My lab is focused on three broad projects:
- How can we manipulate the clock?
Circadian timekeeping is coded in the regulation of “clock gene” expression, a product of precisely regulated accumulation, interaction between and degradation of clock gene products in a negative feedback loop system (see Figure 1). We are very interested in identifying the mechanisms regulating the interaction and degradation of clock proteins, as they likely have high therapeutic potential. The predominant approach we are taking is to leverage the power of cell-based genetics with the ease of setting up high-throughput functional cell based assays to examine specific aspects of clockwork regulation. For example, with John Hogenesch at the University of Pennsylvania School of Medicine, we have recently developed a simple screen to identify which ubiquitin ligases degrade which proteins…an approach that has uncovered several novel potential clockwork regulators that we are currently studying. These types of focused, mechanism-based assays combined with cell-based genetics has tremendous potential to rapidly uncover many new clock regulators and potentially open new avenues for circadian manipulation.
- Why are mice nocturnal?
A hallmark of circadian timekeeping is the rhythmic expression of many of the clock genes. It is currently thought that stimuli that acute alter the expression level of one clock gene family (the Period genes) directly, reset the clock. However, clocks from all mammals do not reset to the same time in response to the same stimuli, implying that clock-resetting mechanisms may differ organisms. We are applying a comparative systems-biology to uncover differences in circadian network responses to clock resetting between organisms, with the hypothesis that these differences will reveal new clock resetting mechanisms, and potentially help address why some animals are day active, and other nocturnal.
- Is stopping the clock useful?
Circadian systems are, by design, difficult to reset – they can only be shifted by 1-2 hours a day. This resistance to resetting prevents unwanted resetting, but it also is the root cause of the most common circadian-related disorders. This raises the question: is it better not to have a circadian clock? We are starting to address the basics of this question using modern genetic approaches (i.e. conditional knockout mice, RNAi), to identify what therapeutic strategies are likely to work, and for which endpoints.
Figure 1. Wire-diagram of mammalian circadian clock design principles. Circadian timekeeping is coded in the regulation of “clock gene” expression, a product of precisely regulated accumulation, interaction between and degradation of clock gene products in a negative feedback loop system. The wire-diagram depicts five transcriptional regulatory ‘modules’ made up of different combinations of gene promoter response elements (E/E’-box, D-box, RRE). Depending on combination of elements, the timing of the genes regulated is such that they peak at one of roughly 5 different times of day (right side). Transcriptional activators and their pathways are in light green, repressors and their pathways in dark red. Note all transcription factors involved are also rhythmically transcribed, and the rhythmic abundance of their proteins carries out their rhythmic duties.
Research Key Words: Circadian rhythm, functional genomics, transcription, ubiquitin ligase