Modeling an evolutionary conserved circadian cis-element using functional and comparative genomics

Discussion of two problems in computational circadian biology: 1. Stochastic phase oscillators and circadian bioluminescence recordings cultured circadian oscillators from peripheral tissues were recently shown to be both cell autonomous and self-sustained. Therefore the dominant cause for amplitude reduction observed in bioluminescence recordings of cultured fibroblasts is desynchronization rather than the damping of individual oscillators. We propose a generic model for quantifying luminescence signals from biochemical oscillators, based on noisy phase oscillators. Our model incorporates 3 essential features of circadian clocks: stability of the limit cycle, fluctuations and inter-cellular coupling. The model is then used to analyze bioluminescence recording from immortalized and primary fibroblasts. Fits to population recordings allow simultaneous estimation of the stability of the limit cycle (or equivalently the stiffness of individual frequencies), the period dispersion and the interaction strength between cells. Consistently with other work, coupling is found to be weak and insufficient to synchronize cells. Interestingly, we find frequency fluctuations remain correlated for longer than one clock cycle, which is confirmed from individual cell recordings. We discuss how to link the generic model with more microscopic models, which suggests mechanisms by which circadian oscillators resist fluctuations and maintain accurate timing in the periphery. 2. Modeling an evolutionary conserved circadian cis-element Circadian oscillator networks rely on a transcriptional activator called CLOCK. Identifying the targets of this heterodimeric bHLH transcription factor poses challenges and it has been difficult to decipher its specific sequence affinity beyond a canonical E-box motif, except perhaps for some flanking bases contributing weakly to the binding energy. Here we use a comparative genomics approach and first study of the conservation properties of the best-known circadian enhancer in the Drosophila melanogaster period gene. This shows a signal involving the presence of two closely spaced sequence motifs, a configuration we can also detect in the other 4 prominent CLOCK targets genes in flies: timeless, vrille, Pdp1 and cwo. The examples allow training a probabilistic model that we can test using functional genomics datasets. We find the sequences predicted from our model are overrepresented in promoters of genes induced in a recent study by a glucocorticoid receptor-CLOCK fusion protein. We then scanned the mouse genome with the fly model and found that many known CLOCK/BMAL1 targets harbour sequences matching our consensus. The phase of predicted cyclers in liver agreed with known CLOCK/BMAL1 regulation. Felix Naef studied theoretical physics at ETHZ and obtained his PhD from EPFL in 2000, then pursued postdoc training at the Center for Studies in Physics and Biology, Rockefeller University, NYC. His research focuses on modeling and interpretation of high-throughput functional data and study of biomolecular oscillators. He joined ISREC as associate scientist in the NCCR Molecular Oncology program in 2004 and was nominated Tenure Track Assistant Professor in the School of Life Sciences, EPFL, in 2005.