Cell-type-specific chromatin occupancy by the pioneer factor Zelda drives key developmental transitions in Drosophila

During early Drosophila embryogenesis, the essential pioneer factor Zelda defines hundreds of cis-regulatory regions and in doing so reprograms the zygotic transcriptome. While Zelda is essential later in development, it is unclear how the ability of Zelda to define cis-regulatory regions is shaped by cell-type specific chromatin architecture established during differentiation. Asymmetric division of neural stem cells (neuroblasts) in the fly brain provide an excellent paradigm for investigating the cell-type specific functions of this pioneer factor. Zelda is expressed in neuroblasts, and we show that Zelda synergistically functions with Notch to maintain neuroblasts in an undifferentiated state. Zelda misexpression can reprogram progenitor cells to neuroblasts, but this capacity is limited by transcriptional repressors critical for progenitor commitment. Zelda genomic occupancy in neuroblasts is reorganized as compared to the embryo, despite sharing many target genes in these two developmental stages. This reorganization is likely driven by differences in chromatin accessibility and cofactor availability. We propose that Zelda regulates essential transitions in the neuroblasts and embryo through a shared gene regulatory network by defining cell-type specific enhancers. Overall design: ChIP-seq of Zelda in type II neuroblasts was performed in duplicate using a-Zelda antibody (Harrison et al., 2011). As a control, a single replicate of Zelda ChIP-seq was performed on superfolder GFP-tagged Zelda using a-GFP antibody (Abcam, Cambridge, UK, Cat #ab290). All ChIP experiments were performed with input controls. ATAC-seq in type II neuroblasts was performed in duplicate. ATAC-seq using the time-release differentiation system was performed in duplicate or triplicate.