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*601851
Table of Contents

* 601851

CLOCK CIRCADIAN REGULATOR; CLOCK


Alternative titles; symbols

CIRCADIAN LOCOMOTOR OUTPUT CYCLES KAPUT
CLOCK, MOUSE, HOMOLOG OF


HGNC Approved Gene Symbol: CLOCK

Cytogenetic location: 4q12   Genomic coordinates (GRCh38) : 4:55,427,903-55,546,909 (from NCBI)


TEXT

Description

Circadian rhythmicity of biologic processes is a fundamental property of all eukaryotic and some prokaryotic organisms. These rhythms are driven by an internal time-keeping system. Changes in the external environment, particularly in the light-dark cycle, entrain this biologic clock. Under constant environmental conditions devoid of time cues, rhythms driven by the biologic clock show a period near, but usually not equal to, 24 hours. The bilaterally paired suprachiasmatic nuclei (SCN) of the hypothalamus are thought to contain the master circadian clock that regulates most, if not all, circadian rhythms in mammals. The CLOCK gene encodes a basic helix-loop-helix (bHLH)-PAS (see 603349) transcription factor that is essential for circadian rhythm (King et al., 1997).


Cloning and Expression

King et al. (1997) used positional cloning to identify the Clock gene in mice. They found that it is a large transcription unit from which mRNA transcripts of 7.5 and approximately 10 kb arise. The gene encodes an 855-amino acid polypeptide that is a novel member of the bHLH-PAS family of transcription factors and has features predicting DNA binding, protein dimerization, and activation domains. King et al. (1997) noted that the circadian rhythm gene of Drosophila 'Period' (PER1; 602260) also encodes a PAS domain-containing Clock protein, which suggests that this motif may define an evolutionarily conserved feature of the circadian Clock mechanism.

As a complementary approach to positional cloning, Antoch et al. (1997) used in vivo complementation with BAC clones expressed in transgenic mice to identify the circadian Clock gene. A 140-kb BAC transgene completely rescued both the long-period and the loss-of-rhythm phenotypes in Clock mutant mice. Analysis with overlapping BAC transgenes demonstrated that a large transcriptional unit represents the Clock gene and encodes a novel bHLH-PAS domain protein. Overexpression of the Clock gene shortened period length beyond the wildtype range, which provided additional evidence that Clock is an integral component of the circadian pacemaking system. Taken together, their results provided proof of the principle that 'cloning by rescue' is an efficient and definitive method in mice.

By searching an EST database and screening a hypothalamus cDNA library, Steeves et al. (1999) obtained a human cDNA encoding CLOCK. The deduced 846-amino acid protein retains the structural features of the mouse protein, with which it is 96% identical. Northern blot analysis revealed expression of a predominant 10.0-kb transcript and a major 8.0-kb transcript in most tissues tested, with highest levels in testis and skeletal muscle and lowest levels in lung, liver, and thymus. A minor 4.0-kb transcript was also detected in testis only. Elevated levels of the 10-kb transcript were present in cerebellum. In situ hybridization analysis demonstrated intense expression of CLOCK in the suprachiasmatic nucleus, the supraoptic nucleus, and the cerebellum.

Doi et al. (2006) reported that CLOCK has a domain structure similar to that of ACTR (NCOA3; 601937), a member of the SRC family of histone acetyltransferases (HATs). Both proteins contain an N-terminal bHLH domain, followed by 2 PAS domains, a serine-rich nuclear receptor interaction domain (NRID), and a C-terminal glutamine-rich region. The glutamine-rich region contains an acetyl-CoA-binding motif, a hallmark of HATs.


Gene Function

Reppert and Weaver (1997) commented that studies on circadian rhythm would yield new insight into the control of sleep and its disorders in humans, the effects of shift work and jet lag, and sleep disorders that occur with advanced age. They reviewed the topic of circadian rhythms and illustrated 3 hypothetical models of how Clock might function as a circadian clock element. They pointed out that 1997 was the silver anniversary of the discovery that the suprachiasmatic nuclei have a circadian clock function.

Gekakis et al. (1998) used a yeast 2-hybrid screen to find proteins that interact with the Clock protein. The mouse Bmal1 (ARNTL; 602550) protein was isolated and found to dimerize with Clock. Bmal1 is found in the suprachiasmatic nucleus and the retina, along with Clock and Per1. The Clock-Bmal1 heterodimers are able to bind DNA and activate transcription from an E-box element (CACGTG), a type of transcription factor-binding site, found adjacent to mouse Per1 and to the Drosophila Per gene. Mutant Clock from the dominant-negative Clock allele forms heterodimers with Bmal1 that bind DNA but fail to activate transcription. The authors concluded that Clock-Bmal1 heterodimers appear to drive the positive component of Per transcriptional oscillations.

Darlington et al. (1998) showed that the Drosophila Clock gene heterodimerizes with the Drosophila homolog of BMAL1. These proteins acted through an E-box sequence in the Per promoter and through an 18-bp element encompassing an E-box sequence in the Timeless (TIM; 603887) promoter to activate Per and Tim transcription. Period and Timeless proteins blocked Clock's ability to activate Tim and Per promoters via the E-box. The authors therefore concluded that Clock drives expression of Period and Timeless, which in turn inhibit Clock's activity and close the circadian loop.

By yeast 2-hybrid analysis of human umbilical vein endothelial cell (HUVEC) cDNA, Maemura et al. (2000) found that CLIF (ARNTL2; 614517) interacted with CLOCK. Mobility shift assays and mutation analysis showed that CLIF formed a heterodimer with CLOCK and bound to the E-box of the PER1 promoter. Coexpression of CLIF with CLOCK in HUVECs resulted in elevated CLOCK-dependent PAI1 (SERPINE1; 173360) expression, and mutation of the E-boxes within the PAI1 promoter abrogated binding by CLIF/CLOCK. PER2 (603426) and CRY1 (601933) inhibited CLIF/CLOCK-dependent transactivation of the PAI1 promoter.

McNamara et al. (2001) reported a hormone-dependent interaction of the nuclear receptors RARA (180240) and RXRA (180245) with CLOCK and MOP4 (NPAS2; 603347). They found that these interactions negatively regulate CLOCK-BMAL1 and MOP4-BMAL1 heterodimer-mediated transcriptional activation of clock gene expression in vascular cells. MOP4 exhibited a robust rhythm in the vasculature, and retinoic acid could phase shift PER2 mRNA rhythmicity in vivo and in serum-induced smooth muscle cells in vitro, providing a molecular mechanism for hormonal control of clock gene expression. McNamara et al. (2001) proposed that circadian or periodic availability of nuclear hormones may play a critical role in resetting a peripheral vascular clock.

Shearman et al. (2000) demonstrated that in the mouse, the core mechanism for the master circadian clock consists of interacting positive and negative transcription and translation feedback loops. Analysis of Clock/Clock mutant mice, homozygous Per2 mutants, and Cry-deficient mice revealed substantially altered Bmal1 rhythms, consistent with a dominant role of Per2 in the positive regulation of the Bmal1 loop. In vitro analysis of Cry inhibition of Clock:Bmal1-mediated transcription showed that the inhibition was through direct protein-protein interactions, independent of the Per and Tim proteins. Per2 is a positive regulator of the Bmal1 loop, and Cry1 and Cry2 (603732) are the negative regulators of the Period and Cryptochrome cycles.

Rutter et al. (2001) demonstrated that the DNA binding activity of the Clock:BMAL1 and NPAS2:BMAL1 heterodimers is regulated by the redox state of nicotinamide adenine dinucleotide (NAD) cofactors in a purified system. The reduced forms of the redox cofactors, NAD(H) and NADP(H), strongly enhance DNA binding of the Clock:BMAL1 and NPAS2:BMAL1 heterodimers, whereas the oxidized forms inhibit. Rutter et al. (2001) suggested the possibility that food, neuronal activity, or both may entrain the circadian clock by direct modulation of cellular redox state.

Etchegaray et al. (2003) demonstrated that transcriptional regulation of the core clock mechanism in mouse liver is accompanied by rhythms in H3 histone (see 602810) acetylation, and that H3 acetylation is a potential target of the inhibitory action of Cry. The promoter regions of the Per1, Per2, and Cry1 genes exhibited circadian rhythms in H3 acetylation and RNA polymerase II (see 180660) binding that were synchronous with the corresponding steady-state mRNA rhythms. The histone acetyltransferase p300 (602700) precipitated with Clock in vivo in a time-dependent manner. Moreover, the Cry proteins inhibited a p300-induced increase in Clock/Bmal1-mediated transcription. Etchegaray et al. (2003) concluded that the delayed timing of the Cry1 mRNA rhythm, relative to the Per rhythms, was due to the coordinated activities of Rev-Erb-alpha (602408) and Clock/Bmal1, and defined a novel mechanism for circadian phase control.

