The miRNA-192/194 cluster regulates the Period gene family and the circadian clock (original) (raw)
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A positive role for PERIOD in mammalian circadian gene expression
Cell reports, 2014
In the current model of the mammalian circadian clock, PERIOD (PER) represses the activity of the circadian transcription factors BMAL1 and CLOCK, either independently or together with CRYPTOCHROME (CRY). Here, we provide evidence that PER has an entirely different function from that reported previously, namely, that PER inhibits CRY-mediated transcriptional repression through interference with CRY recruitment into the BMAL1-CLOCK complex. This indirect positive function of PER is consistent with previous data from genetic analyses using Per-deficient or mutant mice. Overall, our results support the hypothesis that PER plays different roles in different circadian phases: an early phase in which it suppresses CRY activity, and a later phase in which it acts as a transcriptional repressor with CRY. This buffering effect of PER on CRY might help to prolong the period of rhythmic gene expression. Additional studies are required to carefully examine the promoter- and phase-specific roles...
Dual role of the CLOCK/BMAL1 circadian complex in transcriptional regulation
The FASEB Journal, 2006
The basic helix-loop-helix (bHLH) -PAS domain containing transcription factors CLOCK and BMAL1 are two major components of the circadian molecular oscillator. It is known that the CLOCK/BMAL1 complex positively regulates the activity of E-box containing promoters. Here we demonstrate that the CLOCK/BMAL1 complex can also suppress the activity of some promoters upon its interaction with CRYPTOCHROME (CRY). Such a dual function of the circadian transcriptional complex provides a mechanistic explanation for the unpredicted pattern of circadian gene expression in the tissues of Bmal1 null mice. We speculate that the switch from transcriptional activation to transcriptional repression may provide a highly efficient mechanism for circadian control of gene expression. We also show that CLOCK/BMAL1 can interfere with promoter regulation by other, non-circadian, transcription factors including N-MYC and ETS, leading to attenuation or abrogation of transcription of CLOCK/BMAL1-controlled stressinduced genes. We propose that, based upon these results, both circadian repression and activation of the transcription of different target genes are required for circadian responses to various external stimuli, including genotoxic stress induced by anticancer treatment.
2008
The mammalian circadian clockwork is composed of a core PER/CRY feedback loop and additional interlocking loops. In particular, the ROR/REV/Bmal1 loop, consisting of ROR activators and REV-ERB repressors that regulate Bmal1 expression, is thought to ''stabilize'' core clock function. However, due to functional redundancy and pleiotropic effects of gene deletions, the role of the ROR/REV/Bmal1 loop has not been accurately defined. In this study, we examined cell-autonomous circadian oscillations using combined gene knockout and RNA interference and demonstrated that REV-ERBa and b are functionally redundant and are required for rhythmic Bmal1 expression. In contrast, the RORs contribute to Bmal1 amplitude but are dispensable for Bmal1 rhythm. We provide direct in vivo genetic evidence that the REV-ERBs also participate in combinatorial regulation of Cry1 and Rorc expression, leading to their phase-delay relative to Rev-erba. Thus, the REV-ERBs play a more prominent role than the RORs in the basic clock mechanism. The cellular genetic approach permitted testing of the robustness of the intracellular core clock function. We showed that cells deficient in both REV-ERBa and b function, or those expressing constitutive BMAL1, were still able to generate and maintain normal Per2 rhythmicity. Our findings thus underscore the resilience of the intracellular clock mechanism and provide important insights into the transcriptional topologies underlying the circadian clock. Since REV-ERB function and Bmal1 mRNA/protein cycling are not necessary for basic clock function, we propose that the major role of the ROR/REV/Bmal1 loop and its constituents is to control rhythmic transcription of clock output genes.
