Skip to main content

Pathophysiology and pathogenesis of circadian rhythm sleep disorders


Metabolic, physiological and behavioral processes exhibit 24-hour rhythms in most organisms, including humans. These rhythms are driven by a system of self-sustained clocks and are entrained by environmental cues such as light-dark cycles as well as food intake. In mammals, the circadian clock system is hierarchically organized such that the master clock in the suprachiasmatic nuclei of the hypothalamus integrates environmental information and synchronizes the phase of oscillators in peripheral tissues. The transcription and translation feedback loops of multiple clock genes are involved in the molecular mechanism of the circadian system. Disturbed circadian rhythms are known to be closely related to many diseases, including sleep disorders. Advanced sleep phase type, delayed sleep phase type and nonentrained type of circadian rhythm sleep disorders (CRSDs) are thought to result from disorganization of the circadian system. Evaluation of circadian phenotypes is indispensable to understanding the pathophysiology of CRSD. It is laborious and costly to assess an individual's circadian properties precisely, however, because the subject is usually required to stay in a laboratory environment free from external cues and masking effects for a minimum of several weeks. More convenient measurements of circadian rhythms are therefore needed to reduce patients' burden. In this review, we discuss the pathophysiology and pathogenesis of CRSD as well as surrogate measurements for assessing an individual's circadian phenotype.

Mammalian circadian clock system

The circadian clock system regulates daily rhythms of physiology and behavior, such as the sleep-wake cycle and hormonal secretion, body temperature and mood [1]. These rhythms are entrained by environmental cues, light-dark (LD) cycles and food intake. In mammals, the master clock in the suprachiasmatic nuclei (SCN) of the hypothalamus incorporates environmental information and coordinates the phase of oscillators in peripheral cells, tissues and organs [2, 3]. Light is one of the most potent environmental cues that enable the organisms to adapt to the 24-hour environmental LD cycle. Photic signals are delivered from the eye to the SCN via the retinohypothalamic tract, thereby mediating the entrainment of the circadian clock system [4]. The circadian clock system involves transcription-translation negative feedback loops of multiple clock genes and posttranscriptional modification and degradation of clock proteins [46] (Figure 1). The basic helix-loop-helix and Per-Arnt-Sim transcription factors CLOCK and BMAL1 form heterodimers and activate transcription of Period 1 (Per1), Per2, Per3, Cryptochrome 1 (Cry1), Cry2 and retinoid-related orphan receptor α (Rorα), Rorβ, Rorγ, Rev-Erbα and Rev-Erbβ by binding to E-box motifs on their promoter regions. PER and CRY proteins gradually accumulate in the cytoplasm and phosphorylation of PER and CRY occurs with casein kinase Iδ (CKIδ) and CKIε. PER, CRY and CKI proteins form complexes that translocate to the nucleus and interact with CLOCK-BMAL1 heterodimers, thereby inhibiting transcription of the Per, Cry, Ror and Rev-Erb genes. Meanwhile, Bmal1 transcription is regulated positively by retinoid-related orphan receptor (ROR) and negatively by REV-ERB via the ROR element (RORE) motif on the Bmal1 promoter.

Figure 1
figure 1

Molecular mechanism of circadian clock system.

Circadian rhythm sleep disorders

A two-process model is a major model of sleep regulation. Two components, homeostatic drive and circadian drive, interact with each other and regulate the sleep-wake cycle [7]. The sleep-wake cycle is controlled by sleep homeostasis. The desire to sleep increases gradually with extended wakefulness and decreases during sleep. Additionally, sleep and wakefulness occur in turn, and the timing of their occurrence is controlled by the circadian clock system. Circadian rhythm sleep disorders (CRSDs) are defined by a persistently or recurrently disturbed sleep pattern. CRSD is attributed etiologically to alterations of the circadian timekeeping system and/or a misalignment between endogenous circadian rhythm and exogenous factors that affect sleep timing [8]. The intrinsic circadian period (τ, the free-running period of circadian rhythms in the absence of external cues) is considered to be a critical factor in the pathophysiology of CRSD [9, 10].

