In mammals, circadian control of physiology and behavior is driven by a master pacemaker located in the suprachiasmatic nuclei (SCN) of the hypothalamus. We have used gene expression profiling to identify cycling transcripts in the SCN and in the liver. Our analysis revealed approximately 650 cycling transcripts and showed that the majority of these were specific to either the SCN or the liver. Genetic and genomic analysis suggests that a relatively small number of output genes are directly regulated by core oscillator components. Major processes regulated by the SCN and liver were found to be under circadian regulation. Importantly, rate-limiting steps in these various pathways were key sites of circadian control, highlighting the fundamental role that circadian clocks play in cellular and organismal physiology.

Mice deficient in the circadian transcription factor BMAL1 (brain and muscle ARNT-like protein) have impaired circadian behavior and demonstrate loss of rhythmicity in the expression of target genes. Here we report that Bmal1 −/− mice have reduced lifespans and display various symptoms of premature aging including sarcopenia, cataracts, less subcutaneous fat, organ shrinkage, and others. The early aging phenotype correlates with increased levels of reactive oxygen species in some tissues of the Bmal1 −/− animals. These findings, together with data on CLOCK/BMAL1-dependent control of stress responses, may provide a mechanistic explanation for the early onset of age-related pathologies in the absence of BMAL1.Supplemental material is available at http://www.genesdev.org.Received March 22, 2006; revised version accepted May 9, 2006. BMAL1 (brain and muscle ARNT-like protein, also known as MOP3 or ARNT3) belongs to the family of the basic helix-loop-helix (bHLH)-PAS domain-containing transcription factors. In a complex with another member of this family, CLOCK, BMAL1 regulates expression of genes through E-box elements in their promoters. BMAL1, CLOCK, and some of their transcriptional targets (PERIODs and CRYPTOCHROMEs) are the key components of the molecular oscillator that generates circadian rhythms. These 24-h oscillations in behavior, physiology, and metabolism are thought to ensure adaptation of organisms to the 24-h periodicity of the Earth's rotation (Panda et al. 2002b;Lowrey and Takahashi 2004). Although the master circadian clock is located within the hypothalamic suprachiasmatic nucleus (SCN), the key circadian proteins are expressed in many peripheral tissues, determining circadian periodicity in gene expression and physiology for many organs (Reppert and Weaver 2002). Indeed, microarray data show that up to 10% of genes in different tissues are directly or indirectly regulated by the circadian clock system (Panda et al. 2002a;Storch et al. 2002). At the same time, only a few oscillating genes (most of them encoding components of the molecular clock itself) are common to all organs tested. Since different tissues have characteristic sets of genes with clock-regulated timing and amplitude of expression (Panda et al. 2002a;Storch et al. 2002), it is likely that the circadian clock is involved in control of homeostasis in different organs.Mice with mutations or targeted disruptions of core circadian genes that have been generated during the last decade all show impaired circadian behavior and deregulation of circadian patterns in gene expression (Lowrey and Takahashi 2004). In addition to this universal phenotype, other pathological defects are specific for particular circadian mutants. Thus, Clock mutation results in reduced fertility and complications of pregnancy (Miller et al. 2004), obesity and metabolic syndrome (Turek et al. 2005), and sensitization to cocaine (McClung et al. 2005). Period2 deficiency leads to the enhanced voluntary alcohol consumption and alterations in the glutamatergic syste...

We used positional cloning to identify the circadian Clock gene in mice. Clock is a large transcription unit with 24 exons spanning approximately 100,000 bp of DNA from which transcript classes of 7.5 and approximately 10 kb arise. Clock encodes a novel member of the bHLH-PAS family of transcription factors. In the Clock mutant allele, an A-->T nucleotide transversion in a splice donor site causes exon skipping and deletion of 51 amino acids in the CLOCK protein. Clock is a unique gene with known circadian function and with features predicting DNA binding, protein dimerization, and activation domains. CLOCK represents the second example of a PAS domain-containing clock protein (besides Drosophila PERIOD), which suggests that this motif may define an evolutionarily conserved feature of the circadian clock mechanism.

