Examination of Kinase-Regulated Transcriptional Networks Using Pharmacological and Chemical Genetic Tools
In response to external cues, kinases function in signaling networks to orchestrate a transcriptional response that results in a precisely altered cellular state. Chapter 1 introduces how kinases regulate histones and histone modifiers, the basal transcriptional machinery, and transcription factors and cofactors to control inducible gene expression. Due to an overwhelming number of cellular phosphorylated substrates and limited methods for studying kinase function, it is oftentimes difficult to link kinases to their transcriptional outputs. Chapter 2 describes how a new generation of ATP-competitive mammalian target of rapamycin (mTOR) inhibitors has revealed a new role for mTOR in regulating cholesterol biosynthetic gene expression and a global gene expression profile that is resistant to inhibition using the natural product rapamycin. Although pharmacological inhibitors have their advantages, they do not allow for discrimination between primary and secondary consequences of kinase inhibition. I have developed a method to identify the primary transcriptional targets of the direct substrates of an individual kinase. Chapter 3 describes a chemical genetic affinity labeling scheme for tracing the direct substrates of an individual kinase and Chapter 4 illustrates how this method may be combined with chromatin immunoprecipitation to elucidate the transcriptional regulatory networks controlled by a single kinase.