The regulation of gene expression is an essential process required for proper cellular function. This process is especially important within multi-cellular organisms which contain a variety of cell types with specialized roles. Key to the proper regulation of genes are transcription factors (TFs) which can be stimulus-specific or general components of the transcriptional machinery. Throughout this thesis, I will present work on development of computational methods to infer the activity of stimulus-specific TFs and investigate the role of Mediator kinases, a component of the general transcriptional machinery, in cellular signaling. The first half of this thesis involves work I performed making use of transcriptional signals to infer TF activity using motif co-localization. I helped develop the first method to perform this quantification called the motif displacement (MD) score. I then improved upon the method developing transcription factor enrichment analysis (TFEA). I show that TFEA outperforms existing techniques and can be widely applied to different types of sequencing data. Next, I present work on how Mediator kinases affect the interferon response. I apply the MD-Score to show that CDK8 activity is responsible for activation of STAT and Irf family of TFs - the main effectors of the interferon pathway. Finally, I show that Mediator kinase activity is crucial for proper cellular response to serum. Using a variety of -omics techniques, I quantify the effects of Mediator kinase inhibition on immediate transcriptional changes, late gene expression changes, differential phosphorylation of key signaling proteins, changes in cellular metabolism, and defects in cellular proliferation. Overall, this thesis seeks to expand our understanding of how cells regulate gene transcription/expression and the key players involved in cellular signaling.
|Advisor:||Taatjes, Dylan J., Dowell, Robin D.|
|Commitee:||Goodrich, James A., Spencer, Sabrina L., Layer, Ryan M.|
|School:||University of Colorado at Boulder|
|School Location:||United States -- Colorado|
|Source:||DAI-B 82/6(E), Dissertation Abstracts International|
|Subjects:||Biology, Bioinformatics, Biochemistry, Cellular biology, Genetics|
|Keywords:||CDK8, Enhancer RNA, Mediator kinase, Motif enrichment, Omics, Transcription factor, Gene expression, Cellular function|
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