Genetics of Circadian Rhythms in Mammalian Model Organisms

Abstract

The mammalian circadian system is a complex hierarchical temporal network which is organized around an ensemble of uniquely coupled cells comprising the principal circadian pacemaker in the suprachiasmatic nucleus of the hypothalamus. This central pacemaker is entrained each day by the environmental light/dark cycle and transmits synchronizing cues to cell-autonomous oscillators in tissues throughout the body. Within cells of the central pacemaker and the peripheral tissues, the underlying molecular mechanism by which oscillations in gene expression occur involves interconnected feedback loops of transcription and translation. Over the past 10 years, we have learned much regarding the genetics of this system, including how it is particularly resilient when challenged by single-gene mutations, how accessory transcriptional loops enhance the robustness of oscillations, how epigenetic mechanisms contribute to the control of circadian gene expression, and how, from coupled neuronal networks, emergent clock properties arise. Here, we will explore the genetics of the mammalian circadian system from cell-autonomous molecular oscillations, to interactions among central and peripheral oscillators and ultimately, to the daily rhythms of behavior observed in the animal.

Introduction

The rising and setting of the sun each day causes predictable environmental changes to which most organisms on earth have adapted by evolving endogenous biological timing systems with a period of approximately 24 h (Young and Kay, 2001). These circadian (∼ 24 h) clocks anticipate environmental cycles and control daily rhythms in biochemistry, physiology, and behavior. Across phyla, all circadian clocks share several fundamental properties: they are synchronized (entrained) each day to external cues, they are self-sustained and produce oscillations that persist in the absence of any external cues, they are temperature compensated such that temperature changes in the physiological range do not alter their endogenous period, and of particular relevance to this review, they are cell-autonomous and genetically determined. In all of the major model organisms in which circadian rhythms have been studied, there has emerged a central organizing principle of the molecular clockwork: within cells, a set of clock genes and their protein products together participate in autoregulatory feedback loops of transcription and translation to produce an oscillation with a period of about 24 h (Lowrey and Takahashi, 2004, Takahashi et al., 2008).

Recent work, however, has prompted a reappraisal of the transcription/translation model as the sole generative mechanism of the molecular circadian oscillator in mammals. For example, it is now clear that oscillations of some mammalian core clock components are dispensable for circadian function (Fan et al., 2007, Liu et al., 2008), and there is some evidence, albeit preliminary, for circadian rhythms in the absence of transcription in some mammalian cells (O'Neill and Reddy, 2011). Perhaps more importantly, however, limitations of the conventional perturbation analysis methods that helped elucidate the transcription/translation model have become apparent. No longer is it sufficient to knock out a clock gene in a mouse and then assess the consequences on behavior (locomotor activity) or gene expression (changes in RNA and protein levels in cells) alone. We now appreciate that the mammalian circadian clock is a more complex hierarchical system than originally imagined, and thus understanding it requires analysis at many levels.

New technologies and clock models have revealed higher-order genetic properties of the mammalian clock system in which the elimination of one component may be compensated for by other components in ways that are more complex than simple redundancy, and they have demonstrated the important roles of accessory feedback loops and gene networks in conferring stability and robustness on the system (Baggs et al., 2009, Ueda et al., 2005, Ukai-Tadenuma et al., 2008). Further, novel approaches have elucidated the importance of networks of coupled cells from which emergent circadian clock properties arise and even buffer the system against the effects of mutations (Abraham et al., 2010, Buhr et al., 2010, Ko et al., 2010, Liu et al., 2007b). These, and other advances, are making clearer the fundamental properties of each level of organization of the mammalian circadian system from cell-autonomous molecular oscillations to tissue-specific properties, to the interaction of central and peripheral oscillators, and ultimately, to the overt daily rhythms of behavior observed in the animal.

Here, we present some of the key findings in the field of mammalian circadian biology over the past 10 years and introduce many of the new technologies that are revolutionizing our understanding of the clock system. Our emphasis will be primarily on work from the principal model organism used to study mammalian biology—the mouse. Indeed, for no other mammalian model is there the extensive repertoire of experimental resources and techniques as for the mouse (Adams and van der Weyden, 2008, Blake et al., 2010, Fox et al., 2007, Hedrich and Bullock, 2004, Nagy et al., 2003, Silver, 1995). We will not, however, explore in depth the intriguing link between the mammalian circadian clock and metabolism, first proposed by McKnight and colleagues a decade ago (Rutter et al., 2002), and now well established, as it is beyond the scope of this review. Instead, we refer the reader to several recent comprehensive treatments of this specific topic (Asher and Schibler, 2011, Bass and Takahashi, 2010, Green et al., 2008, Maury et al., 2010).