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PubMed2002

The 3111 Clock gene polymorphism is not associated with sleep and circadian rhythmicity in phenotypically characterized human subjects.

Mutations in clock genes are associated with abnormal circadian parameters, including sleep. An association has been reported previously between a polymorphism (3111C), situated in the 3'-untranslated region (3'-UTR) of the circadian gene Clock and evening preference. In the present study, this polymorphism was assessed in: (1) 105 control subjects with defined diurnal preference, (2) 26 blind subjects with free-running circadian rhythms and characterized with regard to circadian period (tau) and (3) 16 delayed sleep phase syndrome patients. The control group was chosen from a larger population (n = 484) by Horne-Ostberg questionnaire analysis, from which three subgroups were selected (evening, intermediate and morning preference). Data from sleep diaries completed by 90% of these subjects showed a strong correlation between preferred and estimated timings of sleep and wake. The mean timings of activities for the evening group were at least 2 h later than the morning group. Genetic analysis showed that, in contrast with the previously published finding, there was no association between 3111C and eveningness. Neither was there an association between 3111C and tau, nor a significant difference in 3111C frequency between the normal and delayed sleep phase syndrome groups. To assess the effect of this polymorphism on messenger RNA (mRNA) translatability, luciferase reporter gene constructs containing the two Clock polymorphic variants in their 3'-UTR were transfected into COS-1 cells and luciferase activity measured. No significant difference was observed between the two variants. These results do not support Clock 3111C as a marker for diurnal preference, tau, or delayed sleep phase syndrome in humans.

Alleles↗
PubMed2000

Clock genes, feedback loops and their possible role in the etiology of bipolar disorders: an integrative model.

Clock genes, which are found in all higher organisms including humans, play a central role in the generation and control of circadian rhythms. For example, the amount of protein encoded by the per gene in mice oscillates with a circadian frequency. The per gene is activated by a constitutively expressed heterodimeric protein encoded by the bmal1 and clock genes, and this activation is suppressed by the PER protein itself. The negative feedback of the PER protein on the expression of the per gene provides a framework for a basic circadian autoregulatory loop in mammals. These elements of biomolecular feedback loops are interpreted within a system theory as an elementary behavioral cycle consisting of intentional programs (the per gene), environmental objects (the BMAL1-CLOCK heterodimer) and the experiential realization of the intended programs (the level of PER protein). This single model enables the deduction of disturbances, which can be transferred to the criteria of bipolar disorders. It is hypothesized that mutations in clock genes lead to disturbances in molecular feedback loops, which on a behavioral level could appear as bipolar disorders. Finally, some implications for research and treatment of bipolar disorders are discussed.

Animals↗
PubMed2004

Structure of the C-terminal domain of the clock protein KaiA in complex with a KaiC-derived peptide: implications for KaiC regulation.

Circadian clocks are widespread endogenous mechanisms that control the temporal pattern of diverse biological processes, including gene transcription. KaiA is the positive element of the cyanobacterial clock because KaiA overexpression elevates transcription levels of clock components. Recently, we showed that the structure of KaiA is that of a domain-swapped homodimer. The N-terminal domain is a pseudo-receiver; thus, it is likely to be involved in signal transduction in the clock-resetting pathway. The C-terminal domain of KaiA is structurally novel and enhances the KaiC autokinase activity directly. Here, we report the NMR structure of the C-terminal domain of KaiA (ThKaiA180C) in complex with a KaiC-derived peptide from the cyanobacterium Thermosynechococcus elongatus BP-1. The protein-peptide interface is revealed to be different from a model that was proposed earlier, is stabilized by a combination of hydrophobic and electrostatic interactions, and includes many residues known to produce a circadian-period phenotype upon substitution. Although the structure of the monomeric subunit of ThKaiA180C is largely unchanged upon peptide binding, the intersubunit dimerization angle changes. It is proposed that modulation of the C-terminal KaiA domain dimerization angle regulates KaiA-KaiC interactions.

Bacterial Proteins↗
PubMed2004

Stochastic simulation of the mammalian circadian clock.

