Department of Molecular Biology and Biochemistry
Rutgers–New Brunswick, School of Arts and Sciences
Ph.D., 1988, McGill University
Telephone: (848) 445-9896
Fax: (732) 235-5318
Circadian rhythms, sleep and seasonal adaptation
By means of endogenous circadian (approx. 24 hr) "clocks" that can be synchronized to the daily and seasonal changes in external time cues, most notably visible light and ambient temperature, life forms anticipate environmental transitions, perform activities at biologically advantageous times during the day and undergo characteristic seasonal responses. Malfunctions in the human circadian timing system are implicated in many disorders and diseases including affective disorders such as "winter' depression, chronic sleep problems in the elderly, a range of metabolic syndromes and even susceptibility to cancer and alcoholism. We use the model organism D. melanogaster, which has been instrumental in our understanding of clock mechanisms in general and mammalian ones in particular. In addition, work in the last decade has established Drosophila as an excellent model system to understand the neurobiological and genetic underpinnings for sleep. Below is a summary of current major goals in the lab:
Mechanisms underlying circadian clocks: In general, clock mechanisms are biochemical oscillators built on interlocked loops of transcriptional negative feedback and protein turnover, wherein a central clock heterodimeric transcription factor drives expression of one or more key repressor proteins that after a time-delay feedback to inhibit the transcription factors until the repressor(s) decline in abundance, enabling another round of transcription. These feedback circuits not only perpetuate daily cycles in the expression of clock genes but also drive rhythmic expression of about 10% of a cell's transcripts, a task that involves chromatin remodeling and ultimately underlies many of the circadian rhythms exhibited by organisms. Based on many lines of evidence obtained from a range of model systems it is now established that time-of-day specific changes in the phosphorylation state of one or more central clock proteins is the key 'state-variable' setting the pace of circadian clocks. In animals, PERIOD (PER) proteins are the clock components behaving as the primary 'phospho-timer'. A major effect of phosphorylation on regulating clock pace is via evoking temporal changes in the stability of PER proteins, which yields daily cycles in their levels that are inextricably linked to clock progression. The importance of PER phosphorylation to human health is highlighted by studies showing that mutations in either a phosphorylation site on human PER2 or a kinase that phosphorylates PER underlie several familial advanced sleep phase syndromes (FASPS). Moreover, a critical feature of phospho-timing clock proteins such as PER is that they connect to gene expression by acting in a phase-specific manner as 'scaffolds' to promote timely interactions of regulatory factors with central clock transcription factors, inhibiting their transcriptional activities. A major goal of our lab is to better understand the biochemical basis for circadian rhythm generation.
We showed that phosphorylated PER is recognized by the F-box protein, SLIMB (homolog of β-TrCP) and targeted to the 26S proteasome for rapid degradation (Ko et al., 2002, Nature). Using mass spectrometry and phospho-specific antibodies we identified the critical phosphorylation events that promote the binding of SLIMB to PER (Chiu et al., 2008, Genes & Development). Converting key phospho-sites to Ala or Asp (phospho-mimetic) leads to decreases or increases in the pace of the clock, respectively (Chiu et al., 2008, Genes & Development). In more recent work we identified a novel clock kinase, NEMO, and showed that different phospho-clusters on PER collaborate with each other to set clock speed (Chiu et al., Cell, 2011). Our findings also suggest that a key aspect of the timing mechanism is progressive increases in phosphorylation, which act to slowly open the conformation of PER rendering it more susceptible to degradation (Chiu et al., Cell, 2011). Ongoing work is aimed at identifying the roles of different phospho-clusters on PER and the relevant kinases and phosphatases. We are also applying these techniques to other central clock proteins. Proteomic strategies are being utilized to identify constituent factors of native clock protein complexes and how they change throughout a daily cycle, critical to understanding how cyclical gene expression is generated. In related work we are investigating the roles of micro RNAs (miRNAs) in clock function.
