Nuclear receptors rock around the clock

Abstract

Circadian rhythms characterize almost every aspect of human physiology, endocrinology, xenobiotic detoxification, cell growth, and behavior. Modern lifestyles that disrupt our normal circadian rhythms are increasingly thought to contribute to various disease conditions ranging from depression and metabolic disorders to cancer. This self-sustained time-keeping system is generated and maintained by an endogenous molecular machine, the circadian clock, which is a transcriptional mechanism composed of the transcription factors CLOCK and BMAL and their co-repressors, PER and CRY. Nuclear receptors (NRs) represent a large family of hormone-sensitive transcriptional regulators involved in a myriad of biological processes such as development, energy metabolism, reproduction, inflammation, and tissue homeostasis. Recent studies point not only to NR regulation by the clock, but also to NR regulation of the clock itself. Here, we discuss recent studies that functionally and mechanistically implicate NRs as key components of both the universal and adaptive circadian clock mechanisms. As proven pharmacological targets, nuclear receptors are promising targets for therapeutic control of many pathological conditions associated with the disruption of circadian rhythm.

Figure 1. Canonical model of the circadian clock and the emerging model of the circadian clock in mammals

(A) In the canonical model of the circadian clock, CLOCK and BMAL1 regulate the expression of Cry and Per. PER and CRY inhibit CLOCK and BMAL1 transcriptional activity, forming a negative feedback loop. This has long been thought to be sufficient to explain the transcriptional timing mechanism. Other factors such as REV-ERB were thought to act as a “stabilizer” , or “output” . (B) In the emerging model of the molecular clock, nuclear receptors (NRs), evidenced most prominently by REV-ERBs, bind to NREs found in all core clock genes and help to orchestrate positive and negative gene expression. Many NRs are thought to share occupancy at these NREs , suggesting multiple orders of redundancy, compensation, and/or co-regulation at these circadian control points in the genome. Evidence of collaboration between canonical circadian clock components, such as CLOCK, PER, and CRY, arises from genome-wide ChIP-sequencing experiments, as well as classical biochemistry experiments (summarized in Table 1). Furthermore, classical NR co-regulators have been implicated in circadian time keeping.

Figure 2. The activities of NRs are controlled by co-regulators

Co-activators recruit histone acetyltransferases (HATs) such as CBP/p300 to activate gene expression. Examples of co-activators are SRC family members, RIP140, PGC-1α, MAGED1. Co-repressors, such as SMRT and NCoR, recruit histone deacetylase 3 (HDAC3) to repress gene expression. In addition, canonical circadian clock regulators such as Cry and Per are also important cofactors to regulate the activities of NRs in circadian rhythms and metabolism.

Figure 3. Post-translational regulation of NRs controls their circadian activities

Rev-erbα is subject to several post-translational modifications such as phosphorylation and ubiquitination. These modifications change the protein stability and transcriptional activity of Rev-erbα. Other core circadian clock components such as BMAL1, CLOCK, PER, and CRY are also subject to a wide variety of post-translational modifications, such as sumoylation, acetylation, phosphorylation, and ubiquitination. Nocturnin, encoding a deadenylase that follows a 24-h oscillatory expression pattern, has been shown to be a downstream target of the nuclear receptor PPARγ as well as of BMAL1/CLOCK. Nocturnin also interacts with PPARγ and promotes its nuclear translocation.

Figure 4. The cellular metabolite NAD⁺ is involved in the regulation of circadian clocks

The NAD⁺-dependent deacetylase SIRT1 deacetylates and thereby activates the core clock components BMAL1 and PER2. Nicotinamide phosphoribosyltransferase (NAMPT), the enzyme that catalyzes the rate-limiting step of NAD⁺ biosynthesis and NAD⁺ salvage pathways, is a direct downstream target of BMAL1 and exhibits an oscillatory expression pattern inside cells. Therefore, the NAD⁺ level also oscillates inside cells and controls the activity of SIRT1 in this feedback loop. SIRT1 also modulates the activities of several NRs such as LXR and PPARγ as well as the cofactor PGC-1α. In this way, SIRT1 functions to integrate nuclear receptor-regulated metabolic processes with circadian clocks via cellular NAD⁺ levels. At the same time, the level of NAD⁺ is also subject to regulation by environmental cues such as food intake or exercise. It could serve as an important mechanism of circadian clock entrainment.