Neuron, 1998
until recently, it has remained unclear whether the circadian pacemakers of these various organisms share a common molecular mechanism (Dunlap, 1998). Perhaps the circadian system that has been best characterized at the molecular genetic level is that of Drosophila melanogaster (Rosato et al., 1997a; Young, Michael W. Young, § Charles J. Weitz, ‡ 1998). Two oscillator components, period (per) and and Joseph S. Takahashi* † timeless tim), express rhythms in messenger RNA and * Department of Neurobiology and Physiology and protein abundance (Hardin et al., 1990; Edery et al., National Science Foundation Center for 1994; Sehgal et al., 1995; Myers et al., 1996). Mutations Biological Timing in these genes affect both overt circadian rhythms of † Howard Hughes Medical Institute eclosion and locomotor activity (Konopka and Benzer, Northwestern University 1971; Sehgal et al., 1994) as well as molecular oscilla-Evanston, Illinois 60208 tions of per and tim gene products (Hardin et al., 1990; ‡ Department of Neurobiology Sehgal et al., 1995). The per and tim genes are involved in Harvard Medical School a negative autoregulatory feedback loop that underlies Boston, Massachusetts 02115 overt rhythm generation (Hardin et al., 1990; Zeng et al., § Laboratory of Genetics and 1994; Sehgal et al., 1995). The TIMELESS (dTIM) and National Science Foundation Center PERIOD (dPER) proteins physically interact and regulate for Biological Timing the expression of their own mRNAs following nuclear The Rockefeller University entry (Gekakis et al., 1995; Saez and Young, 1996). New York, New York 10021 Work over the past year has demonstrated a striking parallel between the mammalian and Drosophila circadian systems. The Clock gene regulates the period and Summary persistence of circadian rhythms in mice (Vitaterna et al., 1994). The molecular identification of Clock first hinted at We report the cloning and mapping of mouse (mTim) the conservation of the circadian system between flies and human (hTIM) orthologs of the Drosophila timeless and mammals as it encodes a novel basic helix-loop-(dtim) gene. The mammalian Tim genes are widely exhelix (bHLH) PAS (PER-ARNT-SIM) transcription factor pressed in a variety of tissues; however, unlike Dro-(Antoch et al., 1997; King et al., 1997). Subsequently, sophila, mTim mRNA levels do not oscillate in the suthree mammalian Per homologs, mPer1, mPer2, and prachiasmatic nucleus (SCN) or retina. Importantly, mPer3, have been identified. All three genes show oscil-hTIM interacts with the Drosophila PERIOD (dPER) lations in mRNA abundance in the SCN and retina (Alprotein as well as the mouse PER1 and PER2 proteins brecht et al., 1997; Shearman et al., 1997; Shigeyoshi in vitro. In Drosophila (S2) cells, hTIM and dPER interet al., 1997; Sun et al., 1997; Tei et al., 1997; Takumi et act and translocate into the nucleus. Finally, hTIM and al., 1998a, 1998b; Zylka et al., 1998). Recent work has mPER1 specifically inhibit CLOCK-BMAL1-induced shown that CLOCK heterodimerizes with a bHLH-PAS transactivation of the mPer1 promoter. Taken topartner known as BMAL1 or MOP3 (Gekakis et al., 1998; gether, these results demonstrate that mTim and hTIM Hogenesch et al., 1998). The CLOCK-BMAL1 complex are mammalian orthologs of timeless and provide a transactivates the mPer1 promoter specifically via E box framework for a basic circadian autoregulatory loop elements contained within the first 1.2 kb upstream of in mammals. the gene (Gekakis et al., 1998). Concomitantly, the corresponding genes in Drosophila were discovered with the
Biochemical and Biophysical Research Communications, 2000
BMAL1 is a putative clock gene which encodes a basic helix-loop-helix (bHLH)-PAS transcription factor. To examine whether the CLOCK protein is required for the circadian expression of BMAL1 mRNA, in situ hybridization and Northern blot analysis were performed in the suprachiasmatic nucleus (SCN) and peripheral tissues of homozygous Clock mutant mice. In the SCN of Clock mutants, BMAL1 mRNA did not oscillate significantly but apparently expressed with low levels, while in wild-type mice the mRNA was robustly oscillated in a circadian manner. The peaktrough amplitudes of BMAL1 mRNA levels were 6.5-, 8.6-, and 6.7-fold in liver, heart, and kidney of wildtype mice, respectively. In Clock mutants, the amplitudes were extremely damped to 1.2-, 2.1-, and 1.4-fold, respectively. Furthermore, expressions of BMAL1 mRNA in the peripheral of Clock mutant mice were close to the peak level in wild-type mice, whereas mPer2 mRNA levels were severely blunted at trough values. Daily expression of albumin site D-binding protein (DBP), a clock controlled output gene (CCG), was also abolished at trough values by the Clock mutation in all tissues examined. These observations suggest that the circadian expression of BMAL1 mRNA is affected by the CLOCK-induced transcriptional feedback loop in the SCN and peripheral tissues in a different way and that the regulation mechanism appeared to be different from those in mPer2 and DBP expressions in vivo.
Genes To Cells, 2006
A new reporter system for monitoring expressions of two clock genes, Per1 and Bmal1 , from a single tissue in culture was developed in mice. Reporters are Vargula hilgendorfii luciferase (VL) and firefly luciferase (FL), whose activities are increased in parallel with Per1 and Bmal1 expressions, respectively. Formal properties of the circadian system in transgenic mice are indistinguishable from those in wild-type animals. Circadian rhythms in Per1 -VL and Bmal1 -FL in the suprachiasmatic nucleus (SCN) were robust and anti-phasic, although they were phase delayed by 4 -8 h as compared with circadian rhythms in respective transcript levels in vivo . In peripheral tissues such as liver, circadian rhythms in Bmal1 -FL persisted for more than 3 weeks. In the course of prolonged culture, circadian rhythms apparently damped out, but were restored immediately by refreshment of the culture medium. Restoration of the circadian rhythm is unlikely to be due to resetting of desynchronized population oscillation, because peripheral circadian rhythms did not show a type 0 phase response curve (PRC) for medium refreshment, a requirement for instantaneous resetting of circadian oscillation. Long-term persistence of circadian oscillation in spite of external perturbations supports an idea that circadian oscillations in peripheral tissues are self-sustained.
