64][65,66]. In this context, it is important to note that traditional sleep deprivation protocols using sensory-motor stimulation induces stress associated with a rise in circulating corticosterone ^[67][69], an important temporal signal within the circadian system. Corticosterone strongly contributes to the sleep-deprivation-induced forebrain transcriptome ^[68][70]. Among the genes assigned to the corticosterone surge are clock genes, as well as genes implicated in sleep homeostasis, cell metabolism, and protein synthesis, while the transcripts that respond to sleep loss independent of corticosterone relate to neuroprotection ^[68][70]. The time-of-day-dependent oscillation in hippocampal transcriptome and proteome is affected by temporal lobe epilepsy ^[69][71]. Although epilepsy could be considered a chronic stress model ^[70][72], little is known on the contribution of glucocorticoids in these alterations. More research avoiding stress as a confounder is needed to explore the effect of sleep and neurological disorders on rhythmic brain function.