The Transcriptional Repressor STRA13 Regulates a Subset of Peripheral Circadian Outputs

Circadian clocks during embryonic and fetal development

Circadian rhythmicity is a fundamental characteristic of organisms, which helps ensure that vital functions occur in an appropriate and precise temporal sequence and in accordance with cyclic environmental changes. Living beings are endowed with a system of biological clocks that measure time on a 24-hr basis, termed the circadian timing system. In mammals, the system is organized as a master clock located in the suprachiasmatic nucleus (SCN) of the hypothalamus, commanding peripheral clocks located in almost every tissue of the body. At the cell level, interlocking transcription/translation feedback loops of the genes Bmal-1, Clock, Per1-2, and Cry1-2, named clock genes, and their protein products results in circadian oscillation of clock genes and of genes involved in almost every cellular function. During gestation, the conceptus follows a complex and dynamic program by which it is simultaneously fit to develop and live in a circadian environment provided by its mother and to prepare for the very different environment that it will experience after birth. It has been known for a number of years that the mother tells the fetus the time of day and season of the year, and that the fetus uses this information to set the phase of fetal and neonatal circadian rhythms. There is evidence that the maternal rhythm of melatonin is one of the time signals to the fetus. In the last few years, the study of the development of the circadian system has turned to the investigation of the oscillatory expression of clock genes and their possible role in development, and to answering questions on the organization of the fetal circadian system. Emerging evidence shows that clock genes are expressed in the oocyte and during early and late development in embryo/fetal organs in the rat and in a fetal primate. The data available raise the intriguing possibility that the fetal SCN and fetal tissues may be peripheral clocks commanded by separate maternal signals. The rapid methodological and conceptual advances on chronobiology may help to unravel how the developing embryo and fetus faces time in this plastic period of life.

bHLH-Orange Transcription Factors in Development and Cancer

Basic helix-loop-helix (bHLH) proteins are a large superfamily of transcription factors that play critical roles in many physiological processes including cellular differentiation, cell cycle arrest and apoptosis. Based on structural and phylogenetic analysis, mammalian bHLH-Orange (bHLH-O) proteins, which constitute the repressor family of bHLH factors, can be grouped into four subfamilies: Hes, Hey, Helt and Stra13/Dec. In addition to the bHLH domain that mediates DNA-binding and protein dimerization, all members of this family are characterized by a distinctive motif called the "Orange domain" which is present exclusively in these factors. Genetic studies using targeted mutagenesis in mice have revealed essential roles for many bHLH-O genes in embryonic development, cell fate decisions, differentiation of a number of cell types and in apoptosis. Furthermore, growing evidence of crosstalk between bHLH-O proteins with the tumor suppressors p53 and hypoxia-inducible factor, have started to shed light on their possible roles in oncogenesis. Consistently, deregulated expression of several bHLH-O factors is associated with various human cancers. Here, we review the structure and biological functions of bHLH-O factors, and discuss recent studies that suggest a potential role for these factors in tumorigenesis and tumor progression.

Are circadian rhythms the code of hypothalamic-immune communication? Insights from natural killer cells

Circadian rhythms in physiology and behavior are ultimately regulated at the hypothalamic level by the suprachiasmatic nuclei (SCN). This central oscillator transduces photic information to the cellular clocks in the periphery through the autonomic nervous system and the neuroendocrine system. The fact that these two systems have been shown to modulate leukocyte physiology supports the concept that the circadian component is an important aspect of hypothalamic-immune communication. Circadian disruption has been linked to immune dysregulation, and recent reports suggest that several circadian clock genes, in addition to their time-keeping role, are involved in the immune response. In this overview, we summarize the findings demonstrating that Natural Killer (NK) cell function is under circadian control.

A functional genomics strategy reveals clockwork orange as a transcriptional regulator in the Drosophila circadian clock

The Drosophila circadian clock consists of integrated autoregulatory feedback loops, making the clock difficult to elucidate without comprehensively identifying the network components in vivo. Previous studies have adopted genome-wide screening for clock-controlled genes using high-density oligonucleotide arrays that identified hundreds of clock-controlled genes. In an attempt to identify the core clock genes among these candidates, we applied genome-wide functional screening using an RNA interference (RNAi) system in vivo. Here we report the identification of novel clock gene candidates including clockwork orange (cwo), a transcriptional repressor belonging to the basic helix-loop-helix ORANGE family. cwo is rhythmically expressed and directly regulated by CLK-CYC through canonical E-box sequences. A genome-wide search for its target genes using the Drosophila genome tiling array revealed that cwo forms its own negative feedback loop and directly suppresses the expression of other clock genes through the E-box sequence. Furthermore, this negative transcriptional feedback loop contributes to sustaining a high-amplitude circadian oscillation in vivo. Based on these results, we propose that the competition between cyclic CLK-CYC activity and the adjustable threshold imposed by CWO keeps E-box-mediated transcription within the controllable range of its activity, thereby rendering a Drosophila circadian clock capable of generating high-amplitude oscillation.