Kondratov et al. (2003) showed that circadian regulation of nuclear Clock accumulation in mouse embryonic fibroblasts was dependent on Bmal1 expression. Formation of Clock-Bmal1 dimers following ectopic coexpression in human cells resulted in codependent phosphorylation of both proteins that was tightly coupled to Clock nuclear translocation and degradation. Binding-dependent coregulation was specific for Clock-Bmal1 interaction, as no other PAS domain protein able to form complexes with either Clock or Bmal1 could induce similar effects. All events were tightly coupled with Clock-Bmal1-dependent transcriptional activation, indicating their functional role in the regulation of the circadian clock.

Toward a system-level understanding of the transcriptional circuitry regulating circadian clocks, Ueda et al. (2005) identified clock-controlled elements on 16 clock and clock-controlled genes in a comprehensive surveillance of evolutionarily conserved cis elements and measurement of the transcriptional dynamics. Ueda et al. (2005) found that E boxes (CACGTG) and E-prime boxes (CACGTT) controlled the expression of Per1 (602260), Nr1d2 (602304), Per2, Nr1d1 (602408), Dbp (124097), Bhlhb2 (604256), and Bhlhb3 (606200) transcription following a repressor-precedes-activator pattern, resulting in delayed transcriptional activity. RevErbA/ROR (600825)-binding elements regulated the transcriptional activity of Arntl, Npas2, Nfil3 (605237), Clock, Cry1, and Rorc (602943) through a repressor-precedes-activator pattern as well. DBP/E4BP4-binding elements controlled the expression of Per1, Per2, Per3, Nr1d1, Nr1d2, Rora, and Rorb (601972) through a repressor-antiphasic-to-activator mechanism, which generates high-amplitude transcriptional activity. Ueda et al. (2005) suggested that regulation of E/E-prime boxes is a topologic vulnerability in mammalian circadian clocks, a concept that had been functionally verified using in vitro phenotype assay systems.

Doi et al. (2006) showed that mouse Clock had HAT activity against histones H3 and H4 (see 602822). In the presence of Bmal1, the relative HAT activity of Clock was enhanced about 4-fold. Mutations in the putative acetyl CoA-binding site of Clock reduced HAT activity. The HAT activity of Clock was essential to rescue circadian rhythmicity and activation of clock genes in Clock mutant mouse embryonic fibroblasts.

Hirayama et al. (2007) demonstrated that CLOCK acetylates a nonhistone substrate: its own partner, BMAL1 (602550), which it specifically acetylates on a unique, highly conserved lys537 residue. BMAL1 undergoes rhythmic acetylation in mouse liver, with a timing that parallels the downregulation of circadian transcription of clock-controlled genes. BMAL1 acetylation facilitates recruitment of CRY1 to CLOCK-BMAL1, thereby promoting transcriptional repression. Importantly, ectopic expression of a K537R-mutated BMAL1 was not able to rescue circadian rhythmicity in a cellular model of peripheral clock. Hirayama et al. (2007) concluded that these findings revealed that the enzymatic interplay between 2 clock core components is crucial for the circadian machinery.

O'Neill et al. (2008) showed that cAMP signaling constitutes an additional bona fide component of the oscillatory network of the circadian rhythm. They proposed that daily activation of cAMP signaling, driven by the transcriptional oscillator, in turn sustains progression of transcriptional rhythms. In this way, clock output constitutes an input to subsequent cycles.

Ramsey et al. (2009) reported that both the rate-limiting enzyme in mammalian nicotinamide adenine dinucleotide (NAD) biosynthesis, nicotinamide phosphoribosyltransferase (NAMPT; 608764), and levels of NAD+ display circadian oscillations that are regulated by the core clock machinery in mice. Inhibition of NAMPT promotes oscillation of the clock gene Per2 by releasing CLOCK:BMAL1 (602550) from suppression by SIRT1 (604479). In turn, the circadian transcription factor CLOCK binds to and upregulates Nampt, thus completing a feedback loop involving NAMPT/NAD+ and SIRT1/CLOCK:BMAL1.

Nakahata et al. (2009) showed that intracellular NAD+ levels cycle with a 24-hour rhythm, an oscillation driven by the circadian clock. CLOCK:BMAL1 regulates the circadian expression of NAMPT, an enzyme that provides a rate-limiting step in the NAD+ salvage pathway. SIRT1 is recruited to the Nampt promoter and contributes to the circadian synthesis of its own coenzyme. Using the specific inhibitor FK866, Nakahata et al. (2009) demonstrated that NAMPT is required to modulate circadian gene expression. Nakahata et al. (2009) concluded that their findings in mouse embryo fibroblasts revealed an interlocked transcriptional-enzymatic feedback loop that governs the molecular interplay between cellular metabolism and circadian rhythms.

DiTacchio et al. (2011) found that the JumonjiC and ARID domain-containing histone lysine demethylase-1a (JARID1A; 180202) forms a complex with CLOCK-BMAL1, which is recruited to the PER2 promoter. JARID1A increased histone acetylation by inhibiting histone deacetylase-1 (601241) function and enhanced transcription by CLOCK-BMAL1 in a demethylase-independent manner. Depletion of JARID1A in mammalian cells reduced PER promoter histone acetylation, dampened expression of canonic circadian genes, and shortened the period of circadian rhythms. Drosophila lines with reduced expression of the JARID1A homolog 'lid' had lowered Per expression and similarly altered circadian rhythms. DiTacchio et al. (2011) concluded that JARID1A thus has a nonredundant role in circadian oscillator function.

Koike et al. (2012) interrogated the transcriptional architecture of the circadian transcriptional regulatory loop on a genome scale in mouse liver and found a stereotyped, time-dependent pattern of transcription factor binding, RNA polymerase II (see 180660) recruitment, RNA expression, and chromatin states. They found that the circadian transcriptional cycle of the clock consists of 3 distinct phases: a poised state, a coordinated de novo transcriptional activation state, and a repressed state. Only 22% of mRNA cycling genes are driven by de novo transcription, suggesting that both transcriptional and posttranscriptional mechanisms underlie the mammalian circadian clock. Koike et al. (2012) also found that circadian modulation of RNA polymerase II recruitment and chromatin remodeling occurs on a genomewide scale far greater than that seen previously by gene expression profiling.

Morf et al. (2012) showed that simulated body temperature cycles, but not peripheral oscillators, controlled the rhythmic expression of cold-inducible RNA-binding protein (CIRBP; 602649) in cultured fibroblasts. In turn, loss-of-function experiments indicated that CIRBP was required for high-amplitude circadian gene expression. The transcriptomewide identification of CIRBP-bound RNAs by a biotin-streptavidin-based crosslinking and immunoprecipitation (CLIP) procedure revealed several transcripts encoding circadian oscillator proteins, including CLOCK. Moreover, CLOCK accumulation was strongly reduced in CIRBP-depleted fibroblasts. Because ectopic expression of CLOCK improved circadian gene expression in these cells, Morf et al. (2012) concluded that CIRBP confers robustness to circadian oscillators through regulation of CLOCK expression.

Using chromatin immunoprecipitation analysis, Annayev et al. (2014) found that Bmal1, Clock, and Cry1 bound the promoter region of mouse Ciart (615782), which they called Gm129. Bmal1 and Cry1 rhythmically bound E-boxes in the Gm129 promoter with different binding phases. Epitope-tagged Gm129 bound endogenous Bmal1 in NIH3T3 mouse fibroblasts. Gm129 interacted with Clock-Bmal1 complexes on E-box DNA in vivo and in vitro and repressed expression of a reporter gene activated by Clock and Bmal1. The effect of Gm129 on Clock-Bmal1 activity was similar in magnitude to that of Cry1, but the function of Gm129 appeared to differ, since Gm129 could not compensate for double knockout of Cry1 and Cry2 in mice. Additional studies with Gm129 -/- mice suggested that Gm129 may modulate the phase of Clock-Bmal1-controlled transcriptional oscillations.

Independently, Anafi et al. (2014) found that mouse Ciart, which they called Chrono, interacted with Bmal1 and repressed the Bmal1-Clock transcriptional complex. Chrono repressed transcription by abrogating binding of Bmal1 to its transcriptional coactivator, Cbp (CREBBP; 600140).

