Computational and Experimental Investigations of the Principles of Eukaryotic Transcriptional Regulation Before, During, and After Open Complex Formation

In this work, I describe my doctoral work studying the regulation of transcription with both computational and experimental methods before, during, and after recruitment of RNA Polymerase II and the formation of the open complex at gene promoters. This works spans investigation of the combinatorial binding of sequence specific distal enhancer binding proteins in the developing fly embryo the role of the yeast AAA-ATPase YTA7 in reorganizing the nucleosome positioning at the highly transcribed loci, and the role of the AFF scaffold-associated members of the human super elongation complex.