Familial advanced sleep phase type

Familial advanced sleep phase type (FASPT) is an autosomal dominant genetic disease characterized by extremely early involuntary sleep timing. A missense mutation in the PER2 gene has been identified in a large pedigree with FASPT. This mutation caused a change from serine to glycine at amino acid 662 (S662G) located in the CKIε binding domain of the PER2 protein and resulted in decreased PER2 phosphorylation [11]. Transgenic mice carrying the mutant S662G PER2 gene showed a shorter free-running period, τ [12]. In addition, a missense mutation in the CKIδ gene was found in another FASPT pedigree. The substitution of threonine with alanine at amino acid 44 of CKIδ reduced enzymatic activity of CKIδ, leading to decreased phosphorylation level of PER2, a target of CKI [13]. The CKIδ T44A mutation shortened τ, as well as the PER2 S662G mutation, in mice. It was previously proposed that decreased phosphorylation of PER2 stabilizes the PER2 protein, thereby enhancing nuclear accumulation of PER2 and leading to a shorter circadian period. Recent studies, however, have shown that decreased PER2 phosphorylation enhances destabilization of PER2 by increasing turnover and degradation of PER2 [14, 15]. These findings suggest that the shortening of τ observed in the FASPT models results from enhanced turnover of nuclear PER2 caused either by increased degradation or by reduced nuclear retention. FASPT patients have been reported to have a shorter period of physiological rhythms [16]. Several studies have indicated that the phosphorylation status of circadian clock proteins plays a critical role in regulating circadian periods [17, 18]. Altered τ seems to contribute to the pathogenesis of CRSD.

Delayed sleep phase type

Delayed sleep phase type (DSPT) is characterized by the inability to fall asleep and awaken at a desired time, leading to significantly later sleep onset and wake times. The pathophysiology of DSPT is attributed to longer τ, misaligned phase relationship between endogenous clock and sleep-wake cycles, reduced photic entrainment and/or altered sleep homeostasis. The human PER3 gene has multiple missense polymorphisms that cause amino acid substitution and a variable number tandem repeat (VNTR) polymorphism that encodes either four or five copies of eighteen amino acids [19]. Association studies have shown that the longer allele (five copies) in PER3 VNTR polymorphism (PER35) is associated with extreme morning preference and that the shorter allele (four copies) is associated with extreme evening preference and DSPT [20]. PER35 homozygotes have been reported to show increased slow-wave sleep in non-rapid eye movement sleep and θ/α activity during wakefulness compared to homozygotes for PER34 [21]. These results suggest that the PER3 polymorphism may be linked to homeostatic regulation of human sleep. The mouse Per3 gene was thought to be dispensable for circadian rhythm, as PER3-deficient mice did not show altered expression patterns of circadian clock genes in the SCN or altered behavioral rhythm [22]. However, PER3-deficient mice have recently been reported to have a shorter τ and advanced phase of Per1 rhythm in peripheral tissues compared to wild-type mice. The results suggest that Per3 may play a role in regulating circadian rhythms in the periphery [23]. Another group has found that PER3-deficient mice had a lower light sensitivity and suggested that Per3 may be involved in the light input pathway [24]. These findings imply that the function of the PER3 gene may contribute to the interaction between the circadian system and sleep homeostasis.

Nonentrained type (free-running type)

Nonentrained type is characterized by sleep timing that occurs with a 30-minute to 1-hour delay each day. Nonentrained sleep-wake patterns are usually observed in totally blind people [2527], whereas the nonentrained patterns are rarely observed in sighted people. It is likely that blind individuals have free-running rhythms due to the loss of photic reception (photic entrainment). Because the τ in humans is not extensively longer than 24 hours (average τ = 24.18 hours) [28] and sighted people are capable of perceiving photic signals, impaired photic entrainment as well as prolonged τ may underlie the pathophysiology of sighted patients with the nonentrained type.

Evaluation of individual circadian phenotypes

FASPT, DSPT and nonentrained type of CRSDs are thought to result from malfunction and/or maladaptation of the circadian system. Evaluation of an individual's circadian phenotype is indispensable to understanding the pathophysiology of CRSD. Individual subjects are required to stay in a laboratory environment free from external cues during a couple of weeks' time to assess circadian rhythms precisely [2830]. First, rhythmic characteristics of physiological functions (core body temperature, plasma melatonin and plasma cortisol levels) are measured to estimate individual circadian phases. Blood samples are collected over a 40-hour period under constant routine (CR) conditions where masking effects (for example, physical movement, food intake, ambient temperature and light intensity) are minimized (first CR). Next, patients undergo a 28-hour forced desynchrony (FD) protocol (9.33-hour sleep and 18.67-hour wake cycle) followed by a 40-hour CR (second CR). Individual circadian phases are assessed again during the second CR. The intrinsic circadian period, τ, is determined by the difference in circadian phase between the first and second CRs. As described herein, the CR and FD protocols are laborious and costly to perform in a clinical setting. More convenient measurements of circadian phenotypes are required to reduce the patients' burden.