Using luciferase analysis, Michael et al. (2015) that both isoforms of PASD1 (300993) repressed CLOCK-BMAL1 activity. Immunoprecipitation analysis showed interaction of PASD1 with BMAL1, but not CLOCK. PASD1 regulation of CLOCK-BMAL1 activity occurred through the PASD1 C-terminal coiled-coil domain acting on the exon 19-encoded region of CLOCK. Introduction of PASD1 into cells attenuated the robustness of the molecular circadian oscillator. The authors noted that PASD1 is expressed exclusively in germline tissues in healthy individuals, but that it can be induced in cells of somatic origin upon oncogenic transformation. Knockdown of PASD1 in human cancer cells resulted in a significant increase in amplitude of circadian cycling. Michael et al. (2015) concluded that PASD1 suppresses circadian clock function when upregulated in human cancer and provides a molecular link from oncogenic transformation to suppression of circadian rhythms.


Gene Structure

Steeves et al. (1999) determined that the human CLOCK gene contains 20 exons.

King et al. (1997) found that the mouse Clock gene contains 24 exons and spans about 100 kb.


Mapping

By radiation hybrid analysis, Steeves et al. (1999) mapped the human CLOCK gene to chromosome 4q12.

King et al. (1997) mapped the Clock gene by linkage analysis to the midportion of mouse chromosome 5. Using comparative genomic sequence analysis, Wilsbacher et al. (2000) localized the mouse Clock gene to chromosome 5 in a region showing homology of synteny with human chromosome 4.


Molecular Genetics

The CLOCK gene contains a highly conserved polyglutamine motif that in humans is encoded by CAG repeats. In view of the involvement of CAG repeat expansion in a number of neuropsychiatric disorders, Saleem et al. (2001) sought to determine the polymorphic status of CAG repeats at the CLOCK locus in humans. An analysis of 190 unrelated individuals, who included patients suffering from bipolar disorder (see, e.g., 125480) or schizophrenia (see 181500), indicated that the repeat, which consists of 6 CAG triplets, is not polymorphic in humans. On the other hand, further analysis of the repeat in nonhuman primates and other organisms demonstrated that the glutamine stretch is shortest in humans and baboons and longest in Drosophila and zebrafish. The gene is highly polymorphic in various Drosophila species. Unlike most other microsatellites, the CAG repeat stretch at the CLOCK locus in humans is smaller than its homologs in nonhuman primates. Saleem et al. (2001) proposed that glutamine repeat size is functionally important in the CLOCK gene and thus tightly regulated. Variation in repeat number is probably deleterious to the individual, resulting in the maintenance of a short and invariable repeat structure in the human population.


Animal Model

King et al. (1997) noted that a spontaneous mutation, 'tau,' found in the golden hamster shortens the circadian period by about 2 hours in heterozygous mutants and by about 4 hours in homozygous mutants. Vitaterna et al. (1994) identified a single-gene mutation induced in the mouse by ethylnitrosourea (ENU) that dramatically altered the phenotypic expression of circadian rhythmicity. This mutation, named 'Clock,' affected the length of the free-running period and the persistence of circadian rhythmicity in constant darkness. King et al. (1997) determined that the ENU-induced mutant Clock allele is an A-to-T nucleotide transversion in a splice donor site caused exon skipping and deletion of 51 amino acids in the Clock protein.

Wager-Smith and Kay (2000) reviewed the genetic dissection of the circadian regulation of behavior through phenotype-driven mutagenesis screens in fly and mice. Cloning and biochemical analysis of evolutionarily conserved proteins led to detailed molecular insight into the clock mechanism. Few behaviors enjoyed the degree of understanding that existed for circadian rhythms at the genetic, cellular, and anatomic levels. They discussed the prospects for using homologs of the fly and mouse genes as candidates in the study of human circadian dysrhythmias: Per1, Per2, Per3 (603427), Tim, Clock, cycle, double-time (CSNK1E; 600863), Cry1, and Cry2.

The Clock mutation lengthens periodicity and reduces amplitude of circadian rhythms in mice. The effects of Clock are cell intrinsic and can be observed at the level of single neurons in the suprachiasmatic nucleus. To address how cells of contrasting genotype functionally interact in vivo to control circadian behavior, Low-Zeddies and Takahashi (2001) analyzed a series of Clock mutant-mouse aggregation chimeras. Circadian behavior in Clock/Clock-wildtype (+/+) chimeric individuals was determined by the proportion of mutant versus normal cells. Significantly, a number of intermediate phenotypes, including Clock/+ phenocopies and novel combinations of the parental behavioral characteristics, were seen in balanced chimeras. The results demonstrated that complex integration of cellular phenotypes determines the generation and expression of coherent circadian rhythms at the organismal level.

Nakamura et al. (2002) recorded the spontaneous discharges of individual neurons in the suprachiasmatic nucleus of Clock mutant mice over 5 days in organotypic slice cultures and dispersed cell cultures using a multielectrode dish. Circadian rhythms with periods of about 27 hours were detected in 77% of slice cultures and 15% of dispersed cell cultures derived from Clock -/- homozygotes. Nakamura et al. (2002) concluded that the Clock mutation lengthens the circadian period but does not abolish the circadian oscillation, and suggested an important role of intercellular communication in the expression of circadian rhythm in the suprachiasmatic nucleus.

Pando et al. (2002) studied the rhythmic behavior of mouse embryo fibroblasts (MEFs) surgically implanted in mice with different circadian rhythm deficiencies. MEFs from Per1 -/- mice had a much shorter period in culture than did tissues in the intact animal. When implanted back into mice, however, the Per1 -/- MEFs took on the rhythmic characteristics of the host. A functioning clock was found to be required for oscillations in the target tissues, as arrhythmic clock c/c MEFs remained arrhythmic in implants. These results demonstrated that SCN hierarchical dominance can compensate for severe intrinsic genetic defects in peripheral clocks, but cannot induce rhythmicity in clock-defective tissues.

Turek et al. (2005) found that homozygous Clock mutant mice have a greatly attenuated diurnal feeding rhythm, are hyperphagic and obese, and develop a metabolic syndrome of hyperleptinemia, hyperlipidemia, hepatic steatosis, hyperglycemia, and hypoinsulinemia. Expression of transcripts encoding selected hypothalamic peptides associated with energy balance was attenuated in the Clock mutant mice. Turek et al. (2005) concluded that the circadian clock gene network plays an important role in mammalian energy balance.

McClung et al. (2005) found that Clock-knockout mice showed increased baseline activity, increased locomotor sensitization to cocaine, and increased drug reward compared to wildtype animals. Compared to wildtype, Clock-knockout mice had increased levels of tyrosine hydroxylase (TH; 191290) mRNA and TH phosphorylation, indicating increased dopaminergic transmission, in the midbrain ventral tegmental area (VTA), which is a key component of the brain's reward circuit. McClung et al. (2005) concluded that the circadian-associated Clock protein is involved in regulating dopaminergic transmission in the brain's reward circuit.

In rat/mouse neuronal cell lines, Yujnovsky et al. (2006) found that the dopamine D2 receptor (DRD2; 126450) mediated stimulation of Clock:Bmal1 activity and increased expression of the Per1 gene. The response was mediated by the transcriptional coactivator CREB-binding protein (CREBBP; 600140). Clock:Bmal1-dependent activation and light inducibility of Per1 transcription were drastically dampened in the retinas of Drd2-null mice. The findings suggested a physiologic link between photic input, dopamine signaling, and molecular clock machinery.

Udo et al. (2004) showed that Clock deletion increased the ability of mice to be entrained to different light-dark cycles. Wildtype mice entrained to only a 24-hour light-dark cycle, whereas Clock-null mice could entrain to 24-, 28-, and 32-hour light-dark cycles. Clock deletion also exaggerated the up- or downregulation of Per genes in response to light.

DeBruyne et al. (2006) found that Clock-null mice showed altered response to light, but they continued to express robust circadian locomotor rhythms, even under conditions of constant darkness. The circadian rhythm of Per1, Per2, Rev-erb-alpha, and Bmal1 expression in the suprachiasmatic nucleus of Clock-null mice was similar to that in wildtype mice, but the amplitudes of Per1, Rev-erb-alpha, and Bmal1 rhythms were reduced in Clock-null mice. DeBruyne et al. (2006) concluded that circadian rhythms do not absolutely require CLOCK-BMAL1 heterodimers.