Circadian rhythms and reproduction

There is a growing recognition that the circadian timing system, in particular recently discovered clock genes, plays a major role in a wide range of physiological systems. Microarray studies, for example, have shown that the expression of hundreds of genes changes many fold in the suprachiasmatic nucleus, liver heart and kidney. In this review, we discuss the role of circadian rhythmicity in the control of reproductive function in animals and humans. Circadian rhythms and clock genes appear to be involved in optimal reproductive performance, but there are sufficient redundancies in their function that many of the knockout mice produced do not show overt reproductive failure. Furthermore, important strain differences have emerged from the studies especially between the various Clock (Circadian Locomotor Output Cycle Kaput) mutant strains. Nevertheless, there is emerging evidence that the primary clock genes, Clock and Bmal1 (Brain and Muscle ARNT-like protein 1, also known as Mop3), strongly influence reproductive competency. The extent to which the circadian timing system affects human reproductive performance is not known, in part, because many of the appropriate studies have not been done. With the role of Clock and Bmal1 in fertility becoming clearer, it may be time to pursue the effect of polymorphisms in these genes in relation to the various types of infertility in humans.

Molecular circadian rhythms in central and peripheral clocks in mammals

The last decade has seen tremendous progress in our understanding of the organization and function of the circadian clock. A number of so-called clock genes were discovered, and these genes and their protein products were shown to organize into feedback loops to give a near 24 h rhythmicity. However, the mechanism is much more complicated. First, many new clock components have been identified, increasing both our understanding and the overall complexity of the mechanism. Second, there is now evidence that transcription may not play a central role in determining the functioning of the clock: the identification of post-translational modifications of the clock proteins has revealed new levels of control. Finally, chromatin remodeling seems to be crucial in the regulation of the expression of major clock components. This review describes the recent advances in our knowledge of the molecular clockwork in mammals; in particular, the contribution of new clock components and of post-transcriptional and post-translational events to circadian timekeeping are discussed.

Clockwork orange encodes a transcriptional repressor important for circadian-clock amplitude in Drosophila

Gene transcription is a central timekeeping process in animal clocks. In Drosophila, the basic helix-loop helix (bHLH)-PAS transcription-factor heterodimer, CLOCK/CYCLE (CLK/CYC), transcriptionally activates the clock components period (per), timeless (tim), Par domain protein 1 (Pdp1), and vrille (vri), which feed back and regulate distinct features of CLK/CYC function. Microarray studies have identified numerous rhythmically expressed transcripts, some of which are potential direct CLK targets. Here we demonstrate a circadian function for one such target, a bHLH-Orange repressor, CG17100/CLOCKWORK ORANGE (CWO). cwo is rhythmically expressed, and levels are reduced in Clk mutants, suggesting that cwo is CLK activated in vivo. cwo mutants display reduced-amplitude molecular and behavioral rhythms with lengthened periods. Molecular analysis suggests that CWO acts, in part, by repressing CLK target genes. We propose that CWO acts as a transcriptional and behavioral rhythm amplifier.

Circadian and CLOCK-controlled regulation of the mouse transcriptome and cell proliferation

Circadian rhythms of cell and organismal physiology are controlled by an autoregulatory transcription-translation feedback loop that regulates the expression of rhythmic genes in a tissue-specific manner. Recent studies have suggested that components of the circadian pacemaker, such as the Clock and Per2 gene products, regulate a wide variety of processes, including obesity, sensitization to cocaine, cancer susceptibility, and morbidity to chemotherapeutic agents. To identify a more complete cohort of genes that are transcriptionally regulated by CLOCK and/or circadian rhythms, we used a DNA array interrogating the mouse protein-encoding transcriptome to measure gene expression in liver and skeletal muscle from WT and Clock mutant mice. In WT tissue, we found that a large percentage of expressed genes were transcription factors that were rhythmic in either muscle or liver, but not in both, suggesting that tissue-specific output of the pacemaker is regulated in part by a transcriptional cascade. In comparing tissues from WT and Clock mutant mice, we found that the Clock mutation affects the expression of many genes that are rhythmic in WT tissue, but also profoundly affects many nonrhythmic genes. In both liver and skeletal muscle, a significant number of CLOCK-regulated genes were associated with the cell cycle and cell proliferation. To determine whether the observed patterns in cell-cycle gene expression in Clock mutants resulted in functional dysregulation, we compared proliferation rates of fibroblasts derived from WT or Clock mutant embryos and found that the Clock mutation significantly inhibits cell growth and proliferation.