Circadian (nearly 24-h) clocks are remarkably accurate at timing biological events despite the randomness of their biochemical reactions. Here we examine the causes of their immunity to molecular noise in the context of a detailed stochastic mathematical model of the mammalian circadian clock. This stochastic model is a direct generalization of the deterministic mammalian circadian clock model previously developed. A feature of that model is that it completely specifies all molecular reactions, leaving no ambiguity in the formulation of a stochastic version of the model. With parameters based on experimental data concerning clock protein concentrations within a cell, we find accurate circadian rhythms in our model only when promoter interaction occurs on the time scale of seconds. As the model is scaled up by proportionally increasing the numbers of molecules of all species and the reaction rates with the promoter, the observed variability scales as 1/n(0.5), where n is the number of molecules of any species. Our results show that gene duplication increases robustness by providing more promoters with which the transcription factors of the model can interact. Although PER2 mutants were not rhythmic in the deterministic version of this model, they are rhythmic in the stochastic version.

Animals↗
PubMed2006

Signaling mediated by the dopamine D2 receptor potentiates circadian regulation by CLOCK:BMAL1.

Environmental cues modulate a variety of intracellular pathways whose signaling is integrated by the molecular mechanism that constitutes the circadian clock. Although the essential gears of the circadian machinery have been elucidated, very little is known about the signaling systems regulating it. Here, we report that signaling mediated by the dopamine D2 receptor (D2R) enhances the transcriptional capacity of the CLOCK:BMAL1 complex. This effect involves the mitogen-activated protein kinase transduction cascade and is associated with a D2R-induced increase in the recruiting and phosphorylation of the transcriptional coactivator cAMP-responsive element-binding protein (CREB) binding protein. Importantly, CLOCK:BMAL1-dependent activation and light-inducibility of mPer1 gene transcription is drastically dampened in retinas of D2R-null mice. Because dopamine is the major catecholamine in the retina, central for the neural adaptation to light, our findings establish a physiological link among photic input, dopamine signaling, and the molecular clock machinery.

ARNTL Transcription Factors↗
PubMed1987

Nucleotide sequences of immunoglobulin epsilon genes of chimpanzee and orangutan: DNA molecular clock and hominoid evolution.

To determine the phylogenetic relationships among hominoids and the dates of their divergence, the complete nucleotide sequences of the constant region of the immunoglobulin epsilon-chain (C epsilon 1) genes from chimpanzee and orangutan have been determined. These sequences were compared with the human epsilon-chain constant-region sequence. A molecular clock (silent molecular clock), measured by the degree of sequence divergence at the synonymous (silent) positions of protein-encoding regions, was introduced for the present study. From the comparison of nucleotide sequences of alpha1-antitrypsin and beta- and delta-globin genes between humans and Old World monkeys, the silent molecular clock was calibrated: the mean evolutionary rate of silent substitution was determined to be 1.56 X 10(-9) substitutions per site per year. Using the silent molecular clock, the mean divergence dates of chimpanzee and orangutan from the human lineage were estimated as 6.4 +/- 2.6 million years and 17.3 +/- 4.5 million years, respectively. It was also shown that the evolutionary rate of primate genes is considerably slower than those of other mammalian genes.

Animals↗
PubMed1994

Circadian clock locus frequency: protein encoded by a single open reading frame defines period length and temperature compensation.

The frequency (frq) locus encodes a key component, a state variable, in a cellular oscillator generating circadian rhythmicity. Two transcripts have been mapped to this region, and data presented here are consistent with the existence of a third transcript. Analysis of cDNA clones and clock mutants from this region focuses attention on one transcript encoding a protein. FRQ, which is a central clock component: (i) mutations in all of the semidominant frq alleles are the result of single amino acid substitutions and map to the open reading frame (ORF) encoding FRQ; (ii) deletion of this ORF, or a frameshift mutation within it, results in a strain with a recessive clock phenotype characterized by the loss of rhythm stability and compensation. Single amino acid substitutions within, or disruption of, this single ORF are thus sufficient to drive major alterations in both period length and temperature compensation, two canonical characteristics of circadian systems. The 989-amino acid FRQ protein species the circadian function of frq in the assembly of the Neurospora biological clock.

Alleles↗
PubMed2000

Differential regulation of circadian pacemaker output by separate clock genes in Drosophila.

Regulation of the Drosophila pigment-dispersing factor (pdf) gene products was analyzed in wild-type and clock mutants. Mutations in the transcription factors CLOCK and CYCLE severely diminish pdf RNA and neuropeptide (PDF) levels in a single cluster of clock-gene-expressing brain cells, called small ventrolateral neurons (s-LN(v)s). This clock-gene regulation of specific cells does not operate through an E-box found within pdf regulatory sequences. PDF immunoreactivity exhibits daily cycling, but only within terminals of axons projecting from the s-LN(v)s. This posttranslational rhythm is eliminated by period or timeless null mutations, which do not affect PDF staining in cell bodies or pdf mRNA levels. Therefore, within these chronobiologically important neurons, separate elements of the central pacemaking machinery regulate pdf or its product in novel and different ways. Coupled with contemporary results showing a pdf-null mutant to be severely defective in its behavioral rhythmicity, the present results reveal PDF as an important circadian mediator whose expression and function are downstream of the clockworks.