Roybal et al. (2007) found that mice with disruption of the Clock gene demonstrated a behavioral profile similar to human mania, including hyperactivity, decreased sleep, lowered depression-like behavior, lower anxiety, and an increase in the reward value for cocaine, sucrose, and medial forebrain bundle stimulation. Chronic administration of the mood stabilizer lithium returned many of these behaviors to wildtype levels. In addition, the Clock mutant mice had an increase in dopaminergic activity in the ventral tegmental area. Targeted viral delivery of the Clock gene to the ventral tegmental area resulted in decreased hyperactivity. Roybal et al. (2007) concluded that Clock has a role in the dopaminergic system in regulating mood and behavior.

Marcheva et al. (2010) showed that mouse pancreatic islets possessed self-sustained circadian gene and protein oscillations of Clock and Bmal1. The phase of oscillation of islet genes involved in growth, glucose metabolism, and insulin signaling was delayed in circadian mutant mice, and both Clock and Bmal1 mutants showed impaired glucose tolerance, reduced insulin secretion, and defects in size and proliferation of pancreatic islets that worsened with age. Clock disruption led to transcriptome-wide alterations in the expression of islet genes involved in growth, survival, and synaptic vesicle assembly. Conditional ablation of the pancreatic clock caused diabetes mellitus due to defective beta-cell function at the very latest stage of stimulus-secretion coupling. Marcheva et al. (2010) concluded that the beta-cell clock has a role in coordinating insulin secretion with the sleep-wake cycle and that ablation of the pancreatic clock can trigger the onset of diabetes mellitus.


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  19. McNamara, P., Seo, S., Rudic, R. D., Sehgal, A., Chakravarti, D., FitzGerald, G. A. Regulation of CLOCK and MOP4 by nuclear hormone receptors in the vasculature: a humoral mechanism to reset a peripheral clock. Cell 105: 877-889, 2001. [PubMed: 11439184, related citations] [Full Text]

  20. Michael, A. K., Harvey, S. L., Sammons, P. J., Anderson, A. P., Kopalle, H. M., Banham, A. H., Partch, C. L. Cancer/testis antigen PASD1 silences the circadian clock. Molec. Cell 58: 743-754, 2015. [PubMed: 25936801, related citations] [Full Text]

  21. Morf, J., Rey, G., Schneider, K., Stratmann, M., Fujita, J., Naef, F., Schibler, U. Cold-inducible RNA-binding protein modulates circadian gene expression posttranscriptionally. Science 338: 379-383, 2012. [PubMed: 22923437, related citations] [Full Text]

  22. Nakahata, Y., Sahar, S., Astarita, G., Kaluzova, M., Sassone-Corsi, P. Circadian control of the NAD+ salvage pathway by CLOCK:SIRT1. Science 324: 654-657, 2009. [PubMed: 19286518, related citations] [Full Text]

  23. Nakamura, W., Honma, S., Shirakawa, T., Honma, K. hClock mutation lengthens the circadian period without damping rhythms in individual SCN neurons. Nature Neurosci. 5: 399-400, 2002. [PubMed: 11953751, related citations] [Full Text]

  24. O'Neill, J. S., Maywood, E. S., Chesham, J. E., Takahashi, J. S., Hastings, M. H. cAMP-dependent signaling as a core component of the mammalian circadian pacemaker. Science 320: 949-953, 2008. [PubMed: 18487196, related citations] [Full Text]

  25. Pando, M. P., Morse, D., Cermakian, N., Sassone-Corsi, P. Phenotypic rescue of a peripheral clock genetic defect via SCN hierarchical dominance. Cell 110: 107-117, 2002. [PubMed: 12151001, related citations] [Full Text]

  26. Ramsey, K. M., Yoshino, J., Brace, C. S., Abrassart, D., Kobayashi, Y., Marcheva, B., Hong, H.-K., Chong, J. L., Buhr, E. D., Lee, C., Takahashi, J. S., Imai, S., Bass, J. Circadian clock feedback cycle through NAMPT-mediated NAD+ biosynthesis. Science 324: 651-655, 2009. [PubMed: 19299583, related citations] [Full Text]

  27. Reppert, S. M., Weaver, D. R. Forward genetic approach strikes gold: cloning of a mammalian Clock gene. Cell 89: 487-490, 1997. [PubMed: 9160739, related citations] [Full Text]

  28. Roybal, K., Theobold, D., Graham, A., DiNieri, J. A., Russo, S. J., Krishnan, V., Chakravarty, S., Peevey, J., Oehrlein, N., Birnbaum, S., Vitaterna, M. H., Orsulak, P., Takahashi, J. S., Nestler, E. J., Carlezon, W. A., Jr., McClung, C. A. Mania-like behavior induced by disruption of CLOCK. Proc. Nat. Acad. Sci. 104: 6406-6411, 2007. [PubMed: 17379666, related citations] [Full Text]

  29. Rutter, J., Reick, M., Wu, L. C., McKnight, S. L. Regulation of Clock and NPAS2 DNA binding by the redox state of NAD cofactors. Science 293: 510-514, 2001. [PubMed: 11441146, related citations] [Full Text]

  30. Saleem, Q., Anand, A., Jain, S., Brahmachari, S. K. The polyglutamine motif is highly conserved at the Clock locus in various organisms and is not polymorphic in humans. Hum. Genet. 109: 136-142, 2001. [PubMed: 11511917, related citations] [Full Text]

  31. Shearman, L. P., Sriram, S., Weaver, D. R., Maywood, E. S., Chaves, I., Zheng, B., Kume, K., Lee, C. C., van der Horst, G. T. J., Hastings, M. H., Reppert, S. M. Interacting molecular loops in the mammalian circadian clock. Science 288: 1013-1019, 2000. [PubMed: 10807566, related citations] [Full Text]

  32. Steeves, T. D. L., King, D. P., Zhao, Y., Sangoram, A. M., Du, F., Bowcock, A. M., Moore, R. Y., Takahashi, J. S. Molecular cloning and characterization of the human CLOCK gene: expression in the suprachiasmatic nuclei. Genomics 57: 189-200, 1999. [PubMed: 10198158, related citations] [Full Text]

  33. Turek, F. W., Joshu, C., Kohsaka, A., Lin, E., Ivanova, G., McDearmon, E., Laposky, A., Losee-Olson, S., Easton, A., Jensen, D. R., Eckel, R. H., Takahashi, J. S., Bass, J. Obesity and metabolic syndrome in circadian Clock mutant mice. Science 308: 1043-1045, 2005. [PubMed: 15845877, related citations] [Full Text]

  34. Udo, R., Hamada, T., Horikawa, K., Iwahana, E., Miyakawa, K., Otsuka, K., Shibata, S. The role of Clock in the plasticity of circadian entrainment. Biochem. Biophys. Res. Commun. 318: 893-898, 2004. [PubMed: 15147955, related citations] [Full Text]

  35. Ueda, H. R., Hayashi, S., Chen, W., Sano, M., Machida, M., Shigeyoshi, Y., Iino, M., Hashimoto, S. System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nature Genet. 37: 187-192, 2005. [PubMed: 15665827, related citations] [Full Text]

  36. Vitaterna, M. H., King, D. P., Chang, A.-M., Kornhauser, J. M., Lowrey, P. L., McDonald, J. D., Dove, W. F., Pinto, L. H., Turek, F. W., Takahashi, J. S. Mutagenesis and mapping of a mouse gene, Clock, essential for circadian behavior. Science 264: 719-725, 1994. [PubMed: 8171325, related citations] [Full Text]

  37. Wager-Smith, K., Kay, S. A. Circadian rhythm genetics: from flies to mice to humans. Nature Genet. 26: 23-27, 2000. [PubMed: 10973243, related citations] [Full Text]

  38. Wilsbacher, L. D., Sangoram, A. M., Antoch, M. P., Takahashi, J. S. The mouse Clock locus: sequence and comparative analysis of 204 kb from mouse chromosome 5. Genome Res. 10: 1928-1940, 2000. [PubMed: 11116088, related citations] [Full Text]

  39. Yujnovsky, I., Hirayama, J., Doi, M., Borrelli, E., Sassone-Corsi, P. Signaling mediated by the dopamine D2 receptor potentiates circadian regulation by CLOCK:BMAL1. Proc. Nat. Acad. Sci. 103: 6386-6391, 2006. [PubMed: 16606840, related citations] [Full Text]


