Clocks, metabolism, and the epigenome.

[1]  P. Sassone-Corsi,et al.  PER2 controls lipid metabolism by direct regulation of PPARγ. , 2010, Cell metabolism.

[2]  S. Shimba,et al.  Deficient of a Clock Gene, Brain and Muscle Arnt-Like Protein-1 (BMAL1), Induces Dyslipidemia and Ectopic Fat Formation , 2011, PloS one.

[3]  D. Reinberg,et al.  Calorie restriction and the exercise of chromatin. , 2009, Genes & development.

[4]  M. Bucan,et al.  Nuclear Receptor Corepressor-Histone Deacetylase 3 Governs Circadian Metabolic Physiology , 2008, Nature.

[5]  Y. Fujii‐Kuriyama,et al.  Transactivation mechanisms of mouse clock transcription factors, mClock and mArnt3 , 2000, Genes to cells : devoted to molecular & cellular mechanisms.

[6]  Tao Liu,et al.  A Circadian Rhythm Orchestrated by Histone Deacetylase 3 Controls Hepatic Lipid Metabolism , 2011, Science.

[7]  Brian J. Wilson,et al.  Genomic Convergence among ERRα, PROX1, and BMAL1 in the Control of Metabolic Clock Outputs , 2011, PLoS genetics.

[8]  A. Nakashima,et al.  Effects of fasting and re-feeding on the expression of Dec1, Per1, and other clock-related genes. , 2006, Journal of biochemistry.

[9]  P. Sassone-Corsi,et al.  Circadian Control of the NAD+ Salvage Pathway by CLOCK-SIRT1 , 2009, Science.

[10]  U. Schibler,et al.  The mammalian circadian timing system: organization and coordination of central and peripheral clocks. , 2010, Annual review of physiology.

[11]  J. Takahashi,et al.  Regulation of Circadian Behavior and Metabolism by Synthetic REV-ERB Agonists , 2012, Nature.

[12]  Kathryn S Lilley,et al.  Glucocorticoid signaling synchronizes the liver circadian transcriptome , 2007, Hepatology.

[13]  S. Panda,et al.  AMPK Regulates the Circadian Clock by Cryptochrome Phosphorylation and Degradation , 2009, Science.

[14]  Ueli Schibler,et al.  Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions , 2006, Nature Genetics.

[15]  J. Zierath,et al.  Relationship between AMPK and the transcriptional balance of clock-related genes in skeletal muscle. , 2008, American journal of physiology. Endocrinology and metabolism.

[16]  C. Fontaine,et al.  The role of the orphan nuclear receptor Rev-Erbα in adipocyte differentiation and function , 2005 .

[17]  R. Akhtar,et al.  Circadian Cycling of the Mouse Liver Transcriptome, as Revealed by cDNA Microarray, Is Driven by the Suprachiasmatic Nucleus , 2002, Current Biology.

[18]  C. Fontaine,et al.  The role of the orphan nuclear receptor Rev-Erb alpha in adipocyte differentiation and function. , 2005, Biochimie.

[19]  W. Wahli,et al.  Reciprocal regulation of brain and muscle Arnt-like protein 1 and peroxisome proliferator-activated receptor alpha defines a novel positive feedback loop in the rodent liver circadian clock. , 2006, Molecular endocrinology.

[20]  S. Khorasanizadeh,et al.  Identification of heme as the ligand for the orphan nuclear receptors REV-ERBα and REV-ERBβ , 2007, Nature Structural &Molecular Biology.

[21]  O. Froy.  The relationship between nutrition and circadian rhythms in mammals , 2007, Frontiers in Neuroendocrinology.

[22]  A. B. Reddy,et al.  Genetic and molecular analysis of the central and peripheral circadian clockwork of mice. , 2007, Cold Spring Harbor symposia on quantitative biology.

[23]  S. Jitrapakdee.  Transcription factors and coactivators controlling nutrient and hormonal regulation of hepatic gluconeogenesis. , 2012, The international journal of biochemistry & cell biology.

[24]  Ueli Schibler,et al.  System-Driven and Oscillator-Dependent Circadian Transcription in Mice with a Conditionally Active Liver Clock , 2007, PLoS biology.

[25]  Steven A. Brown,et al.  PERIOD1-Associated Proteins Modulate the Negative Limb of the Mammalian Circadian Oscillator , 2005, Science.

