The circadian clock is thought to coordinate aspects of mammalian physiology such as metabolism and the sleep wake cycle. Genetic and molecular characterization of the circadian oscillator shows that interlocked transcriptional/translational feedback loops underlie these rhythms. Recent findings have reinforced the notion that the primary feedback loop plays a vital role in circadian clock function. In this loop, two bHLH-PAS transactivators, Clock and Bmall, heterodimerize and stimulate circadian expression of two potent transcriptional repressors, Cryptochrome 1 and Cryptochrome 2. Once translated, Cry proteins then form a complex with the Period and casein kinase 1 proteins, and translocate to the nucleus where they potently represses Clock/Bmall transcription. This results in the shut down of Cry gene transcription, which eventually results in 'de-repression'of the Clock/BmaM complex and re-initiation of the transcriptional cycle after -24 hours. Although changes in chromatin remodeling and histone acetylation and methylation have been observed to accompany Cry protein repression activity, the molecular mechanism by which Cry proteins act to repress the Clock/Bmall complex remains to be elucidated. Here we propose molecular, cellular, and physiological characterization of the mechanisms underlying clock function including Cry repression. Furthermore, we propose generation of a mouse model that is uncoupled from Cry-mediated feedback repression (a circadian clock knockout) and use this model to investigate the hypothesis that circadian oscillation, rather than the specific clock factors Clock and Bmall, is required to maintain normal metabolic function. Finally, we propose a mechanism-based strategy to identify and characterize small molecules with the capacity to perturb oscillator function via effects on the negative feedback loop. Thus successful completion of the proposed research would result in an important animal model for ascribing circadian clock function in physiology, as well as lay the foundation for mechanism based small molecule perturbation of the clock.

National Institute of Health (NIH)
National Institute of Neurological Disorders and Stroke (NINDS)
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Biological Rhythms and Sleep Study Section (BRS)
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Mitler, Merrill
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University of Pennsylvania
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Anafi, Ron C; Francey, Lauren J; Hogenesch, John B et al. (2017) CYCLOPS reveals human transcriptional rhythms in health and disease. Proc Natl Acad Sci U S A 114:5312-5317
Hughes, Michael E; Abruzzi, Katherine C; Allada, Ravi et al. (2017) Guidelines for Genome-Scale Analysis of Biological Rhythms. J Biol Rhythms 32:380-393
Krishnaiah, Saikumari Y; Wu, Gang; Altman, Brian J et al. (2017) Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism. Cell Metab 25:961-974.e4
Love, Michael I; Hogenesch, John B; Irizarry, Rafael A (2016) Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nat Biotechnol 34:1287-1291
Xu, Lili; Ruan, Guoxiang; Dai, Heng et al. (2016) Mammalian retinal Müller cells have circadian clock function. Mol Vis 22:275-83
Wu, Gang; Anafi, Ron C; Hughes, Michael E et al. (2016) MetaCycle: an integrated R package to evaluate periodicity in large scale data. Bioinformatics 32:3351-3353
Cao, Ruifeng; Gkogkas, Christos G; de Zavalia, Nuria et al. (2015) Light-regulated translational control of circadian behavior by eIF4E phosphorylation. Nat Neurosci 18:855-62
Jang, Christopher; Lahens, Nicholas F; Hogenesch, John B et al. (2015) Ribosome profiling reveals an important role for translational control in circadian gene expression. Genome Res 25:1836-47
DeBruyne, Jason P; Baggs, Julie E; Sato, Trey K et al. (2015) Ubiquitin ligase Siah2 regulates RevErb? degradation and the mammalian circadian clock. Proc Natl Acad Sci U S A 112:12420-5
Lee, Yool; Jang, A Reum; Francey, Lauren J et al. (2015) KPNB1 mediates PER/CRY nuclear translocation and circadian clock function. Elife 4:

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