Paul J. Converse - updated : 03/28/2017
Patricia A. Hartz - updated : 5/12/2014
Ada Hamosh - updated : 11/7/2012
Patricia A. Hartz - updated : 3/2/2012
Ada Hamosh - updated : 11/22/2011
Ada Hamosh - updated : 8/24/2010
Patricia A. Hartz - updated : 8/10/2010
Ada Hamosh - updated : 7/28/2009
Ada Hamosh - updated : 6/11/2008
Ada Hamosh - updated : 4/22/2008
Patricia A. Hartz - updated : 8/30/2007
Cassandra L. Kniffin - updated : 5/29/2007
Cassandra L. Kniffin - updated : 5/24/2006
Patricia A. Hartz - updated : 9/28/2005
Ada Hamosh - updated : 8/5/2005
Cassandra L. Kniffin - updated : 7/11/2005
Ada Hamosh - updated : 6/2/2005
Ada Hamosh - updated : 2/21/2003
Stylianos E. Antonarakis - updated : 7/29/2002
Ada Hamosh - updated : 4/16/2002
Victor A. McKusick - updated : 9/5/2001
Stylianos E. Antonarakis - updated : 7/5/2001
Stylianos E. Antonarakis - updated : 4/26/2001
Paul J. Converse - updated : 4/9/2001
Victor A. McKusick - updated : 8/28/2000
Ada Hamosh - updated : 5/11/2000
Ada Hamosh - updated : 8/17/1998
Creation Date:
Victor A. McKusick : 6/6/1997
carol : 09/08/2025
mgross : 03/28/2017
mgross : 05/12/2014
mgross : 5/12/2014
mgross : 2/8/2013
mgross : 2/5/2013
alopez : 11/7/2012
terry : 11/7/2012
mgross : 3/2/2012
alopez : 11/22/2011
terry : 11/22/2011
mgross : 8/24/2010
terry : 8/24/2010
mgross : 8/18/2010
mgross : 8/16/2010
terry : 8/10/2010
alopez : 8/4/2009
terry : 7/28/2009
alopez : 6/13/2008
terry : 6/11/2008
alopez : 5/15/2008
terry : 4/22/2008
mgross : 10/8/2007
terry : 8/30/2007
wwang : 7/6/2007
ckniffin : 5/29/2007
wwang : 6/5/2006
ckniffin : 5/24/2006
mgross : 10/6/2005
terry : 9/28/2005
terry : 8/5/2005
mgross : 8/3/2005
wwang : 7/29/2005
ckniffin : 7/11/2005
alopez : 6/3/2005
terry : 6/2/2005
alopez : 2/24/2003
alopez : 2/24/2003
terry : 2/21/2003
mgross : 7/29/2002
alopez : 4/30/2002
alopez : 4/17/2002
terry : 4/16/2002
alopez : 9/11/2001
terry : 9/5/2001
cwells : 9/4/2001
cwells : 8/29/2001
cwells : 8/28/2001
terry : 8/27/2001
mgross : 7/5/2001
mgross : 4/26/2001
mgross : 4/9/2001
alopez : 8/28/2000
terry : 8/28/2000
alopez : 5/11/2000
alopez : 7/20/1999
alopez : 6/8/1999
carol : 4/27/1999
carol : 8/17/1998
dholmes : 2/10/1998
mark : 1/25/1998
terry : 1/21/1998
mark : 6/6/1997
mark : 6/6/1997

* 601851

CLOCK CIRCADIAN REGULATOR; CLOCK


Alternative titles; symbols

CIRCADIAN LOCOMOTOR OUTPUT CYCLES KAPUT
CLOCK, MOUSE, HOMOLOG OF


HGNC Approved Gene Symbol: CLOCK

Cytogenetic location: 4q12   Genomic coordinates (GRCh38) : 4:55,427,903-55,546,909 (from NCBI)


TEXT

Description

Circadian rhythmicity of biologic processes is a fundamental property of all eukaryotic and some prokaryotic organisms. These rhythms are driven by an internal time-keeping system. Changes in the external environment, particularly in the light-dark cycle, entrain this biologic clock. Under constant environmental conditions devoid of time cues, rhythms driven by the biologic clock show a period near, but usually not equal to, 24 hours. The bilaterally paired suprachiasmatic nuclei (SCN) of the hypothalamus are thought to contain the master circadian clock that regulates most, if not all, circadian rhythms in mammals. The CLOCK gene encodes a basic helix-loop-helix (bHLH)-PAS (see 603349) transcription factor that is essential for circadian rhythm (King et al., 1997).


Cloning and Expression

King et al. (1997) used positional cloning to identify the Clock gene in mice. They found that it is a large transcription unit from which mRNA transcripts of 7.5 and approximately 10 kb arise. The gene encodes an 855-amino acid polypeptide that is a novel member of the bHLH-PAS family of transcription factors and has features predicting DNA binding, protein dimerization, and activation domains. King et al. (1997) noted that the circadian rhythm gene of Drosophila 'Period' (PER1; 602260) also encodes a PAS domain-containing Clock protein, which suggests that this motif may define an evolutionarily conserved feature of the circadian Clock mechanism.

As a complementary approach to positional cloning, Antoch et al. (1997) used in vivo complementation with BAC clones expressed in transgenic mice to identify the circadian Clock gene. A 140-kb BAC transgene completely rescued both the long-period and the loss-of-rhythm phenotypes in Clock mutant mice. Analysis with overlapping BAC transgenes demonstrated that a large transcriptional unit represents the Clock gene and encodes a novel bHLH-PAS domain protein. Overexpression of the Clock gene shortened period length beyond the wildtype range, which provided additional evidence that Clock is an integral component of the circadian pacemaking system. Taken together, their results provided proof of the principle that 'cloning by rescue' is an efficient and definitive method in mice.

By searching an EST database and screening a hypothalamus cDNA library, Steeves et al. (1999) obtained a human cDNA encoding CLOCK. The deduced 846-amino acid protein retains the structural features of the mouse protein, with which it is 96% identical. Northern blot analysis revealed expression of a predominant 10.0-kb transcript and a major 8.0-kb transcript in most tissues tested, with highest levels in testis and skeletal muscle and lowest levels in lung, liver, and thymus. A minor 4.0-kb transcript was also detected in testis only. Elevated levels of the 10-kb transcript were present in cerebellum. In situ hybridization analysis demonstrated intense expression of CLOCK in the suprachiasmatic nucleus, the supraoptic nucleus, and the cerebellum.

Doi et al. (2006) reported that CLOCK has a domain structure similar to that of ACTR (NCOA3; 601937), a member of the SRC family of histone acetyltransferases (HATs). Both proteins contain an N-terminal bHLH domain, followed by 2 PAS domains, a serine-rich nuclear receptor interaction domain (NRID), and a C-terminal glutamine-rich region. The glutamine-rich region contains an acetyl-CoA-binding motif, a hallmark of HATs.


Gene Function

Reppert and Weaver (1997) commented that studies on circadian rhythm would yield new insight into the control of sleep and its disorders in humans, the effects of shift work and jet lag, and sleep disorders that occur with advanced age. They reviewed the topic of circadian rhythms and illustrated 3 hypothetical models of how Clock might function as a circadian clock element. They pointed out that 1997 was the silver anniversary of the discovery that the suprachiasmatic nuclei have a circadian clock function.

Gekakis et al. (1998) used a yeast 2-hybrid screen to find proteins that interact with the Clock protein. The mouse Bmal1 (ARNTL; 602550) protein was isolated and found to dimerize with Clock. Bmal1 is found in the suprachiasmatic nucleus and the retina, along with Clock and Per1. The Clock-Bmal1 heterodimers are able to bind DNA and activate transcription from an E-box element (CACGTG), a type of transcription factor-binding site, found adjacent to mouse Per1 and to the Drosophila Per gene. Mutant Clock from the dominant-negative Clock allele forms heterodimers with Bmal1 that bind DNA but fail to activate transcription. The authors concluded that Clock-Bmal1 heterodimers appear to drive the positive component of Per transcriptional oscillations.

Darlington et al. (1998) showed that the Drosophila Clock gene heterodimerizes with the Drosophila homolog of BMAL1. These proteins acted through an E-box sequence in the Per promoter and through an 18-bp element encompassing an E-box sequence in the Timeless (TIM; 603887) promoter to activate Per and Tim transcription. Period and Timeless proteins blocked Clock's ability to activate Tim and Per promoters via the E-box. The authors therefore concluded that Clock drives expression of Period and Timeless, which in turn inhibit Clock's activity and close the circadian loop.

