Integrative Genomic Analyses of Chromatin and Epigenetic Regulation Across Eukaryotes: A Journey from Yeast Transcription to Human Cancer

In the past decade, advances in high-throughput DNA sequencing have enabled unprecedented insights into the complex and often highly entangled mechanisms of epigenetics and chromatin regulation. However, many studies have been limited by sequencing costs or informatic complexities of high-throughput sequencing analyses. Oftentimes, only one aspect of chromatin can be investigated at once, limiting the full scope and understanding of epigenetic regulation mechanisms. Large scale consortia, though, such as The Epigenome Roadmap, ENCODE, and The Cancer Genome Atlas, began to pioneer the integration of multiple assays and analytical methods. These efforts have proven fruitful, and revealed many critical mutations, regulatory pathways, and chromatin-based processes that are central to cellular biology and human disease. In the chapters that follow, we take inspiration from these large consortia and describe the use of integrated technologies and analytical methods to reveal chromatin-based dynamics in yeast, in particular that of the histone post-translational modification H3K36me3 and its associated histone methyltransferase, Set2. We demonstrate that H3K36me3 deposition is a directed process, where H3K36me3 removal is a more stochastic process throughout the cell. We also reveal the consequences of losing Set2 and H3K36me3, which limits a yeast cell’s ability to properly respond to nutrient deprivation and results is misregulation of transcriptional fidelity. We use mouse models of congenital heart defects to elucidate how mutations in NuRD, a nucleosome remodeling complex, result in aberrant smooth and skeletal muscle isoform expression in cardiac tissues. We also examine how mutations in the nucleosome remodeling complex SWI/SNF members are conducive for non-small cell lung cancer and clear cell renal cell carcinoma development, from remodeling of nucleosomes at transcription start sites to the activation of oncogenic transcription factors that lead to the establishment of de novo enhancers associated with downstream tumorigenic pathways. Taken together, these studies expand our knowledge of epigenetic regulation mechanisms that could have only been elucidated by the integration of various genome-wide assays and informatics.Doctor of Philosoph