Seasonal and thermal adaptation: Many animals exhibit a bimodal distribution of activity, with ‘morning’ and ‘evening’ bouts of activity that are separated by a mid-day dip in activity or ‘siesta’. Ambient temperature is a key environmental modality regulating the daily distribution of activity in animals. In D. melanogaster, as temperatures rise there is less midday activity and the two bouts of activity are increasingly shifted into the cooler nighttime hours, almost certainly an adaptive response that minimizes the detrimental effects of the hot midday sun (Majercak et al., 1999, Neuron). We showed that the temperature-dependent splicing of the 3'-terminal intron (termed dmpi8) from the D. melanogaster per RNA is a major ‘thermosensor’ that adjusts the distribution of daily wake-sleep cycles, eliciting seasonably appropriate responses (see Figure 1). In more recent work we showed that this mechanism does not operate in several Drosophila species with more restricted and ancestral locations in equatorial Africa wherein temperature and daylength do not show large seasonal variations (Low et al., 2008, Neuron). We investigated the molecular basis for the species-specific splicing phenotypes and found that multiple suboptimal splicing signals on dmpi8 underlie the thermosensitivity (Low et al., 2008, Neuron). Presumably, higher temperatures progressively destabilize interactions between the non-consensus 5’ splice site (ss) and the U1 snRNP, the initial step in the splicing reaction. Ongoing work is aimed at understanding how temperature dependent splicing of per 3’-terminal introns regulate the distribution of daily activity. In addition, we are studying circadian rhythms in different Drosophila species as a means to understand how clocks evolved.
Figure 1. Model for how thermal sensitive splicing of a 3’-terminal intron in the key clock gene period enables D. melanogaster to adapt to seasonal changes in temperature (left panel, adapted from Majercak et al. 1999, Neuron). D. melanogaster colonized temperate regions (right panel). Intriguingly, the thermal sensitive splicing mechanism (left panel) does not operate in Drosophila species indigenous to Afro-equatorial regions, wherein temperature shows little seasonal variation (Low et al. 2008, Neuron).
Cao W, Edery I. (2017) Mid-day siesta in natural populations of D. melanogaster from Africa exhibits an altitudinal cline and is regulated by splicing of a thermosensitive intron in the period clock gene. BMC Evol Biol 17:32
Yildirim E, Chiu JC, Edery I. (2015) Identification of light-sensitive phosphorylation sites on PERIOD that regulate the pace of circadian rhythms in Drosophila. Mol Cell Biol 36:855-70
Kwok RS, Li YH, Lei AJ, Edery I, Chiu JC. (2015) The catalytic and non-catalytic functions of the Brahma chromatin-remodeling protein collaborate to fine-tune circadian transcription in Drosophila. PLoS Genet 11:e1005307
Cao W, Edery I. (2015) A novel pathway for sensory-mediated arousal involves splicing of an intron in the period clock gene. Sleep 38:41-51
Kim EY, Jeong EH, Park S, Jeong HJ, Edery I, Cho JW. (2012) A role for O-GlcNAcylation in setting circadian clock speed. Genes Dev 26:490-502
Chiu JC, Ko HW, Edery I. (2011) NEMO/NLK phosphorylates PERIOD to initiate a time-delay phosphorylation circuit that sets circadian clock speed. Cell 145:357-70
Low KH, Lim C, Ko HW, Edery I. (2008) Natural variation in the splice site strength of a clock gene and species-specific thermal adaptation. Neuron 60:1054-67
Chiu JC, Vanselow JT, Kramer A, Edery I. (2008) The phospho-occupancy of an atypical SLIMB-binding site on PERIOD that is phosphorylated by DOUBLETIME controls the pace of the clock. Genes Dev 22:1758-72
Kim EY, Edery I. (2006) Balance between DBT/CKIε kinase and protein phosphatase activities regulate phosphorylation and stability of Drosophila CLOCK protein. Proc Natl Acad Sci USA 103:6178-83
Ko HW, Jiang J, Edery I. (2002) Role for Slimb in the degradation of Drosophila Period protein phosphorylated by Doubletime. Nature 420:673-8
Majercak J, Sidote D, Hardin PE, Edery I. (1999) How a circadian clock adapts to seasonal decreases in temperature and day length. Neuron 24:219-30
Lee C, Parikh V, Itsukaichi T, Bae K, Edery I. (1996) Resetting the Drosophila clock by photic regulation of PER and a PER-TIM complex. Science 271:1740-4