By yeast 2-hybrid analysis of human umbilical vein endothelial cell (HUVEC) cDNA, Maemura et al. (2000) found that CLIF (ARNTL2; 614517) interacted with CLOCK. Mobility shift assays and mutation analysis showed that CLIF formed a heterodimer with CLOCK and bound to the E-box of the PER1 promoter. Coexpression of CLIF with CLOCK in HUVECs resulted in elevated CLOCK-dependent PAI1 (SERPINE1; 173360) expression, and mutation of the E-boxes within the PAI1 promoter abrogated binding by CLIF/CLOCK. PER2 (603426) and CRY1 (601933) inhibited CLIF/CLOCK-dependent transactivation of the PAI1 promoter.

McNamara et al. (2001) reported a hormone-dependent interaction of the nuclear receptors RARA (180240) and RXRA (180245) with CLOCK and MOP4 (NPAS2; 603347). They found that these interactions negatively regulate CLOCK-BMAL1 and MOP4-BMAL1 heterodimer-mediated transcriptional activation of clock gene expression in vascular cells. MOP4 exhibited a robust rhythm in the vasculature, and retinoic acid could phase shift PER2 mRNA rhythmicity in vivo and in serum-induced smooth muscle cells in vitro, providing a molecular mechanism for hormonal control of clock gene expression. McNamara et al. (2001) proposed that circadian or periodic availability of nuclear hormones may play a critical role in resetting a peripheral vascular clock.

Shearman et al. (2000) demonstrated that in the mouse, the core mechanism for the master circadian clock consists of interacting positive and negative transcription and translation feedback loops. Analysis of Clock/Clock mutant mice, homozygous Per2 mutants, and Cry-deficient mice revealed substantially altered Bmal1 rhythms, consistent with a dominant role of Per2 in the positive regulation of the Bmal1 loop. In vitro analysis of Cry inhibition of Clock:Bmal1-mediated transcription showed that the inhibition was through direct protein-protein interactions, independent of the Per and Tim proteins. Per2 is a positive regulator of the Bmal1 loop, and Cry1 and Cry2 (603732) are the negative regulators of the Period and Cryptochrome cycles.

Rutter et al. (2001) demonstrated that the DNA binding activity of the Clock:BMAL1 and NPAS2:BMAL1 heterodimers is regulated by the redox state of nicotinamide adenine dinucleotide (NAD) cofactors in a purified system. The reduced forms of the redox cofactors, NAD(H) and NADP(H), strongly enhance DNA binding of the Clock:BMAL1 and NPAS2:BMAL1 heterodimers, whereas the oxidized forms inhibit. Rutter et al. (2001) suggested the possibility that food, neuronal activity, or both may entrain the circadian clock by direct modulation of cellular redox state.

Etchegaray et al. (2003) demonstrated that transcriptional regulation of the core clock mechanism in mouse liver is accompanied by rhythms in H3 histone (see 602810) acetylation, and that H3 acetylation is a potential target of the inhibitory action of Cry. The promoter regions of the Per1, Per2, and Cry1 genes exhibited circadian rhythms in H3 acetylation and RNA polymerase II (see 180660) binding that were synchronous with the corresponding steady-state mRNA rhythms. The histone acetyltransferase p300 (602700) precipitated with Clock in vivo in a time-dependent manner. Moreover, the Cry proteins inhibited a p300-induced increase in Clock/Bmal1-mediated transcription. Etchegaray et al. (2003) concluded that the delayed timing of the Cry1 mRNA rhythm, relative to the Per rhythms, was due to the coordinated activities of Rev-Erb-alpha (602408) and Clock/Bmal1, and defined a novel mechanism for circadian phase control.

Kondratov et al. (2003) showed that circadian regulation of nuclear Clock accumulation in mouse embryonic fibroblasts was dependent on Bmal1 expression. Formation of Clock-Bmal1 dimers following ectopic coexpression in human cells resulted in codependent phosphorylation of both proteins that was tightly coupled to Clock nuclear translocation and degradation. Binding-dependent coregulation was specific for Clock-Bmal1 interaction, as no other PAS domain protein able to form complexes with either Clock or Bmal1 could induce similar effects. All events were tightly coupled with Clock-Bmal1-dependent transcriptional activation, indicating their functional role in the regulation of the circadian clock.

Toward a system-level understanding of the transcriptional circuitry regulating circadian clocks, Ueda et al. (2005) identified clock-controlled elements on 16 clock and clock-controlled genes in a comprehensive surveillance of evolutionarily conserved cis elements and measurement of the transcriptional dynamics. Ueda et al. (2005) found that E boxes (CACGTG) and E-prime boxes (CACGTT) controlled the expression of Per1 (602260), Nr1d2 (602304), Per2, Nr1d1 (602408), Dbp (124097), Bhlhb2 (604256), and Bhlhb3 (606200) transcription following a repressor-precedes-activator pattern, resulting in delayed transcriptional activity. RevErbA/ROR (600825)-binding elements regulated the transcriptional activity of Arntl, Npas2, Nfil3 (605237), Clock, Cry1, and Rorc (602943) through a repressor-precedes-activator pattern as well. DBP/E4BP4-binding elements controlled the expression of Per1, Per2, Per3, Nr1d1, Nr1d2, Rora, and Rorb (601972) through a repressor-antiphasic-to-activator mechanism, which generates high-amplitude transcriptional activity. Ueda et al. (2005) suggested that regulation of E/E-prime boxes is a topologic vulnerability in mammalian circadian clocks, a concept that had been functionally verified using in vitro phenotype assay systems.

Doi et al. (2006) showed that mouse Clock had HAT activity against histones H3 and H4 (see 602822). In the presence of Bmal1, the relative HAT activity of Clock was enhanced about 4-fold. Mutations in the putative acetyl CoA-binding site of Clock reduced HAT activity. The HAT activity of Clock was essential to rescue circadian rhythmicity and activation of clock genes in Clock mutant mouse embryonic fibroblasts.

Hirayama et al. (2007) demonstrated that CLOCK acetylates a nonhistone substrate: its own partner, BMAL1 (602550), which it specifically acetylates on a unique, highly conserved lys537 residue. BMAL1 undergoes rhythmic acetylation in mouse liver, with a timing that parallels the downregulation of circadian transcription of clock-controlled genes. BMAL1 acetylation facilitates recruitment of CRY1 to CLOCK-BMAL1, thereby promoting transcriptional repression. Importantly, ectopic expression of a K537R-mutated BMAL1 was not able to rescue circadian rhythmicity in a cellular model of peripheral clock. Hirayama et al. (2007) concluded that these findings revealed that the enzymatic interplay between 2 clock core components is crucial for the circadian machinery.

O'Neill et al. (2008) showed that cAMP signaling constitutes an additional bona fide component of the oscillatory network of the circadian rhythm. They proposed that daily activation of cAMP signaling, driven by the transcriptional oscillator, in turn sustains progression of transcriptional rhythms. In this way, clock output constitutes an input to subsequent cycles.

Ramsey et al. (2009) reported that both the rate-limiting enzyme in mammalian nicotinamide adenine dinucleotide (NAD) biosynthesis, nicotinamide phosphoribosyltransferase (NAMPT; 608764), and levels of NAD+ display circadian oscillations that are regulated by the core clock machinery in mice. Inhibition of NAMPT promotes oscillation of the clock gene Per2 by releasing CLOCK:BMAL1 (602550) from suppression by SIRT1 (604479). In turn, the circadian transcription factor CLOCK binds to and upregulates Nampt, thus completing a feedback loop involving NAMPT/NAD+ and SIRT1/CLOCK:BMAL1.

Nakahata et al. (2009) showed that intracellular NAD+ levels cycle with a 24-hour rhythm, an oscillation driven by the circadian clock. CLOCK:BMAL1 regulates the circadian expression of NAMPT, an enzyme that provides a rate-limiting step in the NAD+ salvage pathway. SIRT1 is recruited to the Nampt promoter and contributes to the circadian synthesis of its own coenzyme. Using the specific inhibitor FK866, Nakahata et al. (2009) demonstrated that NAMPT is required to modulate circadian gene expression. Nakahata et al. (2009) concluded that their findings in mouse embryo fibroblasts revealed an interlocked transcriptional-enzymatic feedback loop that governs the molecular interplay between cellular metabolism and circadian rhythms.

