Understanding the dynamics of rhythmic gene expression in mammalian cells

In mammals, circadian rhythms are driven by a cell-autonomous core-clock mechanism consisting of over a dozen core-clock genes forming transcription-translation feedback loops. The core-clock mechanism also drives the rhythmic expression of downstream genes called clock-controlled genes, which are thought to be important for driving rhythmic biochemical and physiological processes. Mathematical models predict that for a gene to be rhythmically expressed, synthesis, degradation, or a combination of the two must be rhythmic. The purpose of this project was to investigate the contribution of synthesis and degradation of RNA to rhythmic gene expression. To systematically understand the contribution of synthesis, degradation, and other RNA dynamics to rhythmic gene expression, I used metabolic labeling and a novel computational pipeline to analyze transcriptomic data in synchronized NIH3T3 cells. I identified 685 rhythmically expressed RNAs with a period of 24-hour in my dataset, of those 389 were rhythmically synthesized and 24 were rhythmically degraded. Low amplitude degradation rhythms were detected more broadly in the 685 rhythmically expressed RNAs, but these were not statistically significant. Although synthesis was the primary driver of rhythmic 24-hour RNA expression, core-clock gene RNAs were regulated by both synthesis and degradation, presumably to sustain high amplitude of rhythmic expression. I also identified rhythmic RNA expression with a period of 12 and 8 hours; interestingly, degradation primarily drove rhythmic expression of these RNAs. Overall this dissertation revealed RNA dynamics that drive rhythmic gene expression. This will provide insights into how diverse circadian clock mechanisms ultimately drive tissue-specific rhythmic gene expression.