Genomic reprogramming in the early embryo

PROJECT SUMMARY Our long-term goal is to elucidate the molecular mechanisms that restructure the genome to allow for developmental transitions. This process is orchestrated by sequence-specific, DNA-binding, transcription factors that occupy discrete regulatory regions and drive gene expression. However, the packaging of the genome into chromatin limits the ability of many transcription factors to bind the underlying DNA. A specialized class of transcription factors, called pioneer factors, are uniquely capable of binding histone-wrapped DNA, establishing accessible chromatin domains, and facilitating the binding of additional transcription factors. These distinctive properties enable pioneer factors to act at the top of gene-regulatory networks to drive changes in cell state. Indeed, pioneer factors are required for reprogramming the early embryonic genome in all species studied. We identified two pioneer factors in Drosophila, Zelda and GAGA factor, that are each essential for embryonic development and together partition the embryonic genome into transcriptionally active and inactive states. Nonetheless, the mechanisms by which these two factors function to drive this conserved developmental transition remains unclear. Despite the powerful ability of pioneer factors to restructure the genome, there are barriers to both their binding and activity. By combining our development of novel tools to interrogate transcription-factor function in the early embryo with the strengths of the well-studied fly system, we are uniquely positioned to determine essential features of pioneer-factor mediated genomic reprogramming. We will use genetic, genomic, biochemical, and imaging strategies to determine how pioneer factors partition the early embryonic genome into the transcriptionally active and inactive compartments and identify pioneer- specific features that promote their ability to restructure the genome. Our proposed research is significant because we will identify unifying principles by which pioneer factors drive the changes in gene-regulatory networks that promote developmental transitions and, when dysregulated, disease.