Let's talk about SOX : diverse key players in the transcriptional regulation of neural stem cells

The development of the central nervous system relies on neural stem cells. How these stem cells either maintain their identity as self-renewing progenitors or differentiate into cells of the neuronal or glial lineage are fundamental questions. The work presented in this thesis investigates how different SOX transcription factors orchestrate the mechanisms and gene expression programs that govern these processes. In paper I, we investigate how SOX2, SOX3 and SOX11 regulate specific gene sets in embryonic stem cells (ESCs), neural progenitor cells (NPCs) and neurons, respectively. We propose a model of sequentially acting SOX transcription factors that control neural lineage-specific gene expression by predisposing gene sets to become activated in NPCs and during neuronal differentiation. In paper II, we expand our sequential binding model to cells of the glial lineage. Binding studies in NPCs and glial precursor cells (GPCs) show that astrocyte and oligodendrocyte specific gene sets are extensively preselected prior to the onset of gliogenesis, through prebinding of SOX3 and SOX9. This prebinding serves to prevent premature activation of a subset of genes, but also promotes the formation of permissive chromatin, which facilitates their activation at a later stage during astrocytic and oligodendrocytic differentiation. In paper III, we use ChIP-seq and RNA-seq analysis to investigate the binding profile of SOX2 in neural stem cells of four different tissues from two germlayers. We demonstrate that although SOX2 binds few regions that are common, the majority of its target regions are cell type specific. The target sites are enriched for distinct binding motifs of putative cofactors that are either commonly expressed or cell type specific. Furthermore, the bound regions function as cis-regulatory modules (CRMs) that instruct tissue specific gene expression. In paper IV, we examine the initial binding events of SOX2 and FOXG1 during early reprogramming. When misexpressed alone in mouse embryonic fibroblasts (MEFs), FOXG1 preferably targets chromatin regions that were already open in native MEFs. In contrast, SOX2 can target regions that were previously closed and inaccessible, hence displaying pioneering activity. When co-expressed, both factors potentiate each other’s binding to neural genes, while the regions that are co-targeted by SOX2 and FOXG1 together correspond to genes that are mainly associated with proliferation