DiTacchio et al. (2011) found that the JumonjiC and ARID domain-containing histone lysine demethylase-1a (JARID1A; 180202) forms a complex with CLOCK-BMAL1, which is recruited to the PER2 promoter. JARID1A increased histone acetylation by inhibiting histone deacetylase-1 (601241) function and enhanced transcription by CLOCK-BMAL1 in a demethylase-independent manner. Depletion of JARID1A in mammalian cells reduced PER promoter histone acetylation, dampened expression of canonic circadian genes, and shortened the period of circadian rhythms. Drosophila lines with reduced expression of the JARID1A homolog 'lid' had lowered Per expression and similarly altered circadian rhythms. DiTacchio et al. (2011) concluded that JARID1A thus has a nonredundant role in circadian oscillator function.

Koike et al. (2012) interrogated the transcriptional architecture of the circadian transcriptional regulatory loop on a genome scale in mouse liver and found a stereotyped, time-dependent pattern of transcription factor binding, RNA polymerase II (see 180660) recruitment, RNA expression, and chromatin states. They found that the circadian transcriptional cycle of the clock consists of 3 distinct phases: a poised state, a coordinated de novo transcriptional activation state, and a repressed state. Only 22% of mRNA cycling genes are driven by de novo transcription, suggesting that both transcriptional and posttranscriptional mechanisms underlie the mammalian circadian clock. Koike et al. (2012) also found that circadian modulation of RNA polymerase II recruitment and chromatin remodeling occurs on a genomewide scale far greater than that seen previously by gene expression profiling.

Morf et al. (2012) showed that simulated body temperature cycles, but not peripheral oscillators, controlled the rhythmic expression of cold-inducible RNA-binding protein (CIRBP; 602649) in cultured fibroblasts. In turn, loss-of-function experiments indicated that CIRBP was required for high-amplitude circadian gene expression. The transcriptomewide identification of CIRBP-bound RNAs by a biotin-streptavidin-based crosslinking and immunoprecipitation (CLIP) procedure revealed several transcripts encoding circadian oscillator proteins, including CLOCK. Moreover, CLOCK accumulation was strongly reduced in CIRBP-depleted fibroblasts. Because ectopic expression of CLOCK improved circadian gene expression in these cells, Morf et al. (2012) concluded that CIRBP confers robustness to circadian oscillators through regulation of CLOCK expression.

Using chromatin immunoprecipitation analysis, Annayev et al. (2014) found that Bmal1, Clock, and Cry1 bound the promoter region of mouse Ciart (615782), which they called Gm129. Bmal1 and Cry1 rhythmically bound E-boxes in the Gm129 promoter with different binding phases. Epitope-tagged Gm129 bound endogenous Bmal1 in NIH3T3 mouse fibroblasts. Gm129 interacted with Clock-Bmal1 complexes on E-box DNA in vivo and in vitro and repressed expression of a reporter gene activated by Clock and Bmal1. The effect of Gm129 on Clock-Bmal1 activity was similar in magnitude to that of Cry1, but the function of Gm129 appeared to differ, since Gm129 could not compensate for double knockout of Cry1 and Cry2 in mice. Additional studies with Gm129 -/- mice suggested that Gm129 may modulate the phase of Clock-Bmal1-controlled transcriptional oscillations.

Independently, Anafi et al. (2014) found that mouse Ciart, which they called Chrono, interacted with Bmal1 and repressed the Bmal1-Clock transcriptional complex. Chrono repressed transcription by abrogating binding of Bmal1 to its transcriptional coactivator, Cbp (CREBBP; 600140).

Using luciferase analysis, Michael et al. (2015) that both isoforms of PASD1 (300993) repressed CLOCK-BMAL1 activity. Immunoprecipitation analysis showed interaction of PASD1 with BMAL1, but not CLOCK. PASD1 regulation of CLOCK-BMAL1 activity occurred through the PASD1 C-terminal coiled-coil domain acting on the exon 19-encoded region of CLOCK. Introduction of PASD1 into cells attenuated the robustness of the molecular circadian oscillator. The authors noted that PASD1 is expressed exclusively in germline tissues in healthy individuals, but that it can be induced in cells of somatic origin upon oncogenic transformation. Knockdown of PASD1 in human cancer cells resulted in a significant increase in amplitude of circadian cycling. Michael et al. (2015) concluded that PASD1 suppresses circadian clock function when upregulated in human cancer and provides a molecular link from oncogenic transformation to suppression of circadian rhythms.


Gene Structure

Steeves et al. (1999) determined that the human CLOCK gene contains 20 exons.

King et al. (1997) found that the mouse Clock gene contains 24 exons and spans about 100 kb.


Mapping

By radiation hybrid analysis, Steeves et al. (1999) mapped the human CLOCK gene to chromosome 4q12.

King et al. (1997) mapped the Clock gene by linkage analysis to the midportion of mouse chromosome 5. Using comparative genomic sequence analysis, Wilsbacher et al. (2000) localized the mouse Clock gene to chromosome 5 in a region showing homology of synteny with human chromosome 4.


Molecular Genetics

The CLOCK gene contains a highly conserved polyglutamine motif that in humans is encoded by CAG repeats. In view of the involvement of CAG repeat expansion in a number of neuropsychiatric disorders, Saleem et al. (2001) sought to determine the polymorphic status of CAG repeats at the CLOCK locus in humans. An analysis of 190 unrelated individuals, who included patients suffering from bipolar disorder (see, e.g., 125480) or schizophrenia (see 181500), indicated that the repeat, which consists of 6 CAG triplets, is not polymorphic in humans. On the other hand, further analysis of the repeat in nonhuman primates and other organisms demonstrated that the glutamine stretch is shortest in humans and baboons and longest in Drosophila and zebrafish. The gene is highly polymorphic in various Drosophila species. Unlike most other microsatellites, the CAG repeat stretch at the CLOCK locus in humans is smaller than its homologs in nonhuman primates. Saleem et al. (2001) proposed that glutamine repeat size is functionally important in the CLOCK gene and thus tightly regulated. Variation in repeat number is probably deleterious to the individual, resulting in the maintenance of a short and invariable repeat structure in the human population.


Animal Model

King et al. (1997) noted that a spontaneous mutation, 'tau,' found in the golden hamster shortens the circadian period by about 2 hours in heterozygous mutants and by about 4 hours in homozygous mutants. Vitaterna et al. (1994) identified a single-gene mutation induced in the mouse by ethylnitrosourea (ENU) that dramatically altered the phenotypic expression of circadian rhythmicity. This mutation, named 'Clock,' affected the length of the free-running period and the persistence of circadian rhythmicity in constant darkness. King et al. (1997) determined that the ENU-induced mutant Clock allele is an A-to-T nucleotide transversion in a splice donor site caused exon skipping and deletion of 51 amino acids in the Clock protein.

Wager-Smith and Kay (2000) reviewed the genetic dissection of the circadian regulation of behavior through phenotype-driven mutagenesis screens in fly and mice. Cloning and biochemical analysis of evolutionarily conserved proteins led to detailed molecular insight into the clock mechanism. Few behaviors enjoyed the degree of understanding that existed for circadian rhythms at the genetic, cellular, and anatomic levels. They discussed the prospects for using homologs of the fly and mouse genes as candidates in the study of human circadian dysrhythmias: Per1, Per2, Per3 (603427), Tim, Clock, cycle, double-time (CSNK1E; 600863), Cry1, and Cry2.

The Clock mutation lengthens periodicity and reduces amplitude of circadian rhythms in mice. The effects of Clock are cell intrinsic and can be observed at the level of single neurons in the suprachiasmatic nucleus. To address how cells of contrasting genotype functionally interact in vivo to control circadian behavior, Low-Zeddies and Takahashi (2001) analyzed a series of Clock mutant-mouse aggregation chimeras. Circadian behavior in Clock/Clock-wildtype (+/+) chimeric individuals was determined by the proportion of mutant versus normal cells. Significantly, a number of intermediate phenotypes, including Clock/+ phenocopies and novel combinations of the parental behavioral characteristics, were seen in balanced chimeras. The results demonstrated that complex integration of cellular phenotypes determines the generation and expression of coherent circadian rhythms at the organismal level.

Nakamura et al. (2002) recorded the spontaneous discharges of individual neurons in the suprachiasmatic nucleus of Clock mutant mice over 5 days in organotypic slice cultures and dispersed cell cultures using a multielectrode dish. Circadian rhythms with periods of about 27 hours were detected in 77% of slice cultures and 15% of dispersed cell cultures derived from Clock -/- homozygotes. Nakamura et al. (2002) concluded that the Clock mutation lengthens the circadian period but does not abolish the circadian oscillation, and suggested an important role of intercellular communication in the expression of circadian rhythm in the suprachiasmatic nucleus.

Pando et al. (2002) studied the rhythmic behavior of mouse embryo fibroblasts (MEFs) surgically implanted in mice with different circadian rhythm deficiencies. MEFs from Per1 -/- mice had a much shorter period in culture than did tissues in the intact animal. When implanted back into mice, however, the Per1 -/- MEFs took on the rhythmic characteristics of the host. A functioning clock was found to be required for oscillations in the target tissues, as arrhythmic clock c/c MEFs remained arrhythmic in implants. These results demonstrated that SCN hierarchical dominance can compensate for severe intrinsic genetic defects in peripheral clocks, but cannot induce rhythmicity in clock-defective tissues.

Turek et al. (2005) found that homozygous Clock mutant mice have a greatly attenuated diurnal feeding rhythm, are hyperphagic and obese, and develop a metabolic syndrome of hyperleptinemia, hyperlipidemia, hepatic steatosis, hyperglycemia, and hypoinsulinemia. Expression of transcripts encoding selected hypothalamic peptides associated with energy balance was attenuated in the Clock mutant mice. Turek et al. (2005) concluded that the circadian clock gene network plays an important role in mammalian energy balance.

McClung et al. (2005) found that Clock-knockout mice showed increased baseline activity, increased locomotor sensitization to cocaine, and increased drug reward compared to wildtype animals. Compared to wildtype, Clock-knockout mice had increased levels of tyrosine hydroxylase (TH; 191290) mRNA and TH phosphorylation, indicating increased dopaminergic transmission, in the midbrain ventral tegmental area (VTA), which is a key component of the brain's reward circuit. McClung et al. (2005) concluded that the circadian-associated Clock protein is involved in regulating dopaminergic transmission in the brain's reward circuit.

In rat/mouse neuronal cell lines, Yujnovsky et al. (2006) found that the dopamine D2 receptor (DRD2; 126450) mediated stimulation of Clock:Bmal1 activity and increased expression of the Per1 gene. The response was mediated by the transcriptional coactivator CREB-binding protein (CREBBP; 600140). Clock:Bmal1-dependent activation and light inducibility of Per1 transcription were drastically dampened in the retinas of Drd2-null mice. The findings suggested a physiologic link between photic input, dopamine signaling, and molecular clock machinery.

Udo et al. (2004) showed that Clock deletion increased the ability of mice to be entrained to different light-dark cycles. Wildtype mice entrained to only a 24-hour light-dark cycle, whereas Clock-null mice could entrain to 24-, 28-, and 32-hour light-dark cycles. Clock deletion also exaggerated the up- or downregulation of Per genes in response to light.

DeBruyne et al. (2006) found that Clock-null mice showed altered response to light, but they continued to express robust circadian locomotor rhythms, even under conditions of constant darkness. The circadian rhythm of Per1, Per2, Rev-erb-alpha, and Bmal1 expression in the suprachiasmatic nucleus of Clock-null mice was similar to that in wildtype mice, but the amplitudes of Per1, Rev-erb-alpha, and Bmal1 rhythms were reduced in Clock-null mice. DeBruyne et al. (2006) concluded that circadian rhythms do not absolutely require CLOCK-BMAL1 heterodimers.

Roybal et al. (2007) found that mice with disruption of the Clock gene demonstrated a behavioral profile similar to human mania, including hyperactivity, decreased sleep, lowered depression-like behavior, lower anxiety, and an increase in the reward value for cocaine, sucrose, and medial forebrain bundle stimulation. Chronic administration of the mood stabilizer lithium returned many of these behaviors to wildtype levels. In addition, the Clock mutant mice had an increase in dopaminergic activity in the ventral tegmental area. Targeted viral delivery of the Clock gene to the ventral tegmental area resulted in decreased hyperactivity. Roybal et al. (2007) concluded that Clock has a role in the dopaminergic system in regulating mood and behavior.

Marcheva et al. (2010) showed that mouse pancreatic islets possessed self-sustained circadian gene and protein oscillations of Clock and Bmal1. The phase of oscillation of islet genes involved in growth, glucose metabolism, and insulin signaling was delayed in circadian mutant mice, and both Clock and Bmal1 mutants showed impaired glucose tolerance, reduced insulin secretion, and defects in size and proliferation of pancreatic islets that worsened with age. Clock disruption led to transcriptome-wide alterations in the expression of islet genes involved in growth, survival, and synaptic vesicle assembly. Conditional ablation of the pancreatic clock caused diabetes mellitus due to defective beta-cell function at the very latest stage of stimulus-secretion coupling. Marcheva et al. (2010) concluded that the beta-cell clock has a role in coordinating insulin secretion with the sleep-wake cycle and that ablation of the pancreatic clock can trigger the onset of diabetes mellitus.


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Contributors:
Paul J. Converse - updated : 03/28/2017
Patricia A. Hartz - updated : 5/12/2014
Ada Hamosh - updated : 11/7/2012
Patricia A. Hartz - updated : 3/2/2012
Ada Hamosh - updated : 11/22/2011
Ada Hamosh - updated : 8/24/2010
Patricia A. Hartz - updated : 8/10/2010
Ada Hamosh - updated : 7/28/2009
Ada Hamosh - updated : 6/11/2008
Ada Hamosh - updated : 4/22/2008
Patricia A. Hartz - updated : 8/30/2007
Cassandra L. Kniffin - updated : 5/29/2007
Cassandra L. Kniffin - updated : 5/24/2006
Patricia A. Hartz - updated : 9/28/2005
Ada Hamosh - updated : 8/5/2005
Cassandra L. Kniffin - updated : 7/11/2005
Ada Hamosh - updated : 6/2/2005
Ada Hamosh - updated : 2/21/2003
Stylianos E. Antonarakis - updated : 7/29/2002
Ada Hamosh - updated : 4/16/2002
Victor A. McKusick - updated : 9/5/2001
Stylianos E. Antonarakis - updated : 7/5/2001
Stylianos E. Antonarakis - updated : 4/26/2001
Paul J. Converse - updated : 4/9/2001
Victor A. McKusick - updated : 8/28/2000
Ada Hamosh - updated : 5/11/2000
Ada Hamosh - updated : 8/17/1998

Creation Date:
Victor A. McKusick : 6/6/1997

Edit History:
carol : 09/08/2025
mgross : 03/28/2017
mgross : 05/12/2014
mgross : 5/12/2014
mgross : 2/8/2013
mgross : 2/5/2013
alopez : 11/7/2012
terry : 11/7/2012
mgross : 3/2/2012
alopez : 11/22/2011
terry : 11/22/2011
mgross : 8/24/2010
terry : 8/24/2010
mgross : 8/18/2010
mgross : 8/16/2010
terry : 8/10/2010
alopez : 8/4/2009
terry : 7/28/2009
alopez : 6/13/2008
terry : 6/11/2008
alopez : 5/15/2008
terry : 4/22/2008
mgross : 10/8/2007
terry : 8/30/2007
wwang : 7/6/2007
ckniffin : 5/29/2007
wwang : 6/5/2006
ckniffin : 5/24/2006
mgross : 10/6/2005
terry : 9/28/2005
terry : 8/5/2005
mgross : 8/3/2005
wwang : 7/29/2005
ckniffin : 7/11/2005
alopez : 6/3/2005
terry : 6/2/2005
alopez : 2/24/2003
alopez : 2/24/2003
terry : 2/21/2003
mgross : 7/29/2002
alopez : 4/30/2002
alopez : 4/17/2002
terry : 4/16/2002
alopez : 9/11/2001
terry : 9/5/2001
cwells : 9/4/2001
cwells : 8/29/2001
cwells : 8/28/2001
terry : 8/27/2001
mgross : 7/5/2001
mgross : 4/26/2001
mgross : 4/9/2001
alopez : 8/28/2000
terry : 8/28/2000
alopez : 5/11/2000
alopez : 7/20/1999
alopez : 6/8/1999
carol : 4/27/1999
carol : 8/17/1998
dholmes : 2/10/1998
mark : 1/25/1998
terry : 1/21/1998
mark : 6/6/1997
mark : 6/6/1997



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NOTE: OMIM is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the OMIM database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions.
OMIM® and Online Mendelian Inheritance in Man® are registered trademarks of the Johns Hopkins University.
Copyright® 1966-2026 Johns Hopkins University.
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