[26]  Norio Iijima,et al.  Circadian and Light-Induced Transcription of Clock Gene Per1 Depends on Histone Acetylation and Deacetylation , 2004, Molecular and Cellular Biology.

[27]  A. B. Reddy,et al.  Circadian Clocks in Human Red Blood Cells , 2010, Nature.

[28]  H. S. Kang,et al.  Retinoic acid-related orphan receptor γ directly regulates neuronal PAS domain protein 2 transcription in vivo , 2011, Nucleic acids research.

[29]  Florian Kreppel,et al.  SIRT1 Regulates Circadian Clock Gene Expression through PER2 Deacetylation , 2008, Cell.

[30]  M. Gilles-Gonzalez,et al.  Signal transduction by heme-containing PAS-domain proteins. , 2004, Journal of applied physiology.

[31]  M. Lazar,et al.  Negative feedback maintenance of heme homeostasis by its receptor, Rev-erbalpha. , 2009, Genes & development.

[32]  Dmitri A. Nusinow,et al.  Cryptochrome Mediates Circadian Regulation of cAMP Signaling and Hepatic Gluconeogenesis , 2010, Nature Medicine.

[33]  S. Panda,et al.  Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression , 2009, Proceedings of the National Academy of Sciences.

[34]  Joseph S. Takahashi,et al.  Circadian Integration of Metabolism and Energetics , 2010, Science.

[35]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[36]  D. Hems,et al.  Fatty acid synthesis in liver and adipose tissue of normal and genetically obese (ob/ob) mice during the 24-hour cycle. , 1975, The Biochemical journal.

[37]  S. Ragsdale,et al.  Thiol-disulfide Redox Dependence of Heme Binding and Heme Ligand Switching in Nuclear Hormone Receptor Rev-erbβ* , 2010, The Journal of Biological Chemistry.

[38]  J. Takahashi,et al.  Circadian Clock Feedback Cycle Through NAMPT-Mediated NAD+ Biosynthesis , 2009, Science.

[39]  Jared Rutter,et al.  Regulation of Clock and NPAS2 DNA Binding by the Redox State of NAD Cofactors , 2001, Science.

[40]  Kathryn Moynihan Ramsey,et al.  High-fat diet disrupts behavioral and molecular circadian rhythms in mice. , 2007, Cell metabolism.

[41]  G. Eichele,et al.  The circadian rhythm of glucocorticoids is regulated by a gating mechanism residing in the adrenal cortical clock. , 2006, Cell metabolism.

[42]  B. Viollet,et al.  AMPK Regulates Circadian Rhythms in a Tissue- and Isoform-Specific Manner , 2011, PloS one.

[43]  J. Auwerx,et al.  Calorie restriction: is AMPK a key sensor and effector? , 2011, Physiology.

[44]  P. Puigserver,et al.  AMPK regulates energy expenditure by modulating NAD+ metabolism and SIRT1 activity , 2009, Nature.

[45]  D. Freyssenet.  Energy sensing and regulation of gene expression in skeletal muscle. , 2007, Journal of applied physiology.

[46]  M. Lazar,et al.  E3 ligases Arf-bp1 and Pam mediate lithium-stimulated degradation of the circadian heme receptor Rev-erbα , 2010, Proceedings of the National Academy of Sciences.

[47]  Satchidananda Panda,et al.  Regulation of Circadian Behavior and Metabolism by Rev-erbα and Rev-erbβ , 2012, Nature.

[48]  Steven M. Reppert,et al.  Rhythmic histone acetylation underlies transcription in the mammalian circadian clock , 2003, Nature.

[49]  G. Chrousos,et al.  Peripheral CLOCK Regulates Target-Tissue Glucocorticoid Receptor Transcriptional Activity in a Circadian Fashion in Man , 2011, PloS one.

[50]  Kathryn S. Lilley,et al.  Circadian Orchestration of the Hepatic Proteome , 2006, Current Biology.

[51]  Satchidananda Panda,et al.  Histone Lysine Demethylase JARID1a Activates CLOCK-BMAL1 and Influences the Circadian Clock , 2011, Science.

[52]  J. Ripperger,et al.  The mammalian clock component PERIOD2 coordinates circadian output by interaction with nuclear receptors. , 2010, Genes & development.

[53]  B. Christensen,et al.  Epigenomics in Environmental Health , 2011, Front. Gene..

[54]  Logan J Everett,et al.  Rev-erbα and Rev-erbβ coordinately protect the circadian clock and normal metabolic function. , 2012, Genes & development.