Surrogate measurements for assessing circadian phenotypes

Most cells in peripheral tissues as well as cells in the SCN are equipped with circadian clock components. Brown et al. developed a lentiviral luminescence assay system using biopsy samples to measure individual circadian rhythms in fibroblasts [31]. Primary cells derived from skin biopsy samples were introduced with a circadian reporter: the Bmal1 promoter-driven luciferase gene (Bmal1-luc). The luciferase activity under the control of the Bmal1 promoter showed robust daily rhythms in individual primary fibroblast cells. Bmal1-luc rhythms were monitored for several days, and rhythmic characteristics of the luminescence rhythms were evaluated. Independently, we measured clock gene expression in primary fibroblast cells established from individual skin biopsies and observed robust Bmal1-luc rhythms (Figure 2). Brown et al. found that extreme morning types had shorter periods of fibroblast rhythms compared to extreme evening types [32]. Furthermore, they compared the period length of fibroblast rhythms with that of physiological rhythms in the same subjects and observed a significant correlation between the two rhythms. However, they did not observe long fibroblast periods in blind subjects, who had significantly longer physiological rhythms than sighted subjects [33]. The prolonged physiological period observed in the blind subjects may be caused by their previous sleep-wake cycles under constant darkness. The unaltered fibroblast period may be attributed to experimental conditions. Although the reason for this discrepancy is not yet fully understood and further studies are required, surrogate measurements using fibroblast cells should be a powerful tool for assessing individual circadian properties.

Figure 2
figure 2

Surrogate measurements for circadian phenotypes.


Evaluation of circadian phenotypes is indispensable to understanding the pathophysiology and pathogenesis of CRSD. Because conventional protocols for examining individual circadian characteristics are laborious and costly, more convenient measurement methods are required in the clinical setting. The circadian reporter Bmal1-luc showed robust daily rhythms in primary fibroblast cells derived from individual skin biopsies. The fibroblast rhythms are associated with chronotypes (morningness vs eveningness preference) and physiological rhythms. Surrogate measurements using fibroblast cells would be a powerful tool for the assessment of individual circadian properties and could lead to providing personalized medicine for CRSD.


  1. Pittendrigh CS: Temporal organization: reflections of a Darwinian clock-watcher. Annu Rev Physiol. 1993, 55: 16-54.

    Article  CAS  PubMed  Google Scholar 

  2. Yamazaki S, Numano R, Abe M, Hida A, Takahashi R, Ueda M, Block GD, Sakaki Y, Menaker M, Tei H: Resetting central and peripheral circadian oscillators in transgenic rats. Science. 2000, 288: 682-585. 10.1126/science.288.5466.682.

    Article  CAS  PubMed  Google Scholar 

  3. Yoo SH, Yamazaki S, Lowrey PL, Shimomura K, Ko CH, Buhr ED, Siepka SM, Hong HK, Oh WJ, Yoo OJ, Menaker M, Takahashi JS: PERIOD2::LUCIFERASE real-time reporting of circadian dynamics reveals persistent circadian oscillations in mouse peripheral tissues. Proc Natl Acad Sci USA. 2004, 101: 5339-5346. 10.1073/pnas.0308709101.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Lowrey PL, Takahashi JS: Mammalian circadian biology: elucidating genome-wide levels of temporal organization. Annu Rev Genomics Hum Genet. 2004, 5: 407-441. 10.1146/annurev.genom.5.061903.175925.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Reppert SM, Weaver DR: Coordination of circadian timing in mammals. Nature. 2002, 418: 935-941. 10.1038/nature00965.

    Article  CAS  PubMed  Google Scholar 

  6. Takahashi JS, Hong HK, Ko CH, McDearmon EL: The genetics of mammalian circadian order and disorder: implications for physiology and disease. Nat Rev Genet. 2008, 9: 764-775. 10.1038/nrg2430.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Daan S, Beersma DG, Borbely AA: Timing of human sleep: recovery process gated by a circadian pacemaker. Am J Physiol. 1984, 246: R161-R183.

    CAS  PubMed  Google Scholar 

  8. International Classification of Sleep Disorders: Diagnostic and Coding Manual. 2nd edition (ICSD-II). 2005, Darien, IL: American Academy of Sleep Medicine

  9. Barion A, Zee PC: A clinical approach to circadian rhythm sleep disorders. Sleep Med. 2007, 8: 566-577. 10.1016/j.sleep.2006.11.017.

    Article  PubMed Central  PubMed  Google Scholar 

  10. Okawa M, Uchiyama M: Circadian rhythm sleep disorders: characteristics and entrainment pathology in delayed sleep phase and non-24-h sleep-wake syndrome. Sleep Med Rev. 2007, 11: 485-496. 10.1016/j.smrv.2007.08.001.

