Gene expression oscillations are widespread in biological systems. The segmentation clock is one such oscillator controlling segmentation of the vertebral column. Its disruption results in congenital vertebral defects in humans. Oscillations necessitate short half-lives of both mRNAs and proteins to allow rapid changes, and negative feedback loops to allow an oscillation to return to baseline. The Hes/her gene family includes the only oscillating segmentation clock genes conserved in vertebrate species. 

Previously, we demonstrated the importance of the transcriptional negative feedback loop of Her transcriptional repressors in zebrafish, but the mechanisms of mRNA and protein instability remain to be discovered. We have built a mathematical pacemaker model that is based on a transcriptional-feedback loop. Our model predicts that a moderate increase in the stabilities of Her proteins or mRNAs should lengthen the period, while a further increase would abolish the oscillations. To discover how Her family proteins and mRNAs come to have such short half-lives, we have performed mass-spectroscopy and identified ubiquitin-proteasome pathway proteins as binding partners of Her proteins and RNA-binding proteins as binding partners of her mRNAs. We investigate the mechanisms and dynamics of protein and RNA degradation in the segmentation clock.