Genome Binding and Gene Regulation by Stem Cell Transcription Factors

Nearly all cells of an individual organism contain the same genome. However, each cell type transcribes a different set of genes due to the presence of different sets of cell type-specific transcription factors. Such transcription factors bind to regulatory regions such as promoters and enhancers and regulate their activity in gene transcription. Transcription factors interact with each other and form tissue-specific transcription factor networks. Identification of genome binding and gene regulation by transcription factors will enhance our understanding of how transcription factors specify cell types.

Chapter 1 serves as a general introduction into eukaryotic transcription regulation and describes the role of enhancers and transcription factors. Chapters 2 – 4 describe the experimental work of this thesis. Chapter 2 describes Chromatin Immunoprecipitation followed by Mass Spectrometry (ChIP-MS), a technique used to identify transcription factors and other genome binding proteins that bind to promoters, enhancers or heterochromatin. Chapter 2 specifically describes the genome-binding pattern of transcription- and pluripotency factor Dppa2, which we identify by ChIP-MS and ChIP-seq to bind to promoters outside the classical pluripotency network. Chapter 3 describes a transcription factor interaction network of over 200 proteins in neural stem cells, which was assembled by the identification of interaction partners of four mental disorder-associated transcription factors. Chapter 4 describes work on the genome-wide localization of Oct4, Sox2 and Nanog in embryonic stem cells and investigates the genome localization of these transcription factors upon depletion of Oct4 or Sox2 from embryonic stem cells. The last chapter, Chapter 5, summarizes the results from Chapter 2-4 and provides additional discussion to these chapters, concerning its implications and future directions.