Chromatin accessibility is a two-tier process regulated by transcription factor pioneering and enhancer activation

Summary Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive accessibility and those that do not. Deep learning models that learn complex sequence rules provide an unprecedented opportunity to dissect this problem. Using zygotic genome activation in the Drosophila embryo as a model, we generated high-resolution TF binding and chromatin accessibility data, analyzed the data with interpretable deep learning, and performed genetic experiments for validation. We uncover a clear hierarchical relationship between the pioneer TF Zelda and the TFs involved in axis patterning. Zelda consistently pioneers chromatin accessibility proportional to motif affinity, while patterning TFs augment chromatin accessibility in sequence contexts in which they mediate enhancer activation. We conclude that chromatin accessibility occurs in two phases: one through pioneering, which makes enhancers accessible but not necessarily active, and a second when the correct combination of transcription factors leads to enhancer activation.