The circadian clock mechanism in the mouse is composed of interlocking transcriptional feedback loops. Two transcription factors, CLOCK and BMAL1, are believed to be essential components of the circadian clock. We have used the Cre-LoxP system to generate whole-animal knockouts of CLOCK and evaluated the resultant circadian phenotypes. Surprisingly, CLOCK-deficient mice continue to express robust circadian rhythms in locomotor activity, although they do have altered responses to light. At the molecular and biochemical levels, clock gene mRNA and protein levels in both the master clock in the suprachiasmatic nuclei and a peripheral clock in the liver show alterations in the CLOCK-deficient animals, although the molecular feedback loops continue to function. Our data challenge a central feature of the current mammalian circadian clock model regarding the necessity of CLOCK:BMAL1 heterodimers for clock function.

Heterodimers of CLOCK and BMAL1, bHLH-PAS transcription factors, are believed to be the major transcriptional regulators of the circadian clock mechanism in mammals. However, a recent study shows that CLOCK-deficient mice continue to exhibit robust behavioral and molecular rhythms. Here we report that the transcription factor NPAS2 (MOP4) is able to functionally substitute for CLOCK in the master brain clock in mice to regulate circadian rhythmicity.

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them.

Both casein kinase 1 delta (CK1␦) and epsilon (CK1) phosphorylate core clock proteins of the mammalian circadian oscillator. To assess the roles of CK1␦ and CK1 in the circadian clock mechanism, we generated mice in which the genes encoding these proteins (Csnk1d and Csnk1e, respectively) could be disrupted using the Cre-loxP system. Cre-mediated excision of the floxed exon 2 from Csnk1d led to in-frame splicing and production of a deletion mutant protein (CK1␦ ⌬2 ). This product is nonfunctional. Mice homozygous for the allele lacking exon 2 die in the perinatal period, so we generated mice with liver-specific disruption of CK1␦. In livers from these mice, daytime levels of nuclear PER proteins, and PER-CRY-CLOCK complexes were elevated. In vitro, the half-life of PER2 was increased by ϳ20%, and the period of PER2::luciferase bioluminescence rhythms was 2 h longer than in controls. Fibroblast cultures from CK1␦-deficient embryos also had long-period rhythms. In contrast, disruption of the gene encoding CK1 did not alter these circadian endpoints. These results reveal important functional differences between CK1␦ and CK1: CK1␦ plays an unexpectedly important role in maintaining the 24-h circadian cycle length.Circadian rhythms are rhythms in gene expression, metabolism, physiology, and behavior that persist in constant environmental conditions with a cycle length near 24 h. In mammals, the circadian timing system is hierarchical. The primary pacemaker regulating circadian behavioral rhythms is located in the suprachiasmatic nuclei (SCN) of the hypothalamus. Most cell types express circadian clock genes and will express rhythmicity in vitro. In vivo, the SCN entrains peripheral oscillators through a complex set of physiological and hormonal rhythms (31,32,36).At the molecular level, circadian oscillations are governed by a cell-autonomous negative-feedback loop in which transcription factors drive the expression of their own negative regulators, leading to oscillation between periods of transcriptional activation and repression (reviewed in references 32 and 36). The bHLH-PAS containing transcription factors CLOCK or NPAS2 form heterodimers with BMAL1. These heterodimers binds to E-box elements within regulatory regions of Period (Per1, Per2, and Per3) and Cryptochrome (Cry1 and Cry2) genes to stimulate their transcription. Approximately 12 h after transcriptional activation, PER and CRY proteins reach concentrations sufficient to form repressor complexes that inhibit the activity of the CLOCK/NPAS2:BMAL1 heterodimer, reducing the transcription of Per and Cry genes and subsequently relieving PER/CRY-mediated negative feedback. E-box-mediated expression of other transcription factors, including members of the DBP/HLF/TEF and nuclear orphan receptor families (e.g., Rev-Erb␣ and ROR-A), provides a mechanism for clock control of genes with diverse promoters and with gene expression peaks occurring at a variety of phases.Posttranslational modifications of circadian clock proteins play a well-established role in the re...

We examined the importance of histone methylation by the polycomb group proteins in the mouse circadian clock mechanism. Endogenous EZH2, a polycomb group enzyme that methylates lysine 27 on histone H3, co-immunoprecipitates with CLOCK and BMAL1 throughout the circadian cycle in liver nuclear extracts. Chromatin immunoprecipitation revealed EZH2 binding and di-and trimethylation of H3K27 on both the Period 1 and Period 2 promoters. A role of EZH2 in cryptochrome-mediated transcriptional repression of the clockwork was supported by overexpression and RNA interference studies. Serum-induced circadian rhythms in NIH 3T3 cells in culture were disrupted by transfection of an RNA interfering sequence targeting EZH2. These results indicate that EZH2 is important for the maintenance of circadian rhythms and extend the activity of the polycomb group proteins to the core clockwork mechanism of mammals.The circadian clock mechanism in the mouse is driven by interacting positive and negative transcriptional feedback loops (1, 2). The negative feedback loop is essential for clockwork function and involves CLOCK⅐BMAL1 enhanced expression of three Period genes (mPer 1-3) and two Cryptochrome genes (mCry1 and mCry2) (3-5). Negative feedback is provided by a CRY⅐PER complex that rhythmically enters the nucleus to inhibit CLOCK⅐BMAL1-mediated transcription via a mechanism that does not substantially alter CLOCK⅐BMAL1 binding to mPer1 and mPer2 promoters (3, 6). Other clockcontrolled genes may be regulated by other mechanisms, as CLOCK⅐BMAL1 binds rhythmically to the promoter of the Dbp gene (7).The positive transcriptional feedback loop involves the regulation of Bmal1 transcription by CLOCK⅐BMAL1-mediated transcription of the nuclear orphan receptor genes Rev-erb␣ and Rora (8 -11). The orphan receptor gene products act on the Bmal1 promoter to generate a circadian rhythm in Bmal1 RNA levels that is antiphase to the mPer and mCry RNA rhythms. The positive feedback loop appears to provide stability to the core clock mechanism (12).Changes in chromatin structure due to post-translational modifications of histones are required for transcriptional regulation of gene expression (13,14), and circadian genes are no exception (7,(15)(16)(17)(18). Previously, we showed in the liver clock that the promoter regions of mPer1 and mPer2 undergo rhythmic acetylation of histone H3 that correlates with their transcriptional activation (16). We proposed that at the time of transcriptional inhibition the mCRY proteins disrupt a CLOCK⅐BMAL1⅐coactivator complex thereby reducing histone acetyltransferase activity. As histone deacetylase activity is constantly associated with the CLOCK⅐BMAL1 nuclear complex, the balance between acetylation and deacetylation of H3 on circadian promoters appears to be regulated by the rhythmic regulation of histone acetyltransferase activity, with deacetylation predominating during transcriptional repression. Other groups have also reported H3 acetylation rhythms at circadian promoters (17,18).Our search for other chroma...