The interplay between transcription, histone variants, and chromatin structure in Eukaryotes

Transcription is a fundamental process necessary for life. In Eukaryotes this process is shaped and constrained, in part, by the 3D structure of chromatin –the assemblage of protein and DNA into which the genome is organized. Additionally, chromatin itself is reorganized as conditions change and different transcriptional programs are activated. Within this work, I present an exploration of the dynamic system created by this intricately intertwined regulation between chromatin structure and transcriptional outputs. In Chapter 1, I begin with a review of the determinants of direction in the initiation stage of Eukaryotic transcription. The process of initiation involves numerous forms of regulation, including chromatin based. The next three chapters investigate different aspects of the nucleosome, which has been the primary topic of my research. Chapter 2 presents an overview on researching the nucleosome in the yeast Saccharomyces cerevisiae. Chapter 3 examines the connections between H2A.Z and transcription. Here, I challenge the generally accepted model of H2A.Z incorporation at the +1 and -1 nucleosomes hedging the transcription start site. Chapter 4 focuses specifically on perturbations to nucleosomal structure produced either from gene deletions or in response to environmental changes. Finally, I conclude by summarizing my findings and with a general discussion of questions in the field that remain to be explored.