    Article  PubMed  Google Scholar 

  11. Toh KL, Jones CR, He Y, Eide EJ, Hinz WA, Virshup DM, Ptácek LJ, Fu YH: An hPer2 phosphorylation site mutation in familial advanced sleep phase syndrome. Science. 2001, 291: 1040-1043. 10.1126/science.1057499.

    Article  CAS  PubMed  Google Scholar 

  12. Xu Y, Toh KL, Jones CR, Shin JY, Fu YH, Ptácek LJ: Modeling of a human circadian mutation yields insights into clock regulation by PER2. Cell. 2007, 128: 59-70. 10.1016/j.cell.2006.11.043.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  13. Xu Y, Padiath QS, Shapiro RE, Jones CR, Wu SC, Saigoh N, Saigoh K, Ptácek LJ, Fu YH: Functional consequences of a CKIδ mutation causing familial advanced sleep phase syndrome. Nature. 2005, 434: 640-644. 10.1038/nature03453.

    Article  CAS  PubMed  Google Scholar 

  14. Gallego M, Eide EJ, Woolf MF, Virshup DM, Forger DB: An opposite role for tau in circadian rhythms revealed by mathematical modeling. Proc Natl Acad Sci USA. 2006, 103: 10618-10623. 10.1073/pnas.0604511103.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. Vanselow K, Vanselow JT, Westermark PO, Reischl S, Maier B, Korte T, Herrmann A, Herzel H, Schlosser A, Kramer A: Differential effects of PER2 phosphorylation: molecular basis for the human familial advanced sleep phase syndrome (FASPS). Genes Dev. 2006, 20: 2660-2672. 10.1101/gad.397006.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Jones CR, Campbell SS, Zone SE, Cooper F, DeSano A, Murphy PJ, Jones B, Czajkowski L, Ptácek LJ: Familial advanced sleep-phase syndrome: a short-period circadian rhythm variant in humans. Nat Med. 1999, 5: 1062-1065. 10.1038/12502.

    Article  CAS  PubMed  Google Scholar 

  17. Hirota T, Lewis WG, Liu AC, Lee JW, Schultz PG, Kay SA: A chemical biology approach reveals period shortening of the mammalian circadian clock by specific inhibition of GSK-3β. Proc Natl Acad Sci USA. 2008, 105: 20746-20751. 10.1073/pnas.0811410106.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Isojima Y, Nakajima M, Ukai H, Fujishima H, Yamada RG, Masumoto KH, Kiuchi R, Ishida M, Ukai-Tadenuma M, Minami Y, Kito R, Nakao K, Kishimoto W, Yoo SH, Shimomura K, Takao T, Takano A, Kojima T, Nagai K, Sakaki Y, Takahashi JS, Ueda HR: CKIε/δ-dependent phosphorylation is a temperature-insensitive, period-determining process in the mammalian circadian clock. Proc Natl Acad Sci USA. 2009, 106: 15744-15749. 10.1073/pnas.0908733106.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Ebisawa T, Uchiyama M, Kajimura N, Mishima K, Kamei Y, Katoh M, Watanabe T, Sekimoto M, Shibui K, Kim K, Kudo Y, Ozeki Y, Sugishita M, Toyoshima R, Inoue Y, Yamada N, Nagase T, Ozaki N, Ohara O, Ishida N, Okawa M, Takahashi K, Yamauchi T: Association of structural polymorphisms in the human period3 gene with delayed sleep phase syndrome. EMBO Rep. 2001, 2: 342-346. 10.1093/embo-reports/kve070.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Dijk DJ, Archer SN: PERIOD3, circadian phenotypes, and sleep homeostasis. Sleep Med Rev. 2009, 14: 151-160.

    Article  PubMed  Google Scholar 

  21. Viola AU, Archer SN, James LM, Groeger JA, Lo JC, Skene DJ, von Schantz M, Dijk DJ: PER3 polymorphism predicts sleep structure and waking performance. Curr Biol. 2007, 17: 613-618. 10.1016/j.cub.2007.01.073.

    Article  CAS  PubMed  Google Scholar 

  22. Shearman LP, Jin X, Lee C, Reppert SM, Weaver DR: Targeted disruption of the mPer3 gene: subtle effects on circadian clock function. Mol Cell Biol. 2000, 20: 6269-6275. 10.1128/MCB.20.17.6269-6275.2000.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Pendergast JS, Friday RC, Yamazaki S: Distinct functions of Period2 and Period3 in the mouse circadian system revealed by in vitro analysis. PLoS One. 2010, 5: e8552-10.1371/journal.pone.0008552.

