In-vivo quantitative proteomics reveals a key contribution of post-transcriptional mechanisms to the circadian regulation of liver metabolism

Timing of circadian genes in mammalian tissues

Circadian clocks are endogenous oscillators driving daily rhythms in physiology. The cell-autonomous clock is governed by an interlocked network of transcriptional feedback loops. Hundreds of clock-controlled genes (CCGs) regulate tissue specific functions. Transcriptome studies reveal that different organs (e.g. liver, heart, adrenal gland) feature substantially varying sets of CCGs with different peak phase distributions. To study the phase variability of CCGs in mammalian peripheral tissues, we develop a core clock model for mouse liver and adrenal gland based on expression profiles and known cis-regulatory sites. ‘Modulation factors’ associated with E-boxes, ROR-elements, and D-boxes can explain variable rhythms of CCGs, which is demonstrated for differential regulation of cytochromes P450 and 12 h harmonics. By varying model parameters we explore how tissue-specific peak phase distributions can be generated. The central role of E-boxes and ROR-elements is confirmed by analysing ChIP-seq data of BMAL1 and REV-ERB transcription factors.

Circadian control of tissue homeostasis and adult stem cells

The circadian timekeeping mechanism adapts physiology to the 24-hour light/dark cycle. However, how the outputs of the circadian clock in different peripheral tissues communicate and synchronize each other is still not fully understood. The circadian clock has been implicated in the regulation of numerous processes, including metabolism, the cell cycle, cell differentiation, immune responses, redox homeostasis, and tissue repair. Accordingly, perturbation of the machinery that generates circadian rhythms is associated with metabolic disorders, premature ageing, and various diseases including cancer. Importantly, it is now possible to target circadian rhythms through systemic or local delivery of time cues or compounds. Here, we summarize recent findings in peripheral tissues that link the circadian clock machinery to tissue-specific functions and diseases.

Molecular mechanisms of the circadian clockwork in mammals

Circadian rhythms enable organisms to co-ordinate biological processes with the predictable 24 h cycle of day and night. Given that molecular clocks that coordinate such biological timing have evolved in almost all organisms, it is clear that being synchronous with the external environment confers competitive advantage. Conversely, it is apparent that being out of phase is detrimental, resulting in a number of clinical conditions, many of which are linked to metabolic dysfunction. The canonical clockwork involves a core set of genes that negatively regulate themselves through a so-called transcription translation feedback loop. However, recent studies describing evolutionarily conserved oscillations in redox reactions link circadian rhythms to metabolic processes, and in particular, redox pathways. In this review we describe the evidence for the interaction between transcriptional loops, redox and metabolism in mammals and suggest the clock may be potential target for the treatment of disease.

Circadian regulation of gene expression: at the crossroads of transcriptional and post-transcriptional regulatory networks

Gene expression programs activated in response to, or in anticipation of, environmental changes involve sequential steps, from transcription and RNA processing to nuclear export and translation. Here we review recent advances in our understanding of the multiple regulatory layers that control the oscillations in gene expression associated with daily rhythms in metabolism and physiology across eukaryotic organisms. Whereas many genes show coordinated oscillations in transcription, RNA processing and translation, others show significant temporal disconnections between these processes. Thus, circadian oscillations constitute an ideal system for examining how multiple transcriptional and post-transcriptional regulatory steps are integrated to maximize organismal adjustments to environmental conditions.

Disruption of daily rhythms in gene expression: the importance of being synchronised

Extending a normal 24 hours day by four hours is unexpectedly highly disruptive to daily rhythms in gene expression in the blood. Using a paradigm in which human subjects were exposed to a 28 hours day, Archer and colleagues show how this sleep-altering forced desynchrony protocol caused complex disruption to daily rhythms in distinct groups of genes. Such perturbations in the temporal organisation of the blood transcriptome arise quickly, and point to the fragile nature of coordinated genomic activity. Chronic disruption of the daily and circadian rhythms in sleep compromise health and well-being and this study reveals potential new molecular targets to combat the disruptive effects of shift work and jetlag.