The regulation of eukaryotic gene expression is critical for proper cell homeostasis and development and relies largely on appropriate initiation of transcription. Transcriptional regulators, such as sequence-specific transcription factors, coactivators, general transcription factors, and chromatin remodelers, are often expressed in a cell-type specific manner to drive cell fate decisions and developmental transitions. Recently, the XPC DNA repair factor was identified as the Stem Cell Coactivator (SCC) complex, a key transcriptional coactivator required to assist OCT4 and SOX2 in driving the expression of key pluripotency genes in embryonic stem cells.

Chapter 1 provides an introduction to mechanisms of eukaryotic transcriptional regulation, eukaryotic DNA repair, and the involvement of the XPC/SCC complex in both of these capacities.

In chapter 2, I describe the first structures of the human apo and DNA-bound XPC holo-complex, as solved by electron microscopy. Comparison of the apo and DNA-bound structures identified key regions that become locally disordered upon engagement with DNA. Using a combination of sequence homology, computational docking of a partial homolog crystal structure into the EM density, and mapped interaction domains, I present a predictive model illustrating regions of key contacts on the XPC/SCC complex.

In chapter 3, I describe the involvement of largely non-specific RNA but not DNA or heparin in mediating the interaction between SOX2 and SCC in a dose-dependent fashion, a novel mode of potentially RNA-mediated transcriptional regulation. I provide evidence that there are little or no sequence or structural requirements for the RNA I also show that while this interaction is RNA-dependent, direct contacts can be formed between SCC and SOX2, suggesting that RNA is stabilizing and possibly even multimerizing existing protein-protein contacts between SCC and SOX2.

In summary, the findings described in this dissertation provide a structural and biochemical framework for understanding the molecular and cellular mechanisms of SCC-driven gene regulation.