    Article  PubMed Central  PubMed  Google Scholar 

  24. van der Veen DR, Archer SN: Light-dependent behavioral phenotypes in PER3-deficient mice. J Biol Rhythms. 2010, 25: 3-8. 10.1177/0748730409356680. A published erratum appears in J Biol Rhythms 2010, 25:150

    Article  PubMed  Google Scholar 

  25. Sack RL, Lewy AJ, Blood ML, Keith LD, Nakagawa H: Circadian rhythm abnormalities in totally blind people: incidence and clinical significance. J Clin Endocrinol Metab. 1992, 75: 127-134. 10.1210/jc.75.1.127.

    CAS  PubMed  Google Scholar 

  26. Lockley SW, Skene DJ, Arendt J, Tabandeh H, Bird AC, Defrance R: Relationship between melatonin rhythms and visual loss in the blind. J Clin Endocrinol Metab. 1997, 82: 3763-3770. 10.1210/jc.82.11.3763.

    CAS  PubMed  Google Scholar 

  27. Lockley SW, Skene DJ, Tabandeh H, Bird AC, Defrance R, Arendt J: Relationship between napping and melatonin in the blind. J Biol Rhythms. 1997, 12: 16-25. 10.1177/074873049701200104.

    Article  CAS  PubMed  Google Scholar 

  28. Czeisler CA, Duffy JF, Shanahan TL, Brown EN, Mitchell JF, Rimmer DW, Ronda JM, Silva EJ, Allan JS, Emens JS, Dijk DJ, Kronauer RE: Stability, precision, and near-24-hour period of the human circadian pacemaker. Science. 1999, 284: 2177-2181. 10.1126/science.284.5423.2177.

    Article  CAS  PubMed  Google Scholar 

  29. Wright KP, Hughes RJ, Kronauer RE, Dijk DJ, Czeisler CA: Intrinsic near-24-h pacemaker period determines limits of circadian entrainment to a weak synchronizer in humans. Proc Natl Acad Sci USA. 2001, 98: 14027-14032. 10.1073/pnas.201530198.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  30. Gronfier C, Wright KP, Kronauer RE, Czeisler CA: Entrainment of the human circadian pacemaker to longer-than-24-h days. Proc Natl Acad Sci USA. 2007, 104: 9081-9086. 10.1073/pnas.0702835104.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  31. Brown SA, Fleury-Olela F, Nagoshi E, Hauser C, Juge C, Meier CA, Chicheportiche R, Dayer JM, Albrecht U, Schibler U: The period length of fibroblast circadian gene expression varies widely among human individuals. PLoS Biol. 2005, 3: e338-10.1371/journal.pbio.0030338.

    Article  PubMed Central  PubMed  Google Scholar 

  32. Brown SA, Kunz D, Dumas A, Westermark PO, Vanselow K, Tilmann-Wahnschaffe A, Herzel H, Kramer A: Molecular insights into human daily behavior. Proc Natl Acad Sci USA. 2008, 105: 1602-1607. 10.1073/pnas.0707772105.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  33. Pagani L, Semenova EA, Moriggi E, Revell VL, Hack LM, Lockley SW, Arendt J, Skene DJ, Meier F, Izakovic J, Wirz-Justice A, Cajochen C, Sergeeva OJ, Cheresiz SV, Danilenko KV, Eckert A, Brown SA: The physiological period length of the human circadian clock in vivo is directly proportional to period in human fibroblasts. PLoS One. 2010, 5: e13376-10.1371/journal.pone.0013376.

    Article  PubMed Central  PubMed  Google Scholar 

Download references


This study was supported by Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, and Technology of Japan and from the Ministry of Health, Labour, and Welfare of Japan. A part of this study is the result of "Understanding of molecular and environmental bases for brain health" carried out under the Strategic Research Program for Brain Sciences by the Ministry of Education, Culture, Sports, Science and Technology of Japan.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Akiko Hida.

Additional information

Competing interests

The authors declare that they have no competing interests.

Authors' contributions

AH wrote the manuscript and performed circadian phenotyping. SK and KM edited the manuscript. All authors read and approved the final manuscript.

Authors’ original submitted files for images

Below are the links to the authors’ original submitted files for images.

Authors’ original file for figure 1

Authors’ original file for figure 2

Rights and permissions

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Reprints and permissions

About this article

Cite this article

Hida, A., Kitamura, S. & Mishima, K. Pathophysiology and pathogenesis of circadian rhythm sleep disorders. J Physiol Anthropol 31, 7 (2012).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: