The circadian clock acts at the genomic level to coordinate internal behavioral and physiologic rhythms via the CLOCK-BMAL transcriptional heterodimer. Although the nuclear receptors REV-ERBα and β have been proposed to form an accessory feedback loop that contributes to clock function1,2, their precise roles and importance remain unresolved. To establish their regulatory potential we generated comparative cistromes of both REV-ERB isoforms, which revealed shared recognition at over 50% of their total sites and extensive overlap with the master circadian regulator BMAL1. While Rev-erbα has been shown to directly regulate Bmal1 expression1,2, the cistromic analysis reveals a direct connection between Bmal1 and Rev-erbα and β regulatory circuits than previously suspected. Genes within the intersection of the BMAL1, REV-ERBα and REV-ERBβ cistromes are highly enriched for both clock and metabolic functions. As predicted by the cistromic analysis, dual depletion of Rev-erbα/β function by creating double-knockout mice (DKOs) profoundly disrupted circadian expression of core circadian clock and lipid homeostatic gene networks. As a result, DKOs show strikingly altered circadian wheel-running behavior and deregulated lipid metabolism. These data now ally Rev-erbα/β with Per, Cry and other components of the principal feedback loop that drives circadian expression and suggest a more integral mechanism for the coordination of circadian rhythm and metabolism.

Obesity and the related disorders of dyslipidemia and diabetes (components of syndrome X) have become global health epidemics. Over the past decade, the elucidation of key regulators of energy balance and insulin signaling have revolutionized our understanding of fat and sugar metabolism and their intimate link. The three 'lipid-sensing' peroxisome proliferator-activated receptors (PPAR-alpha, PPAR-gamma and PPAR-delta) exemplify this connection, regulating diverse aspects of lipid and glucose homeostasis, and serving as bona fide therapeutic targets. With molecular underpinnings now in place, new pharmacologic approaches to metabolic disease and new questions are emerging.

Mammalian metabolism is highly circadian and major hormonal circuits involving nuclear hormone receptors (NRs) display interlinked diurnal cycling1,2. However, mechanisms that logically explain the coordination of NRs and the clock are poorly understood. Here we show that two circadian co-regulators, cryptochromes 1 (Cry1) and 2 (Cry2), interact with the glucocorticoid receptor (GR) in a ligand-dependent fashion and globally alter the transcriptional response to glucocorticoids in mouse embryonic fibroblasts (MEFs): Cry deficiency vastly decreases gene repression and approximately doubles the number of dexamethasone (Dex) induced genes suggesting that cryptochromes broadly oppose GR activation and promote repression. In mice, genetic loss of Cry1 and/or Cry2 resulted in glucose intolerance and constitutively high levels of circulating corticosterone, suggesting reduced suppression of the hypothalamic-pituitary-adrenal (HPA) axis coupled with increased glucocorticoid transactivation in the liver. Genomically, Cry1 and Cry2 associate with a glucocorticoid response element (GRE) in the phosphoenolpyruvate carboxykinase 1 (Pck1) promoter in a hormone-dependent manner, and Dex-induced transcription of pck1 was strikingly increased in Cry-deficient livers. These results reveal a specific mechanism through which cryptochromes couple the activity of clock and receptor target genes to complex genomic circuits underpinning normal metabolic homeostasis.

SUMMARY Liver fibrosis is a reversible wound-healing response involving TGFβ1 activation of hepatic stellate cells (HSCs). Here we show that vitamin D receptor (VDR) ligands inhibit HSC activation and abrogate liver fibrosis, while Vdr knockout mice spontaneously developed hepatic fibrosis. Mechanistically, we describe a pronounced redistribution of genome wide VDR binding sites (VDR cistrome) in HSCs elicited by a TGFβ1 pro-fibrotic insult. This TGFβ1-induced VDR cistrome overlaps extensively with SMAD3 binding sites, with co-occupancy at numerous cis-regulatory elements identified on a large set of pro-fibrotic genes. Addition of VDR ligand reduces SMAD3 occupancy at co-regulated genes, revealing an intersecting VDR/SMAD genomic circuit that regulates hepatic fibrogenesis. These results define a role for VDR as a endocrine checkpoint to modulate the wound healing response in liver, and suggest VDR ligands as a potential therapy for liver fibrosis.

Obesity is a growing threat to global health by virtue of its association with insulin resistance, glucose intolerance, hypertension, and dyslipidemia, collectively known as the metabolic syndrome or syndrome X. The nuclear receptors PPARα and PPARγ are therapeutic targets for hypertriglyceridemia and insulin resistance, respectively, and drugs that modulate these receptors are currently in clinical use. More recent work on the less-described PPAR isotype PPARδ has uncovered a dual benefit for both hypertriglyceridemia and insulin resistance, highlighting the broad potential of PPARδ in the treatment of metabolic disease. PPARδ enhances fatty acid catabolism and energy uncoupling in adipose tissue and muscle, and it suppresses macrophage-derived inflammation. Its combined activities in these and other tissues make it a multifaceted therapeutic target for the metabolic syndrome with the potential to control weight gain, enhance physical endurance, improve insulin sensitivity, and ameliorate atherosclerosis. IntroductionThe prevalence of adult obesity has increased an alarming 75% since 1980, rendering a third of men and women obese in the US (1). This unabated rise has spawned proportionate increases in obesity-associated metabolic disorders, including glucose intolerance, insulin resistance, dyslipidemia, and hypertension, that are well-established risk factors for cardiovascular disease. Known as the metabolic syndrome or syndrome X, this dangerous cluster of pathologies accounts for 6-7% of all-cause mortality and is an expanding health threat. In fact, it is predicted that life expectancy will plateau or decline in the US within the first half of this century because of the magnitude of obesity-associated conditions and the increased rates of obesity in younger populations, particularly children (2, 3). The global obesity problem will require complex solutions, including public health efforts to diminish portion sizes, improve food choices, increase physical activity levels, and raise public awareness. In addition to social and behavioral changes, however, pharmacological interventions to diminish diabetic and cardiovascular complications of the metabolic syndrome are urgently needed.The pathophysiology underlying the metabolic syndrome is incompletely understood, but insulin resistance appears to be an important component (4, 5). Insulin resistance is marked by hyperinsulinemia, enhanced hepatic gluconeogenesis, and impaired insulin-stimulated glucose uptake into skeletal muscle and fat. Elevated levels of circulating FFAs, associated with obesity and insulin resistance, increase fat accumulation in insulin target tissues and contribute to defective insulin action. Indeed, intramuscular fat, based on NMR spectroscopy, correlates strongly with insulin resistance (6). Obese adipose tissue-derived inflammation and altered adipokine secretion may also inhibit insulin signals and affect systemic metabolism (7). The resulting hyperglycemia, dyslipidemia, and hypertension of the metabolic syndrome cause endothelial...

The mammalian transcription factors CLOCK and BMAL1 are essential components of the molecular clock that coordinate behavior and metabolism with the solar cycle. Genetic or environmental perturbation of circadian cycles contributes to metabolic disorders including type 2 diabetes. To study the impact of the cell-autonomous clock on pancreatic β-cell function, we examined islets from mice with either intact or disrupted BMAL1 expression both throughout life and limited to adulthood. We found pronounced oscillation of insulin secretion that was synchronized with the expression of genes encoding secretory machinery and signaling factors that regulate insulin release. CLOCK/BMAL1 co-localized with the pancreatic transcription factor PDX1 within active enhancers distinct from those controlling rhythmic metabolic gene networks in liver. β-cell clock ablation in adult mice caused severe glucose intolerance. Thus cell-type specific enhancers underlie the circadian control of peripheral metabolism throughout life and may help explain its deregulation in diabetes.

Summary How the glucocorticoid receptor (GR) activates some genes while potently repressing others remains an open question. There are three current models for suppression: trans-repression via GR ‘tethering’ to AP-1/NF-κB sites, direct GR association with inhibitory elements (nGREs), and GR recruitment of the corepressor GRIP1. To gain insights into GR suppression, we used genomic analyses and genome-wide profiling of GR, p65, and c-Jun in LPS-stimulated macrophages. We show that GR mediates both activation and repression at tethered sites, GREs, and GRIP1-bound elements, indicating that motif classification is insufficient to predict regulatory polarity of GR binding. Interestingly, sites of GR repression utilize GRIP1’s corepressor function and display reduced histone acetylation. Together, these findings suggest that while GR occupancy confers hormone responsiveness, the receptor itself may not participate in the regulatory effects. Furthermore, transcriptional outcome is not established by sequence, but is influenced by epigenetic regulators, context, and other unrecognized regulatory determinants.

Transcriptional coregulators control the activity of many transcription factors and are thought to have wide ranging effects on gene expression patterns. We show here that muscle-specific nuclear receptor corepressor 1 (NCoR1) knockout mice have rather selective phenotypic changes, characterized by enhanced exercise endurance due to an increase of both muscle mass and of mitochondrial number and activity. The activation of selected transcription factors that control muscle function, such as MEF2, PPARβ/δ and ERRs, underpinned these phenotypic alterations. NCoR1 levels are decreased in conditions that require fat oxidation resetting transcriptional programs to boost oxidative metabolism. The capacity of NCoR1 to modulate oxidative metabolism may be conserved as the knockdown of gei-8, the sole C.elegans NCoR homolog, also robustly increased muscle mitochondria and respiration. Collectively, our data suggest that NCoR1 plays an adaptive role in muscle physiology and that interference with NCoR1 action could be used to improve muscle function.