The tau mutation is a semidominant autosomal allele that dramatically shortens period length of circadian rhythms in Syrian hamsters. We report the molecular identification of the tau locus using genetically directed representational difference analysis to define a region of conserved synteny in hamsters with both the mouse and human genomes. The tau locus is encoded by casein kinase I epsilon (CKIɛ), a homolog of the Drosophila circadian gene double-time. In vitro expression and functional studies of wild-type and tau mutant CKIɛ enzyme reveal that the mutant enzyme has a markedly reduced maximal velocity and autophosphorylation state. In addition, in vitro CKIɛ can interact with mammalian PERIOD proteins, and the mutant enzyme is deficient in its ability to phosphorylate PERIOD. We conclude that tau is an allele of hamster CKIɛ and propose a mechanism by which the mutation leads to the observed aberrant circadian phenotype in mutant animals.Daily rhythms in biochemical, physiological, and behavioral processes are regulated by biological clocks (1, 2). In natural conditions, the endogenous circadian rhythms that are generated by these clocks are synchronized (entrained) to the 24-hour cycles of the external world by time cues such as the daily light/dark cycle (2). While these clocks are found in organisms as divergent as cyanobacteria, plants, fruit flies, and mammals, there is an extraordinary degree of evolutionary conservation of the underlying generative molecular mechanisms (3-9). The first mammalian circadian gene, Clock, was cloned and characterized in mouse (10-12). Clock encodes a novel member of the basic helix-loop-helix (bHLH) PER-ARNT-SIM (PAS) family of transcription factors. Shortly following the cloning of Clock, three mouse Period orthologs, denoted mPer1 (13,14), and mPer3 (18, 19), as well as a Timeless (mTim) ortholog, were cloned (20)(21)(22)(23)(24). At the same time, another gene, BMAL1 (25), was found to encode the protein dimerization partner for CLOCK (26), and together the CLOCK/BMAL complex was shown to transactivate mPer1 via conserved E-box elements found in the promoters of Drosophila and mouse period genes (26-28). Finally, in Drosophila and mammals, the negative feedback effects of PER and TIM were shown to act at the level of the CLOCK/BMAL complex (20, 28) in a surprisingly direct manner (29, 30).

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 CLOCKregulated 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.cell cycle ͉ circadian rhythms ͉ Clock mutation ͉ gene expression ͉ protein-encoding transcriptome M any organisms have Ϸ24-h rhythms in metabolism, physiology, and behavior that are driven by cell autonomous circadian pacemakers (1). These circadian rhythms allow organisms to coordinate a myriad of physiological processes with the changing environment. In mammals, the circadian pacemaker is composed of interlocked transcription-translation feedback loops: the primary loop is composed of the basic helix-loophelix transcription factors CLOCK and BMAL1, which drive transcription of the Period (Per1, Per2) and Cryptochrome (Cry1, Cry2) genes (1, 2). PER and CRY proteins form the negative limb of the feedback loop by inhibiting their own CLOCK: BMAL1-induced transcription; turnover of PER and CRY allows the cycle to begin anew. The interlocked loop consists of REV-ERB-␣ and ROR␣, which repress and activate the Bmal1 gene, thereby modulating its function (3, 4). Mutation or deletion of Clock (5), Bmal1 (6), Per1/2 genes (7, 8), or Cry1/2 (9, 10) genes results in behavioral arrhythmicity and disruption of the autoregulatory loop, whereas disruption of components of the secondary loop results in short period-length phenotypes (3, 4).The molecular components of the circadian clock are present in the majority of neurons in the suprachiasmatic nucleus (SCN), a bilateral body in the anterior hypot...