Animals↗
PubMed2003

Histone acetyltransferase-dependent chromatin remodeling and the vascular clock.

Rhythmic gene expression is central to the circadian control of physiology in mammals. Transcriptional activation of Per and Cry genes by heterodimeric bHLH-PAS proteins is a key event in the feedback loop that drives rhythmicity; however, the mechanism is not clearly understood. Here we show the transcriptional coactivators and histone acetyltransferases, p300/CBP, PCAF, and ACTR associate with the bHLH-PAS proteins, CLOCK and NPAS2, to regulate positively clock gene expression. Furthermore, Cry2 mediated repression of NPAS2:BMAL1 is overcome by overexpression of p300 in transactivation assays. Accordingly, p300 exhibits a circadian time-dependent association with NPAS2 in the vasculature, which precedes peak expression of target genes. In addition, a rhythm in core histone H3 acetylation on the mPer1 promoter in vivo correlates with the cyclical expression of their mRNAs. Temporal coactivator recruitment and HAT-dependent chromatin remodeling on the promoter of clock controlled genes in the vasculature permits the mammalian clock to orchestrate circadian gene expression.

Acetyltransferases↗
PubMed2005

SCFbeta-TRCP controls clock-dependent transcription via casein kinase 1-dependent degradation of the mammalian period-1 (Per1) protein.

Circadian rhythms are controlled by the periodic accumulation of Period proteins, which act as transcriptional repressors of Clock-dependent genes. Period genes are themselves Clock targets, thereby establishing a negative transcriptional feedback circuit controlling circadian periodicity. Previous data have implicated the CK1epsilon isolog Doubletime (Dbt) and the F-box protein Slimb in the regulation of Drosophila Period (Per) through an unknown mechanism. In this work, we have identified components of the machinery involved in regulating the abundance of human Per1 in tissue culture cells. CK1epsilon and CK1gamma2 were found to bind to Per1 and to promote its degradation in an in vivo degradation assay. Per1 turnover was blocked by a dominant negative version of the Cul1 protein, a component of the SCF (Skp1-Cul1-F-box protein) ubiquitin ligase. We screened a panel of F-box proteins for those that would associate with Per1 in a CK1epsilon-dependent manner, and we identified beta-TRCP1 and beta-TRCP2, isologs of the Drosophila Slimb protein. RNA interference against beta-transducin repeat-containing protein (beta-TRCP) stabilizes endogenous and exogenous Per1. beta-TRCP associates with sequences near the N terminus of Per1 in a region distinct from the previously characterized CK1epsilon-binding site. beta-TRCP and CK1epsilon promote Per1 ubiquitination in vitro. Finally, RNA interference against beta-TRCP greatly decreases Clock-dependent gene expression in tissue culture cells, indicating that beta-TRCP controls endogenous Per1 activity and the circadian clock by directly targeting Per1 for degradation.

Binding Sites↗
PubMed2006

Mapping of binding regions for the circadian regulators BMAL1 and CLOCK within the mouse Rev-erbalpha gene.

Two major interconnected feedback loops govern circadian rhythmicity in mammals. The transcriptional activators BMAL1/MOP3 and CLOCK drive one loop by binding to E-box motifs in the regulatory regions of circadian target genes. Time-of-day-dependent inhibition of the activity of BMAL1 and CLOCK by PERIOD (PER) and CRYPTOCHROME (CRY) proteins provokes consequent rhythmic gene expression. In this fashion, the Per and Cry genes can feedback onto their own synthesis. The orphan nuclear receptor Rev-erbalpha manifests the second feedback loop. Genetically linked to the molecular oscillator, it was identified as a repressor of the Bmal1 and Clock genes. In an attempt to understand the circadian regulation of the mouse Rev-erbalpha gene, we developed a screening technique for BMAL1 and CLOCK binding regions consisting of chromatin-immunoprecipitation. Here we show that the mouse Rev-erbalpha gene contains at least two binding regions for the transcriptional activators close to its previously identified promoter region and in its first intron. However, our data also indicate that not all potential E-box motifs in vitro are occupied in vivo.

ARNTL Transcription Factors↗
PubMed2006

How temperature affects the circadian clock of Neurospora crassa.