[55]  S. Shimba,et al.  Brain and muscle Arnt-like protein-1 (BMAL1), a component of the molecular clock, regulates adipogenesis. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Cheng Chi Lee,et al.  Reciprocal regulation of haem biosynthesis and the circadian clock in mammals , 2004, Nature.

[57]  Felix Naef,et al.  Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver , 2011, PLoS biology.

[58]  Wilhelm Haas,et al.  Nutrient control of glucose homeostasis through a complex of PGC-1α and SIRT1 , 2005, Nature.

[59]  R. DePinho,et al.  Inactivation of hepatic Foxo1 by insulin signaling is required for adaptive nutrient homeostasis and endocrine growth regulation. , 2008, Cell metabolism.

[60]  A. Jetten.  Retinoid-related orphan receptors (RORs): critical roles in development, immunity, circadian rhythm, and cellular metabolism , 2009, Nuclear receptor signaling.

[61]  Paolo Sassone-Corsi,et al.  The NAD+-Dependent Deacetylase SIRT1 Modulates CLOCK-Mediated Chromatin Remodeling and Circadian Control , 2008, Cell.

[62]  R. Evans,et al.  Cryptochromes mediate rhythmic repression of the glucocorticoid receptor , 2011, Nature.

[63]  Paolo Sassone-Corsi,et al.  CLOCK-mediated acetylation of BMAL1 controls circadian function , 2007, Nature.

[64]  Weimin He,et al.  Nuclear Receptor Expression Links the Circadian Clock to Metabolism , 2006, Cell.

[65]  Jason P. DeBruyne,et al.  The Polycomb Group Protein EZH2 Is Required for Mammalian Circadian Clock Function*♦ , 2006, Journal of Biological Chemistry.

[66]  C. Fontaine,et al.  Regulation of bile acid synthesis by the nuclear receptor Rev-erbalpha. , 2008, Gastroenterology.

[67]  J. Yates,et al.  A Fasting Inducible Switch Modulates Gluconeogenesis Via Activator-Coactivator Exchange , 2008, Nature.

[68]  Siyu Chen,et al.  SWItch/sucrose nonfermentable (SWI/SNF) complex subunit BAF60a integrates hepatic circadian clock and energy metabolism , 2011, Hepatology.

[69]  Hong Wang,et al.  Hepatic Hdac3 promotes gluconeogenesis by repressing lipid synthesis and sequestration , 2012, Nature Medicine.

[70]  Paolo Sassone-Corsi,et al.  The histone methyltransferase MLL1 permits the oscillation of circadian gene expression , 2010, Nature Structural &Molecular Biology.

[71]  T. Kino,et al.  Circadian rhythm transcription factor CLOCK regulates the transcriptional activity of the glucocorticoid receptor by acetylating its hinge region lysine cluster: potential physiological implications , 2009, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[72]  Ueli Schibler,et al.  REV-ERBα Participates in Circadian SREBP Signaling and Bile Acid Homeostasis , 2009, PLoS biology.

[73]  P. Saha,et al.  Absence of the SRC-2 Coactivator Results in a Glycogenopathy Resembling Von Gierke's Disease , 2008, Science.

[74]  Charles E. Vejnar,et al.  Integration of microRNA miR-122 in hepatic circadian gene expression. , 2009, Genes & development.

[75]  Andrew J. Millar,et al.  Circadian rhythms persist without transcription in a eukaryote , 2010, Nature.

[76]  H. Krause,et al.  The Structural Basis of Gas-Responsive Transcription by the Human Nuclear Hormone Receptor REV-ERBβ , 2009, PLoS biology.

[77]  J. Gimble,et al.  Fat circadian biology. , 2009, Journal of applied physiology.

[78]  R. D. Rudic,et al.  Histone Acetyltransferase-dependent Chromatin Remodeling and the Vascular Clock* , 2004, Journal of Biological Chemistry.

[79]  R. A. Reid,et al.  Rev-erbalpha, a heme sensor that coordinates metabolic and circadian pathways. , 2007, Science.

[80]  Y Sakaki,et al.  Entrainment of the circadian clock in the liver by feeding. , 2001, Science.

[81]  M. Lazar,et al.  The N-CoR/Histone Deacetylase 3 Complex Is Required for Repression by Thyroid Hormone Receptor , 2003, Molecular and Cellular Biology.