Microarrays: statistical methods for circadian rhythms

Microarrays are promising tools that are increasingly being applied to the study of circadian rhythms. The large and complex datasets they generate, however, mean they require a new approach on how to design experiments, handle datasets, translate results, and derive conclusions. This technology also requires statistical methods for the correct interpretation of data generated by the microarrays. In this chapter, we provide an overview of analytical methods applied to microarray experiments for the identification of genes with circadian expression.

Cloning and developmental expression of the DEC1 ortholog gene in zebrafish

DEC1/STRA13/SHARP2 is a transcription factor of the bHLH family that has been suggested to play key roles in mammalian cell differentiation, the cell cycle and circadian regulation. However, the function of the DEC1 gene during embryogenesis is not well understood. In the present study, we cloned a zebrafish ortholog of the human DEC1 gene and analyzed its expression during development of zebrafish. The predicted protein encoded by zebrafish DEC1 consists of 403 amino acids, and shares 59%, 60% and 59% identity in overall amino acid sequence with human DEC1, mouse STRA13 and rat SHARP2, respectively. Zebrafish DEC1 contains a bHLH domain exhibiting 97% identity with that of the mammalian ortholog. During zebrafish embryogenesis, DEC1 is expressed in a strong ubiquitous manner before early segmentation. At 15-72 hpf, DEC1 shows a specific and dynamic expression in the developing eyes, somites, pineal gland (epiphysis), heart, brain, spinal cord, notochord, pronephric duct, common cardinal vein and blood cells. In older zebrafish, DEC1 also is expressed in multiple tissues including the brain, eye, gut, liver and pancreas. Our data provide evidence that expression of DEC1 is evolutionally conserved in zebrafish.

Evidence supporting a circadian control of natural killer cell function

Natural killer (NK) cells participate in the immune response against infection and cancer. An emerging body of epidemiological data supports that circadian homeostasis may constitute a factor risk for cancer development. Physiological rhythms under circadian control persist in the absence of light entrainment and ultimately rely on a molecular clock. We have previously shown that NK cell cytolytic activity follows a daily rhythm and that NK cells enriched from light-entrained rats present 24-h oscillations of clock genes, cytolytic factors, and cytokines. To investigate whether these oscillations are under a genuine circadian control, we assessed the daily expression of clock genes (Per1, Per2, Clock, and Bmal1), a clock-controlled gene (Dbp), cytolytic factors (granzyme B and perforin), and cytokines (IFN-gamma and TNF-alpha) in NK cells enriched from rats maintained in constant darkness (DD). In addition, we investigated whether the disruption of the NK cell clock by RNA interference (RNAi) affects the expression of cytolytic factors and cytokines. Persistent 24-h oscillations were found in the expression levels of clock genes, cytolytic factors, and cytokines in NK cells enriched from DD rats. In addition, RNAi-mediated Per2 knockdown caused a significant decrease of granzyme B and perforin levels in the rat derived NK cell line RNK16. Taken together, these results provide evidence supporting that NK cell function is under circadian regulation.

Characterization of peripheral circadian clocks in adipose tissues

First described in the suprachiasmatic nucleus, circadian clocks have since been found in several peripheral tissues. Although obesity has been associated with dysregulated circadian expression profiles of leptin, adiponectin, and other fat-derived cytokines, there have been no comprehensive analyses of the circadian clock machinery in adipose depots. In this study, we show robust and coordinated expression of circadian oscillator genes (Npas2, Bmal1, Per1-3, and Cry1-2) and clock-controlled downstream genes (Rev-erb alpha, Rev-erb beta, Dbp, E4bp4, Stra13, and Id2) in murine brown, inguinal, and epididymal (BAT, iWAT, and eWAT) adipose tissues. These results correlated with respective gene expression in liver and the serum markers of circadian function. Through Affymetrix microarray analysis, we identified 650 genes that shared circadian expression profiles in BAT, iWAT, and liver. Furthermore, we have demonstrated that temporally restricted feeding causes a coordinated phase-shift in circadian expression of the major oscillator genes and their downstream targets in adipose tissues. The presence of circadian oscillator genes in fat has significant metabolic implications, and their characterization may have potential therapeutic relevance with respect to the pathogenesis and treatment of diseases such as obesity, type 2 diabetes, and the metabolic syndrome.

