Developmental regulation of oscillatory expression - Biological oscillators, the rhythmic and regular increases and decreases of gene expression or protein activity, drive many dynamic molecular and morphological processes. Probably the most familiar is the circadian clock, but there are also ultradian clocks that operate on the order of minutes and/or hours. Examples of ultradian clocks are those that regulate periodic root branching in Arabidopsis, molting cycle in C. elegans, timing of mitosis to tightly coordinate cell proliferation and tissue morphogenesis, stem cell maintenance, bulk protein degradation and re-synthesis in proliferating mammalian cells, and tissue patterning during somitogenesis, a fundamental vertebrate developmental process that we have studied for many years. Somitogenesis is the anterior to posterior sequential segmentation of the vertebrate embryonic mesoderm into blocks of tissue called somites, which later give rise to axial skeletal muscle, vertebrae, and dermis This rhythmic and regular process is controlled by a molecular oscillator called the segmentation clock which operates in the unsegmented presomitic mesoderm (PSM) and is characterized by rapid cycles of mRNA and protein expression with a species-specific periodicity. Like many cell-autonomous oscillatory networks, the segmentation clock is regulated by a self-sustaining negative feedback loop, where a core oscillatory factor, a transcriptional repressor, inhibits expression of downstream oscillatory genes, including itself. For segmentation clock oscillations to persist, the transcript and protein molecules of clock genes must be short- lived. In all vertebrates examined to date, transcriptional repressors of the Hes/her gene family are considered the evolutionarily conserved pacemakers of the segmentation clock. For proper somite formation, rates of each oscillatory step, from transcription to translation to decay, must be regulated to ensure correct somite size and number. Computational modeling and experimental perturbations have shown that transcriptional and translational time delays (the amount of time from transcription or translation initiation to the emergence of a mature mRNA or protein, respectively) and degradation rates of both transcript and protein are parameters having the largest influence on clock period and evidence from in vivo studies assessing the impact of timing of mRNA and protein processing and decay mirrors modeling predictions. Transcriptional regulation alone is not sufficient to produce genetic oscillations and we are focusing on understanding the post-transcriptional regulatory mechanisms that promote proper oscillatory expression. The two key questions that we address in this proposal are: (1) What are the key targets of the core Hes/Her oscillators that carry out oscillatory output? and (2) What are the post-transcriptional regulatory mechanisms driving rapid decay of oscillatory gene transcripts. Answering these questions will address how oscillatory gene expression regulates pattern and fate.