Biochemical and Biophysical Research Communications, 1998
lecular mechanisms involved in the circadian clock are A superfamily gene which encodes a bHLH (basic just beginning to be understood in mammals, substanhelix-loop-helix)/PAS transcription factor, BMAL1, tial progress has been made during the past year by was cloned and sequenced from rat cDNA. A robust the cloning of a mouse clock gene Clock (6, 7). Clock was circadian rhythm of rat BMAL1 expression was deshown to encode a transcription factor which contains a tected by in situ hybridization in the suprachiasmatic protein-protein interaction sequence known as a PAS nucleus (SCN), the site of the circadian clock, with the domain and a DNA binding sequence, basic helix-loophighest level at the subjective night. Less prominent helix (bHLH) (7). However, the expression of Clock in and completely reversed circadian rhythms of rBMAL1 the SCN did not oscillate (8, 9). In the same year, sev-mRNA were observed in the piriform and parietal coreral members of a PAS family were cloned from mamtices. The hybridization signals of rBMAL1 mRNA were malian DNA, which includes homologues of human also detected in the olfactory bulb, hippocampus, and Arnt (BMAL1 or MOP3) (10, 11) and of the Drosophila cerebellum. Since the product of rBMAL1 was recently clock gene Per (mPer1 and mPer2) (8, 9). Although the demonstrated to dimerize with the protein of a mammalian clock gene, Clock, and the protein complex was functions of these genes are not yet clarified, mRNA shown to bind the E Box in the promoter region of levels of mPer1 and mPer2 showed circadian oscillation mPer1 (a mouse homologue to Drosophila clock gene, in the mouse SCN (8, 9). In addition, the gene tran-Per), rBMAL1 possibly plays a critical role in the clock script was increased in response to a short light pulse mechanism generating the circadian oscillation in (12-14). Because of structural similarities to Drosophrats. ᭧ 1998 Academic Press EMBL, and GenBank nucleotide sequence databases under Accesbe the mutants of BMAL1 homologue and Drosophila sion No. AB012600.
System-level identification of transcriptional circuits underlying mammalian circadian clocks
Nature Genetics, 2005
Mammalian circadian clocks consist of complexly integrated regulatory loops 1-5 , making it difficult to elucidate them without both the accurate measurement of system dynamics and the comprehensive identification of network circuits 6 . Toward a system-level understanding of this transcriptional circuitry, we identified clock-controlled elements on 16 clock and clock-controlled genes in a comprehensive surveillance of evolutionarily conserved cis elements and measurement of their transcriptional dynamics. Here we report the roles of E/E¢ boxes, DBP/E4BP4 binding elements 7 and RevErbA/ROR binding elements 8 in nine, seven and six genes, respectively. Our results indicate that circadian transcriptional circuits are governed by two design principles: regulation of E/E¢ boxes and RevErbA/ROR binding elements follows a repressor-precedes-activator pattern, resulting in delayed transcriptional activity, whereas regulation of DBP/E4BP4 binding elements follows a repressor-antiphasic-to-activator mechanism, which generates high-amplitude transcriptional activity. Our analysis further suggests that regulation of E/E¢ boxes is a topological vulnerability in mammalian circadian clocks, a concept that has been functionally verified using in vitro phenotype assay systems.
Mammalian Circadian Clock: The Roles of Transcriptional Repression and Delay
Handbook of Experimental Pharmacology, 2013
The circadian clock is an endogenous oscillator with a 24-h period. Although delayed feedback repression was proposed to lie at the core of the clock more than 20 years ago, the mechanism for making delay in feedback repression in clock function has only been demonstrated recently. In the mammalian circadian clock, delayed feedback repression is mediated through E/E 0-box, D-box, and RRE transcriptional cis-elements, which activate or repress each other through downstream transcriptional activators/repressors. Among these three types of cis-elements, transcriptional negative feedback mediated by E/E 0-box plays a critical role for circadian rhythms. A recent study showed that a combination of D-box and RRE elements results in the delayed expression of Cry1, a potent transcriptional inhibitor of the E/E 0-box. The overall interconnection of these cis-elements can be summarized as a combination of two oscillatory motifs: one is a simple delayed feedback repression where only an RRE represses an E/E 0-box, and the other is a repressilator where each element inhibits another in turn (i.e., E/E 0 box represses an RRE, an RRE represses a D-box, and a D-box represses an E/E 0 box). Experimental verification of the roles of each motif as well as post-transcriptional regulation of the circadian oscillator will be the next challenges.