[82]  P. Sassone-Corsi,et al.  Altered behavioral and metabolic circadian rhythms in mice with disrupted NAD+ oscillation , 2011, Aging.

[83]  R. Virk,et al.  The clock gene Per2 links the circadian system to the estrogen receptor , 2007, Oncogene.

[84]  Alec J Davidson,et al.  Daily oscillations in liver function: diurnal vs circadian rhythmicity , 2004, Liver international : official journal of the International Association for the Study of the Liver.

[85]  P. Farnham.  Insights from genomic profiling of transcription factors , 2009, Nature Reviews Genetics.

[86]  T. Key,et al.  Shift work and chronic disease: the epidemiological evidence , 2011, Occupational medicine.

[87]  Joseph S. Takahashi,et al.  Disruption of the Clock Components CLOCK and BMAL 1 Leads to Hypoinsulinemia and Diabetes , 2012 .

[88]  Lei Yin,et al.  The orphan nuclear receptor Rev-erbalpha recruits the N-CoR/histone deacetylase 3 corepressor to regulate the circadian Bmal1 gene. , 2005, Molecular endocrinology.

[89]  U. Schibler,et al.  Poly(ADP-Ribose) Polymerase 1 Participates in the Phase Entrainment of Circadian Clocks to Feeding , 2010, Cell.

[90]  M. Lambert,et al.  Structure of Rev-erbα bound to N-CoR reveals a unique mechanism of nuclear receptor–co-repressor interaction , 2010, Nature Structural &Molecular Biology.

[91]  S. McKnight,et al.  NPAS2: A Gas-Responsive Transcription Factor , 2002, Science.

[92]  C. Weitz,et al.  A Molecular Mechanism for Circadian Clock Negative Feedback , 2011, Science.

[93]  Joseph S. Takahashi,et al.  The Meter of Metabolism , 2008, Cell.

[94]  Steven A. Brown,et al.  Rhythms of Mammalian Body Temperature Can Sustain Peripheral Circadian Clocks , 2002, Current Biology.

[95]  D. Moore,et al.  Circadian Dysregulation Disrupts Bile Acid Homeostasis , 2009, PloS one.

[96]  B. H. Miller,et al.  Coordinated Transcription of Key Pathways in the Mouse by the Circadian Clock , 2002, Cell.

[97]  Kai-Florian Storch,et al.  Physiological significance of a peripheral tissue circadian clock , 2008, Proceedings of the National Academy of Sciences.

[98]  S. Shibata,et al.  Refeeding after Fasting Elicits Insulin-Dependent Regulation of Per2 and Rev-erbα with Shifts in the Liver Clock , 2011, Journal of biological rhythms.

[99]  Steven A. Brown,et al.  Resetting of circadian time in peripheral tissues by glucocorticoid signaling. , 2000, Science.

[100]  F. Fleury-Olela,et al.  Restricted feeding uncouples circadian oscillators in peripheral tissues from the central pacemaker in the suprachiasmatic nucleus. , 2000, Genes & development.

[101]  Kathryn Moynihan Ramsey,et al.  Circadian rhythms, sleep, and metabolism. , 2011, The Journal of clinical investigation.

[102]  The circadian change of gluconeogenesis in the liver in vivo in fed rats. , 1980, Journal of biochemistry.

[103]  Fred W. Turek,et al.  Obesity and Metabolic Syndrome in Circadian Clock Mutant Mice , 2005, Science.

[104]  Satchidananda Panda,et al.  BMAL1 and CLOCK, Two Essential Components of the Circadian Clock, Are Involved in Glucose Homeostasis , 2004, PLoS biology.

[105]  B. Viollet,et al.  Activation of 5′-AMP-activated Kinase with Diabetes Drug Metformin Induces Casein Kinase Iϵ (CKIϵ)-dependent Degradation of Clock Protein mPer2* , 2007, Journal of Biological Chemistry.

[106]  S. Khorasanizadeh,et al.  Identification of heme as the ligand for the orphan nuclear receptors REV-ERBalpha and REV-ERBbeta. , 2007, Nature structural & molecular biology.

[107]  Paolo Sassone-Corsi,et al.  Circadian Regulator CLOCK Is a Histone Acetyltransferase , 2006, Cell.

[108]  Ueli Schibler,et al.  The Orphan Nuclear Receptor REV-ERBα Controls Circadian Transcription within the Positive Limb of the Mammalian Circadian Oscillator , 2002, Cell.