Understanding the dynamics of rhythmic gene expression in mammalian cells

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dc.contributor.authorUnruh, Benjamin Alexen
dc.contributor.committeechairKojima, Shihokoen
dc.contributor.committeememberZhang, Liqingen
dc.contributor.committeememberHauf, Silkeen
dc.contributor.committeememberFinkielstein, Carla V.en
dc.contributor.departmentBiological Sciencesen
dc.date.accessioned2023-06-17T08:00:19Zen
dc.date.available2023-06-17T08:00:19Zen
dc.date.issued2023-06-16en
dc.description.abstractIn 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.en
dc.description.abstractgeneralAlmost all organisms on Earth have an internal timekeeping system, called a circadian clock, that enables them to anticipate and respond to the day/night cycle. The circadian clock regulates diverse body processes such as the sleep/wake cycle, eating and digestion, body temperature, and blood pressure. Disruptions to the circadian clock are detrimental to health and wellbeing. Many organisms, including humans, have a core circadian clock mechanism that drives rhythmic gene expression in thousands of genes that are thought to be ultimately responsible for rhythmic biological and physiological processes. My project investigates how the core clock mechanism drives rhythmic gene expression. I found that rhythmic synthesis of RNA was a primary driver of rhythmic gene expression, but the genes involved in the core circadian clock mechanism itself was regulated by multiple rhythmic processes. Understanding rhythmic gene expression control points is integral for understanding how circadian gene expression can be changed or interrupted.en
dc.description.degreeDoctor of Philosophyen
dc.format.mediumETDen
dc.identifier.othervt_gsexam:38190en
dc.identifier.urihttp://hdl.handle.net/10919/115454en
dc.language.isoenen
dc.publisherVirginia Techen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectGene Expressionen
dc.subjectCircadianen
dc.subjectChronobiologyen
dc.subjectRNAen
dc.subjecttranscriptionen
dc.subjectpost-transcriptionen
dc.subjectregulationen
dc.subjectgenomicsen
dc.subjecttranscriptomicsen
dc.titleUnderstanding the dynamics of rhythmic gene expression in mammalian cellsen
dc.typeDissertationen
thesis.degree.disciplineBiological Sciencesen
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen
thesis.degree.leveldoctoralen
thesis.degree.nameDoctor of Philosophyen

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