A novel role of circadian transcription factor DBP in hippocampal plasticity

In neurons, a variety of extracellular stimuli are capable of inducing transcriptional events that underlie complex processes ranging from learning to disease. The mechanisms linking these long-lasting cellular modifications to behavior remain to be established. Here, we show by microarray analysis that hippocampal activation of glucagon-like peptide-1 receptor (GLP-1R), which is associated with improved learning and neuroprotection, results in suppression of the transcription factor DBP (albumin D-site-binding protein). Recombinant adeno-associated virus (rAAV) based gene expression of DBP in the hippocampus of adult rats caused upregulation of mRNAs encoding constituents of the molecular clock, and the DBP target gene, pyridoxal kinase. Behaviorally, DBP over expression inhibited spatial learning but not memory, and enhanced susceptibility to kainate-induced seizures. This phenotype was paralleled by the activation of MAP kinase in dendritic regions of hippocampal neurons in vivo. These data suggest that DBP may represent an important transcriptional link between GLP-1R activation and neuroplasticity in the hippocampus.

Atypical patterns of circadian clock gene expression in human peripheral blood mononuclear cells

Circadian ( approximately 24 h) rhythms in physiology and behaviour are observed in all mammals, including humans. These rhythms are generated by circadian clocks located in the hypothalamus and also in most peripheral tissues. Clock genes are essential components of circadian clocks, and mutations or polymorphisms within several of them have been associated with circadian disorders in humans. However, information about human clock gene expression has remained very limited. Peripheral blood mononuclear cells (PBMCs) represent an ideal material to investigate non-invasively the human clock at the molecular level. In the present study, we analysed the expression of three key clock genes, PER2, BMAL1 and REV-ERBalpha in PBMCs from ten healthy humans over a 24-h cycle. PER2 and BMAL1 were found to oscillate throughout the light-dark cycle in all subjects. Interestingly, despite normal melatonin and cortisol secretion patterns, two groups of subjects could be distinguished with significantly different mean PER2 and BMAL1 acrophases. BMAL1 oscillated with approximately the same phase as PER2, instead of being anti-phasic as anticipated from data previously obtained in other peripheral tissues. Furthermore, this unusual phase relationship of PER2 and BMAL1 in human PBMCs was associated with a constant expression of REV-ERBalpha, a crucial regulator of BMAL1, which is highly rhythmic in many other systems. These results reveal the existence of different chronotypes of clock gene expression patterns and suggest specific regulatory mechanisms in human PBMCs.

Finding new clock components: past and future

The molecular mechanism of circadian clocks has been unraveled primarily by the use of phenotype-driven (forward) genetic analysis in a number of model systems. We are now in a position to consider what constitutes a clock component, whether we can establish criteria for clock components, and whether we have found most of the primary clock components. This perspective discusses clock genes and how genetics, molecular biology, and biochemistry have been used to find clock genes in the past and how they will be used in the future.

It's all in the timing: many clocks, many outputs

It is thought that circadian regulation of physiology and behavior imparts survival advantages to organisms that use clocks. In mammals, a master clock resident in the SCN synchronizes other central and peripheral oscillators to evoke this regulation. This master oscillator consists of interlocking transcriptional-translational feedback loops, and it regulates both core clock genes necessary for oscillator maintenance as well as specific output genes that directly or indirectly mediate physiology under circadian control. It is now clear that both neuroanatomic and molecular outputs of the clock are necessary for proper circadian clock function. Recent technology has improved our understanding of these processes, elucidating the anatomic outputs of the SCN, as well as the molecular outputs of both central and peripheral oscillators that mediate observed physiological changes.

The role of circadian rhythmicity in reproduction

Circadian rhythmicity is evident in a wide range of physiological systems including the reproductive axis. The recent discoveries of rhythmic clock gene expression in peripheral tissues, including reproductive tissue, suggests that they may play an important role in optimizing fertility. The evidence for rhythmic control of reproduction from studies in laboratory animals is reviewed and where possible this includes evidence from human studies. Clock genes are highly conserved across species including humans and there is no reason to suggest that they are functionless in humans. The challenge issued here is for researchers to probe their function and the consequences of their disruption in both animal and human reproduction.

