Transcription factor function and regulation in development and disease

Transcription factors (TFs) regulate gene expression across biology. Dysregulation of expression secondary to TF perturbation characterizes many disease states including developmental disorders and cancer. Multiple generations of scientists have greatly improved our understanding of TF activity and, by extension, the molecular underpinnings of gene regulation. Recent technological advances allow for queries of TF function at a genome-wide scale and single-nucleotide resolution. The work presented in this dissertation leverages these novel methodologies to study TFs in disease and developmental contexts. Chapter I provides a review of basic TF biology and concepts relevant to the subsequent projects. The study described in Chapter II details the effect of histone deacetylase inhibitor (HDACi) treatment on cutaneous T-cell lymphoma (CTCL) cell chromatin accessibility. We developed an alternative normalization method using reads aligning to the mitochondrial genome to correct for unidirectional shifts in accessibility. Using this approach, we find that the vast majority of differentially accessible regions following HDACi treatment increase in accessibility. These regions are enriched within promoters and are potentially regulated by the RUNX1 TF, suggesting an underappreciated role for this classic hematopoietic factor in CTCL development and response to therapy. In Chapter III, we present our novel approach to transcriptional network inference integrating accessibility and nascent transcription. We apply this approach to 3T3-L1 adipogenesis and infer regulatory TFs as well as putative binding sites and target genes. We identify TWIST2 as a negative regulatory of accessibility, transcription, and differentiation. We propose that TWIST2 forms a negative feedback loop designed to prevent overstimulation of developing cells. Chapter IV describes my contributions to other published projects. Finally in Chapter V I expand on the impact of our findings in 3T3-L1 adipogenesis and propose a number of future inquiries. In summary, this dissertation explores TF function in multiple contexts and reaches a number of intriguing conclusions.