Investigating Transcription Factor Networks That Drive Biological Clocks and Oscillators

<p>Biological systems are highly dynamic, yet our temporal resolution of such</p><p>dynamical processes is often limited or difficult to test in the laboratory. The 24-hour</p><p>circadian rhythm and the approximately 75-minute cell cycle of a budding yeast cell are</p><p>both examples of dynamical processes that contain precisely ordered events, repeating</p><p>over each cycle. Organisms utilize such biological clock processes to time a particular</p><p>function. Dynamic cellular events are ordered, in part, by coordinated programs of</p><p>periodic gene expression. Up to 40% of all mouse genes are periodically expressed with</p><p>respect to the circadian cycle, and almost 20% of all yeast genes are periodic during the</p><p>cell cycle. Furthermore, more than half of the most frequently prescribed drugs in human</p><p>patients target an effector whose expression is under circadian control. Given the large</p><p>proportion of genes that are periodically expressed across different biological processes,</p><p>it is critically important to understand mechanisms that regulate dynamics in biology.</p><p>In this dissertation, I focus on two biological processes that are dynamic and are</p><p>not yet fully understood: the eukaryotic cell cycle and malaria parasite development.</p><p>Large programs of periodic genes emerge when these biological clock processes are</p><p>synchronized and profiled over time. Gene regulatory networks composed of</p><p>transcription factors, kinases, and other transcriptional regulators play a critical role in</p><p>generating periodicity in gene expression programs, ordering clock events, and</p><p>maintaining oscillations in subsequent cycles.</p><p>Many previous studies have profiled gene expression during the cell cycle in the</p><p>budding yeast Saccharomyces cerevisiae. I have added to this detailed body of work by</p><p>demonstrating that regulatory motifs involving negative feedback are required to</p><p>maintain normal gene expression levels. Additionally, I showed that many periodic</p><p>mRNAs are also periodically abundant at the protein level during the cell cycle. Both</p><p>projects provide evidence for the hypothesis that cell-cycle dynamics are driven by a</p><p>network of transcription factors with complex protein dynamics and with negative</p><p>feedback motifs. Using this ground truth cell-cycle network in S. cerevisiae, I next</p><p>performed a comparative transcriptomics study on cell-cycle genes in the less studied,</p><p>but more human health relevant fungal pathogen, Cryptococcus neoformans. This work</p><p>not only begins to identify a cell-cycle network in C. neoformans but also has</p><p>implications for future antifungal drug development, as some genes that are important</p><p>for fungal virulence were found to be expressed periodically during the cell cycle.</p><p>During infection, the human malaria parasite Plasmodium falciparum cyclically</p><p>develops and re-infects red blood cells. Many groups have shown that a very large</p><p>program of gene expression occurs during this red blood cell developmental cycle. In</p><p>this dissertation, I deploy the experimental and analysis tools that I used to characterize</p><p>the fungal cell cycle to ask if a network of transcription factors can explain</p><p>developmental gene expression dynamics and cycle period control in malaria.</p><p>Biological systems are highly dynamic to respond to environmental signals, grow,</p><p>and survive. As the application of genetics and genomics has moved toward</p><p>characterizing complex diseases, host-pathogen interactions, or even the cell cycle of a</p><p>single yeast cell, it has become increasingly clear that networks of interacting genes are</p><p>required to explain biological mechanisms. Results from this dissertation where I</p><p>investigate dynamic gene regulatory networks are broadly applicable to our</p><p>understanding of both basic molecular biology and of human infectious diseases.</p>

Author dc:creator

• Kelliher, Christina Marie

Advisor dc:contributor.advisor

• Haase, Steven B

• Genetics
• cell cycle transcription
• Cryptococcus neoformans
• gene regulatory networks
• Plasmodium falciparum
• Saccharomyces cerevisiae

Handle dc:identifier.uri

https://hdl.handle.net/10161/16224

OAI identifier oai:identifier

oai:dukespace.lib.duke.edu:10161/16224