All embryos start off development with an initial, 'ground state' of chromatin structure. This starting point for all future developmental decisions is built during a period of rapid mitotic proliferation that precedes Zygotic Genome Activation (ZGA). While work over the past decades from many labs around the world has measured how the genome wakes up, and has identified critical mechanisms for this process, we still don't know how these systems coordinate to yield a precise, reproducible, stepwise assembly of the initial epigenetic landscape. We have previously determined that all these changes in chromatin structure (in the context of rapid mitotic activity) triggers the DNA replication checkpoint. Remarkably, the only time in the life history of a fruit fly that an individual absolutely requires a functional DNA replication checkpoint is at the moment of large scale ZGA. Mutants in critical checkpoint components like atr and chk1 die at this exact moment of development. If we slow the rate of ZGA, however, some checkpoint mutant embryos will survive. In other words, the lethal phenotype of checkpoint mutants can be suppressed. We are leveraging this genetic interaction to identify additional limiting factors for the process of ZGA, and are beginning to piece together the complex biological system that governs this process.


The initial epigenetic ground state is mostly homogeneous, meaning that each nucleus in the embryo has roughly the same starting set of promoters, enhancers, insulators, etc. available to begin the process of embryonic patterning and cell fate specification. But, we know that, over time, differentiation drives the emergence of heterogeneous chromatin states. By studying the process from the beginning, and by perturbing patterning mechanisms, we can address the open question of how developmental cues encode the establishment of stable, heritable chromatin states in specific cell lineages. We have previously demonstrated that maternal patterning systems rapidly establish epigenetic heterogeneity through activation of zygotic pioneer factors. We are currently investigating both how zygotic pioneers, like Odd-paired/Zic function to alter the ground state of chromatin structure, as well as exhaustively identifying additional early zygotic pioneers. 


The Drosophila model system is unique in that all of the genes necessary for early embryonic patterning, as well as many of the cis-regulatory elements controlling these genes, have been identified over the past 40 years of investigation. Still, we do not know how these all work together. Many of these genes encode transcription factors and signaling pathways that drive differential gene expression. Gene regulatory systems must contend with chromatin. We have recently demonstrated that the chromatin state over a set of regulatory elements that drive embryonic segmentation undergo changes in accessibility over time. It has also been demonstrated previously that spatially restricted determinants can give rise to cell type specific chromatin states. Chromatin accessibility will have an outsize impact on how transcription factors see available regulatory elements. We are currently measuring how binding states of functionally related transcription factors are affected by the underlying chromatin state, with an aim to understand how accessibility adds a further dimension to the complex regulatory logic that drives development.