Mosley, Amber L.Baldwin, Dominique AdomWek, Ronald C.Motea, Edward A.Linnemann, Amelia K.2023-08-182023-08-182023-08https://hdl.handle.net/1805/34972Indiana University-Purdue University Indianapolis (IUPUI)RNA Polymerase II (RNAPII) plays a pivotal role in cellular homeostasis due to its role of RNA transcription and gene expression. Many protein-protein interactions (PPIs) are required to assist RNAPII during RNA generation and these interactions can be directed by the addition of many post-translational modifications (PTMs) of proteins. Notably, the largest subunit of RNAPII is dynamically phosphorylated to regulate progression through transcription. As such, the coordination of many protein kinases and phosphatases is required to regulate signaling that occurs throughout transcription by RNAPII. These transcriptional regulators play additional roles in other cellular pathways as well such as the unfolded protein response (UPR). To further understand the regulation and dysregulation of RNAPII phosphorylation and the regulatory roles RNAPII kinases and phosphatases play, especially from a disease perspective, it is important to develop and utilize workflows to monitor changes surrounding proteins and their modifications. One method is quantitative mass spectrometry (MS), which allows biomolecules to be directly quantified, thus serving as a powerful tool to better understand the regulation of transcription with high accuracy. This work explores the development and experimental application of various OMICS workflows to answer long-standing questions surrounding transcription biology and onward.en-USAnalytical chemistryBiochemistryMass spectrometryMolecular biologyTranscriptionDissertation