As a complementary approach to positional cloning, we used in vivo complementation with bacterial artificial chromosome (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 demonstrates that a large transcription unit spanning approximately 100,000 base pairs is the Clock gene and encodes a novel basic-helix-loop-helix-PAS domain protein. Overexpression of the Clock transgene can shorten period length beyond the wild-type range, which provides additional evidence that Clock is an integral component of the circadian pacemaking system. Taken together, these results provide a proof of principle that "cloning by rescue" is an efficient and definitive method in mice.

Graphical Abstract Highlights d SIRT6 KO mice accumulate L1 cDNA, triggering interferon response via cGAS pathway d Wild-type aged mice accumulate L1 cDNA and display type I interferon response d Reverse-transcriptase inhibitors rescue type I interferon response and DNA damage d Reverse-transcriptase inhibitors extend lifespan and improve health of SIRT6 KO mice SUMMARYMice deficient for SIRT6 exhibit a severely shortened lifespan, growth retardation, and highly elevated LINE1 (L1) activity. Here we report that SIRT6-deficient cells and tissues accumulate abundant cytoplasmic L1 cDNA, which triggers strong type I interferon response via activation of cGAS.Remarkably, nucleoside reverse-transcriptase inhibitors (NRTIs), which inhibit L1 retrotransposition, significantly improved health and lifespan of SIRT6 knockout mice and completely rescued type I interferon response. In tissue culture, inhibition of L1 with siRNA or NRTIs abrogated type I interferon response, in addition to a significant reduction of DNA damage markers. These results indicate that L1 activation contributes to the pathologies of SIRT6 knockout mice. Similarly, L1 transcription, cytoplasmic cDNA copy number, and type I interferons were elevated in the wild-type aged mice. As sterile inflammation is a hallmark of aging, we propose that modulating L1 activity may be an important strategy for attenuating age-related pathologies. Context and SignificanceMammalian aging is complex and likely reflects accumulated damage to our genes/DNA. Retrotransposons are a special class of parasitic genetic elements that can replicate their DNA within our genes, at times amounting to up to 20% of human DNA. Retrotransposons, such as the commonly occurring L1, have been associated with aging, neurodegeneration, and cancer. University of Rochester scientists uncovered L1 retrotransposons as the culprit in many aspects of accelerated aging in mice, a model for human aging. They also linked these special gene elements to inflammation. Experimentally blocking retrotransposon amplification improved the health and lifespan of mice. Although there is a long road ahead, inhibiting retrotransposon activity, and the related inflammation, could eventually be a therapy for age-related diseases.

Mammalian CLOCK and BMAL1 are two members of bHLH-PAS-containing family of transcription factors that represent the positive elements of circadian autoregulatory feedback loop. In the form of a heterodimer, they drive transcription from E-box enhancer elements in the promoters of responsive genes. We have examined abundance, posttranslational modifications, cellular localization of endogenous and ectopically expressed CLOCK and BMAL1 proteins. Nuclear/cytoplasm distribution of CLOCK was found to be under circadian regulation. Analysis of subcellular localization of CLOCK in embryo fibroblasts of mice carrying different germ-line circadian mutations showed that circadian regulation of nuclear accumulation of CLOCK is BMAL1-dependent. Formation of CLOCK/BMAL1 complex following ectopic coexpression of both proteins is followed by their codependent phosphorylation, which is tightly coupled to CLOCK nuclear translocation and degradation. This binding-dependent coregulation is specific for CLOCK/BMAL1 interaction, as no other PAS domain protein that can form a complex with either CLOCK or BMAL1 was able to induce similar effects. Importantly, all posttranslational events described in our study are coupled with active transactivation complex formation, which argues for their significant functional role. Altogether, these results provide evidence for an additional level of circadian system control, which is based on regulation of transcriptional activity or/and availability of CLOCK/BMAL1 complex.[Keywords: Circadian rhythm; CLOCK/BMAL1 complex; transcriptional activation; phosphorylation; nuclear entry] Supplemental material is available at www.genesdev.org.