Abstract
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.