Light and temperature are major environmental cues that influence circadian clocks. The molecular effects of these zeitgebers on the circadian clock of Neurospora crassa have been studied intensively during the last decade. While signal transduction of light into the circadian clock is quite well characterized, we have only recently begun to understand the molecular mechanisms that underlie temperature sensing. Here we summarize briefly the current knowledge about the effects of temperature on the circadian clock of Neurospora crassa.

Alternative Splicing↗
PubMed2004

Wavelength dependency of light-induced effects on photoperiodic clock in the migratory blackheaded bunting (Emberiza melanocephala).

The effects of light wavelength on photoperiodic clock were determined in the migratory male blackheaded bunting (Emberiza melanocephala). We constructed an action spectrum for photoperiodic induction (body fattening, gain in body mass, and gonadal recrudescence) by exposing birds for 4.5 weeks to 13 h light per day (L:D = 13:11 h) of white (control), blue (450 nm), or red (640 nm) color at irradiances ranging from 0.028 to 1.4Wm(-2). The threshold light irradiance for photoinduction was about 10-fold higher for blue, compared to red and white light. Phase-dependent effects of light wavelength on the photoperiodic clock were further examined in the next two sets of skeleton photoperiods (SKPs). In the first set of SKPs, birds were exposed for four weeks to asymmetrical light periods (L:D:L:D= 6:6:1:11 h) at 0.25+/-0.01 W m(-2); two light periods applied were of the same (450nm: blue:blue, B:B; 640nm, red:red, R:R) or different (blue:red, B:R or red:blue, R:B) wavelengths, or of white:white (W:W, controls). Photoperiodic induction occurred under R:R and B:R, but not under B:B and R:B light conditions; the W:W condition induced an intermediate response. The second set of SKPs used symmetrical light periods (L:D:L:D = 1:11:1:11 h), and measured effects also on the activity rhythm. Birds were first exposed to one of the four SKPs (R:R, B:B, R:B, or B:R) for three weeks, subsequently were released into dim constant light (LLdim; approximately 0.01 Wm(-2), the night light used in an L:D cycle) for two weeks, and then were returned to respective SKPs for another three weeks. Activity was greater in the R:R compared to B:B, and in B:R compared to R:B light condition. Zugunruhe (intense nighttime activity, indicating migratory restlessness in a caged situation) developed under the R:R and B:R, but not the B:B and R:B, light condition. Under LLdim, all birds free-ran with a period >24h, the Zugunruhe had a circadian period longer than the daytime activity, and the re-entrainment to SKPs was influenced by the position of light periods relative to circadian phase of the activity rhythm. Photoperiodic induction at the end of 8 weeks was found in the R:R and B:R, but not in B:B, light conditions; in the R:B condition only one bird had initiated testes. Taken together, these results suggest that in the blackheaded bunting, the circadian photoperiodic clock is differentially responsive to light wavelengths; this responsiveness is phase-dependent, and the development of Zugunruhe reflects a true circadian function. Wavelength-dependent response of the photoperiodic clock could be part of an adaptive strategy in evolution of the seasonality in reproduction and migration among photoperiodic species under wild conditions.

Animals↗
PubMed1997

Isolation and characterization of a temperature-sensitive circadian clock mutant of Neurospora crassa.

A new circadian clock mutant has been isolated in Neurospora crassa. This new mutation, called period-6 (prd-6), has two features novel to known clock mutations. First, the mutation is temperature sensitive. At restrictive temperatures (above 21 degrees) the mutation shortens circadian period length from a wild-type value of 21.5 hr to 18 hr. At permissive temperatures (below 21 degrees) the mutant has a 20.5-hr period length close to that of the wild-type strain. Second, the prd-6 mutation is epistatic to the previously isolated clock mutation period-2 (prd-2). This epistasis is unusual in that the prd-2 prd-6 double mutant strain has an 18-hr period length at both the restrictive and permissive temperatures. That is, the temperature-sensitive aspect of the phenotype of the prd-6 strain is lost in the prd-2 prd-6 double mutant strain. This suggests that the gene products of the prd-2 and prd-6 loci may interact physically and that the presence of a normal prd-2+ protein is required for low temperature to "rescue" the prd-6 mutant phenotype. These results, combined with our recent finding that prd-2 and some alleles of the frq gene show genetic synergy, suggest that it may be possible to establish a more comprehensive model of the Neurospora circadian clock.

Biological Clocks↗
PubMed2000

A compound poisson process for relaxing the molecular clock.

