Circadian rhythms (CR) are a series of endogenous autonomous oscillators generated by the molecular circadian clock which acting on coordinating internal time with the external environment in a 24-h daily cycle. The circadian clock system is a major regulatory factor for nearly all physiological activities and its disorder has severe consequences on human health. CR disruption is a common issue in modern society, and researches about people with jet lag or shift works have revealed that CR disruption can cause cognitive impairment, psychiatric illness, metabolic syndrome, dysplasia, and cancer. In this review, we summarized the synchronizers and the synchronization methods used in experimental research, and introduced CR monitoring and detection methods. Moreover, we evaluated conventional CR databases, and analyzed experiments that characterized the underlying causes of CR disorder. Finally, we further discussed the latest developments in understanding of CR disruption, and how it may be relevant to health and disease. Briefly, this review aimed to synthesize previous studies to aid in future studies of CR and CR-related diseases.
Circadian rhythms (CR) are endogenous autonomous oscillators of physiological activities resulting 24-h day/night cycles, which allow organisms to adapt to a fluctuating environment. The core pacemaker of CR lies in the SCN, which plays crucial roles in maintenance of systemic CR and regulates peripheral tissue clocks through secretion of endogenous regulatory factors. The molecular clock of the CR system, which is present in all cells, is made up of oscillating clock-related proteins that compose TTFLs. The core TTFL is composed of the transcriptional activator proteins CLOCK and BMAL1, and the repressor proteins Period-1 (PER1), PER2, PER3, Cryptochrome-1 (CRY1) and CRY2. Other loops are coupled to the core TTFL to maintain oscillation. The first sub-loop is composed of RORs and nuclear REV-ERB receptors. The second sub-loop comprises D-box-related genes, which include DBP, TEF, and HLF. Moreover, recent studies have suggested that circadian regulation is heavily involved in gene expression. A considerable portion (approximately 10%) of genes expressed in cells or tissues have been found to display circadian oscillations, resulting in identification of these genes as “CCGs”.
Mammalian tissues and cells have an autonomous circadian oscillator with a period of roughly 24 h. External stimuli are essential for maintaining the appropriate circadian oscillations. In vivo, CR is mainly entrained by environmental signals such as light, food, and arousal stimuli. In the SCN, the circadian clock mainly responds to the LD cycle. In peripheral tissues, CR can be synchronized by food or temperature. Moreover, internal signals such as circulating hormones, cytokines, metabolites, sympathetic nervous activation, and body temperature are significant timing cues that regulate peripheral clocks. In vitro, CR are difficult to observe due to lack of SCN signals. As such, external stimuli should be applied to induce CR in cultured cells or explants.
The field of chronobiology requires detection of features of CR in tissues or cells. Through chronological collection or luminescence monitoring, the basic data resulting from circadian fluctuations in vivo or in vitro can be accurately recorded. Approaches such as FFT, JTK-Cycle, or autocorrelation can be used to analyze the rhythmic features of CR. Subsequently, we introduced several circadian databases established in recent years.
Finally, we summarized in vivo and in vitro factors that can alter CR. In vivo factors include entrainments such as light, food, and temperature, while the in vitro factors include cell density, osmotic pressure, PH, mechanical stimulus, temperature, oxygen concentration, and microorganisms. These factors can lead to circadian disruptions, and result in various diseases such as cancer, dysplasia, and metabolic and behavioral disorders.
The circadian clock system is the totality of all oscillators in organisms coupled to various physiological processes. This system generally consists of three parts in mammals including the input pathway, the core circadian clock, and the output pathway. The input pathway senses external timing signals, for example, light/dark, and sends information to the core circadian clock. The core circadian clock forms endogenous CR according to external time cues to allow for adaptation to the environment. Based on changes in the core circadian clock, the output pathway adjusts the physiological activities in various tissues and organs through neurohumoral regulation.
In mammals, the core pacemaker of the CR system exists in the SCN, which exhibits endogenous rhythmic oscillations both at the tissue and cell levels, plays a vital role in maintenance and alterations of CR, and provides outputs to peripheral tissues after synchronization by external time cues. The SCN can be distinguished into two main areas: the VL core area and the DM shell area. The core area mainly expresses the neuropeptide VIP, while the shell area expresses AVP. The VL-SCN, which controls essential physiological activities such as exercise, body temperature, heart rate, and hormone synthesis, serves to couple the circadian system. VIP is released periodically from the VL core region, binding to VPAC2 on the neuronal surface, resulting in cell depolarization and induction of PER1 and PER2. VIP deficiency impairs synchronization of the cells, leading to weakening of whole-body rhythms. AVP-deficient rats exhibit weakened rhythms, but do not experience changes in circadian pacemaking. As such, the AVP-SCN is considered to function as the output. In addition to VIP and AVP, other neurotransmitters such as glutamate and GABA, which are present in the SCN, conduce to regulate areas upstream and downstream of the circadian clock system. The SCN has historically been considered to be the only endogenous circadian clock with autonomous oscillations, and peripheral clocks were not believed to spontaneously oscillate, but could oscillate under pacing by the SCN. However, studies have demonstrated that the peripheral clocks also have the ability to oscillate autonomously and keep their internal rhythms. The predominant theory is that the SCN, as the master pacemaker, can drive peripheral clock rhythms. Peripheral clocks are under the regulation of endogenous regulatory factors from the SCN. In an organized CR system, the connection between the SCN and peripheral tissues is a complex network, and the gene expression patterns of peripheral tissues are under the control of various complex factors including autonomic innervations, endocrine signaling, temperature, and local signals.
Within cells, the CR system regulates cell biological behaviors either directly through the TTFLs or indirectly. The core TTFL contains two transcription activators, CLOCK and BMAL1, which generate a heterodimer, bind to the cis-acting element E-box (5′-CACGTG-3′), and activates transcription of the PER and CRY genes at the beginning of the cycle. After several hours, PER and CRY proteins accumulate, dimerize, and generate a complex which translocates to the nucleus and inhibits the CLOCK/BMAL1 heterodimer. Other loops are coupled to the core TTFL to complete the oscillation. The first sub-loop comprises RORs and REV-ERB, which directly targets at CLOCK/BMAL1 or ROREs. The second CLOCK/BMAL1-driven sub-loop contains the PAR-bZip factors DBP, TEF, and HLF. The repressor NFIL3 (or E4BP4), driven by the REV-ERB/ROR loop, interacts with these proteins at sites containing D-boxes. These three interlocking TTFLs form 24-h cycles of transcription with diverse expression phases, resting with the combination of cis-elements (E-box, RORE, D-box) in the promoters and enhancers of specific CCGs.
Nearly every eukaryote has a cell-autonomous circadian clock which exhibits 24-h physiological oscillations and can be influenced by external timing cues. These external timing cues, also called “synchronizers,” “zeitgeber,” or ”entraining agents” can reset the body’s circadian clock and place all cells at the same phase of circadian oscillation, a process called circadian rhythm synchronization. The word “ZT” is used to describe external cues that synchronize CR such as LD cycles or temperature cycles, and the word “CT” is utilized to describe timing without external signals. In the field of chronobiology research, whether in vivo or in vitro, researchers use these entraining agents to synchronize CR of the experimental animals or cells. A variety of factors which act as synchronizers are summarized.
Most organisms acquire the time information through changing light intensity throughout the day to reset their own clock, referred to as “photic entrainment”. In chronobiology experiments, light is often served as a stimulus to induce responses from the circadian clock. The light signaling cascades that entrain the circadian clock are fairly complex. In vivo, pRGCs receive light information, which is transmitted to the SCN directly throu