Functional analysis of the basic helix-loop-helix transcription factor DEC1 in circadian regulation. Interaction with BMAL1

The basic helix-loop-helix transcription factor DEC1 is expressed in a circadian manner in the suprachiasmatic nucleus where it seems to play a role in regulating the mammalian circadian rhythm by suppressing the CLOCK/BMAL1-activated promoter. The interaction of DEC1 with BMAL1 has been suggested as one of the molecular mechanisms of the suppression [Honma, S., Kawamoto, T., Takagi, Y., Fujimoto, K., Sato, F., Noshiro, M., Kato, Y. & Honma, K. (2002) Nature 419, 841-844]. Deletion analysis of DEC1 demonstrated that its N-terminal region, which includes the basic helix-loop-helix domain, was essential for both the suppressive activity and the interaction with BMAL1, as DEC1 lacking the basic region did not show any suppression or interaction. Furthermore, we found that Arg65 in the basic region, which is conserved among group B basic helix-loop-helix proteins, was responsible for the suppression, for the interaction with BMAL1 and for its binding to CACGTG E-boxes. However, substitution of His57 for Ala significantly reduced the E-box binding activity of DEC1, although it did not affect the interaction with BMAL1 or suppression of CLOCK/BMAL1-induced transcription. On the other hand, the basic region-deleted DEC1 acted in a dominant-negative manner for DEC1 activity, indicating that the basic region was not required for homodimer formation of DEC1. Moreover, mutant DEC1 also counteracted DEC2-mediated suppressive activity in a dominant-negative manner. The heterodimer formation of DEC1 and DEC2 was confirmed by pull-down assay. These findings suggest that the basic region of DEC1 participates in the transcriptional regulation through a protein-protein interaction with BMAL1 and DNA binding to the E-box.

Expression of the gene for Dec2, a basic helix-loop-helix transcription factor, is regulated by a molecular clock system

Dec2, a member of the basic helix-loop-helix superfamily, is a recently confirmed regulatory protein for the clockwork system. Transcripts of Dec2, as well as those of its related gene Dec1, exhibit a striking circadian oscillation in the suprachiasmatic nucleus, and Dec2 inhibits transcription from the Per1 promoter induced by Clock/Bmal1 [Honma, Kawamoto, Takagi, Fujimoto, Sato, Noshiro, Kato and Honma (2002) Nature (London) 419, 841-844]. It is known that mammalian circadian rhythms are controlled by molecular clockwork systems based on negative-feedback loop(s), but the molecular mechanisms for the circadian regulation of Dec2 gene expression have not been clarified. We show here that transcription of the Dec2 gene is regulated by several clock molecules and a negative-feedback loop. Luciferase and gel retardation assays showed that expression of Dec2 was negatively regulated by binding of Dec2 or Dec1 to two CACGTG E-boxes in the Dec2 promoter. Forced expression of Clock/Bmal1 and Clock/Bmal2 markedly increased Dec2 mRNA levels, and up-regulated the transcription of the Dec2 gene through the CACGTG E-boxes. Like Dec, Cry and Per also suppressed Clock/Bmal-induced transcription from the Dec2 promoter. Moreover, the circadian expression of Dec2 transcripts was abolished in the kidney of Clock/Clock mutant mice. These findings suggest that the Clock/Bmal heterodimer enhances Dec2 transcription via the CACGTG E-boxes, whereas the induced transcription is suppressed by Dec2, which therefore must contribute to its own rhythmic expression. In addition, Cry and Per may also modulate Dec2 transcription.

Resetting Mechanism of Central and Peripheral Circadian Clocks in Mammals

Almost all organisms on earth exhibit diurnal rhythms in physiology and behavior under the control of autonomous time-measuring system called circadian clock. The circadian clock is generally reset by environmental time cues, such as light, in order to synchronize with the external 24-h cycles. In mammals, the core oscillator of the circadian clock is composed of transcription/translation-based negative feedback loops regulating the cyclic expression of a limited number of clock genes (such as Per, Cry, Bmal1, etc.) and hundreds of output genes in a well-concerted manner. The central clock controlling the behavioral rhythm is localized in the hypothalamic suprachiasmatic nucleus (SCN), and peripheral clocks are present in other various tissues. The phase of the central clock is amenable to ambient light signal captured by the visual rod-cone photoreceptors and non-visual melanopsin in the retina. These light signals are transmitted to the SCN through the retinohypothalamic tract, and transduced therein by mitogen-activated protein kinase and other signaling molecules to induce Per gene expression, which eventually elicits phase-dependent phase shifts of the clock. The central clock controls peripheral clocks directly and indirectly by virtue of neural, humoral, and other signals in a coordinated manner. The change in feeding time resets the peripheral clocks in a SCN-independent manner, possibly by food metabolites and body temperature rhythms. In this article, we will provide an overview of recent molecular and genetic studies on the resetting mechanism of the central and peripheral circadian clocks in mammals.