The molecular clock hypothesis remains an important conceptual and analytical tool in evolutionary biology despite the repeated observation that the clock hypothesis does not perfectly explain observed DNA sequence variation. We introduce a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process. Events of substitution rate change are placed onto a phylogenetic tree according to a Poisson process. When an event of substitution rate change occurs, the current rate of substitution is modified by a gamma-distributed random variable. Parameters of the model can be estimated using Bayesian inference. We use Markov chain Monte Carlo integration to evaluate the posterior probability distribution because the posterior probability involves high dimensional integrals and summations. Specifically, we use the Metropolis-Hastings-Green algorithm with 11 different move types to evaluate the posterior distribution. We demonstrate the method by analyzing a complete mtDNA sequence data set from 23 mammals. The model presented here has several potential advantages over other models that have been proposed to relax the clock because it is parametric and does not assume that rates change only at speciation events. This model should prove useful for estimating divergence times when substitution rates vary across lineages.

Bayes Theorem↗
PubMed2025

Multiomic clocks to predict phenotypic age in mice.

Biological age refers to a person's overall health in aging, as distinct from their chronological age. Diverse measures of biological age, referred to as "clocks," have been developed in recent years and enable risk assessments and an estimation of the efficacy of longevity interventions in animals and humans. Although most clocks are trained to predict chronological age, clocks have been developed to predict more complex composite biological age outcomes, at least in humans. These composite outcomes can be made up of a combination of phenotypic data, chronological age, and disease or mortality risk. Here, we develop the first such composite biological age measure for mice: the mouse phenotypic age model (Mouse PhenoAge). This outcome is based on frailty measures, complete blood counts, and mortality risk in a longitudinally assessed cohort of male and female C57BL/6 mice. We then develop clocks to predict Mouse PhenoAge, based on multiomic models using metabolomic and DNA methylation data. Our models accurately predict Mouse PhenoAge, and residuals of the models are associated with remaining lifespan, even for mice of the same chronological age. These methods offer novel ways to accurately predict mortality in laboratory mice, thus reducing the need for lengthy and costly survival studies.

Animals↗
PubMed2003

Mammalian cultured cells as a model system of peripheral circadian clocks.

The mammalian circadian system consists of multiple oscillators with basically hierarchical relationship, in which the hypothalamic suprachiasmatic nucleus (SCN) is the master pacemaker and the other oscillators in the periphery are subordinate. Although peripheral oscillators have been preceded by the SCN in circadian studies, accumulating data have revealed the importance and characteristics of peripheral oscillators. Cultured cell lines have also provided valuable information about intracellular mechanisms of circadian rhythms. This review outlines the properties of peripheral clocks in several perspectives such as the mechanisms of autonomous oscillations, the clock resetting, and the clock outputs, and describes the usefulness of immortalized cultured cells as a model system of mammalian circadian clocks by introducing some fruits of related works.

Animals↗
PubMed2002

Slow molecular clocks in Old World monkeys, apes, and humans.

Two longstanding issues on the molecular clock hypothesis are studied in this article. First, is there a global molecular clock in mammals? Although many authors have observed unequal rates of nucleotide substitution among mammalian lineages, some authors have proposed a global clock for all eutherians, i.e., a single global rate of 2.2 x 10(-9) substitutions per nucleotide site per year. We reexamine this issue using noncoding, nonrepetitive DNA from Old World monkeys (OWMs), chimpanzee, and human. First, using the minimal date of 6 MYA for the human-chimpanzee divergence and more than 2.5 million base pairs of genomic sequences from human and chimpanzee, we estimate a maximal rate of 0.99 x 10(-9) for noncoding, nonrepetitive genomic regions for these two species. This estimate is less than half of the proposed global rate and much smaller than the commonly used rate (3.5 x 10(-9)) for eutherians. Further, using a minimal date of 23 MYA for the human-OWM divergence, we estimate a maximal rate of 1.5 x 10(-9) for both introns and fourfold degenerate sites in humans and OWMs. In addition, with the New World monkey (NWM) lineage as an outgroup, we estimate that the rate of substitution in introns is 30% higher in the OWM lineage than in the human lineage. Clearly, there is no global molecular clock in eutherians. Second, although many studies have indicated considerable variation in the mutation rate among regions of the mammalian genome, a recent study proposed a uniform rate. Using new and existing intron sequence data from higher primates, we find significant rate variation among genomic regions and a positive correlation between the rate of substitution and the GC content, refuting the claim of a uniform rate.

Animals↗