The broad goal of my research program is to understand the molecular mechanisms that control early embryonic development. We use genetic, biochemical, and genomic approaches to study gene regulatory networks in the early Drosophila embryo. Initially the embryo relies on maternally deposited gene products to begin developing, and the transition to reliance on its own zygotic-gene activity is called the maternal-to-zygotic transition (MZT). The MZT represents a major cellular reprogramming event whereby thousands of maternal RNAs are degraded and hundreds of new zygotic RNAs are transcribed during the time between egg fertilization and blastoderm formation. Recently we discovered a key transcriptional regulator called Zelda, which plays a key role in this reprogramming event. Our goal is to understand how Zelda mediates the rapid and robust activation of the zygotic genome and how it works together with the other key transcription factors to prepare the embryo for major developmental processes such as gastrulation and tissue differentiation.
Currently, the major project in the lab aims to understand how Zelda functions at the mechanistic level. Zelda is a zinc-finger transcription factor, and binds to CAGGTAG and related sites (Liang et al., 2008). Interestingly, our genome-wide binding analysis (ChIP-chip/seq) showed that Zelda binds to known enhancers in the early embryo to such an extent that Zelda binding is a predictive indicator of the location of an enhancer (Nien et al., 2012). Zelda is the major hub in the early gene network (Liang et al., 2008; Nien et al., 2011). Zelda binds enhancers well before the gene is activated (Harrision et al., 2012; Nien et al., 2010), suggesting that Zelda might act as a pioneer factor, a special class of transcription factors that bind target sites in chromatin, allowing other factors access to enhancers (reviewed in Zaret and Carroll, 2011). In this way, Zelda may potentiate the activity of other transcription factors such as the patterning morphogens, an exciting hypothesis that points to the significance of Zelda function in embryonic patterning. We believe that Zelda works together with morphogens, and though we do not yet know how they interact, one fact is clear - that without Zelda, morphogens cannot function to their full potential, particularly when at low concentrations, and target genes are not activated at the right time and in the right place. Mechanistically, Zelda may act as a beacon on chromatin for other transcription factors. Without Zelda, these factors may not position correctly, and redistribute to other regions of the genome. In collaboration with the Zeitlinger lab at Stowers Institute, we are examining the chromatin landscape in wild type and zelda mutant embryos to determine how Zelda cooperates with other key regulators during the MZT.
A second Zelda project stems from the observation that Zelda is expressed in older embryos and larva, specifically in imaginal discs and the brain. For example in the eye disc and optic lobe of the brain, Zelda is expressed in the undifferentiated cells and is down-regulated upon differentiation. In the opitc lobe neuroepithelium, which comprises stem cells that give rise to neuroblasts/neurons, loss of Zelda causes premature differentiation. We propose that Zelda establishes the neural stem cell gene network, which prepares cells for the neuropeithelial to neuroblast transition.
The projects in the my lab require the use of several types of approaches from manipulating genes and transgenes and observing the output phenotypes, to systems/genome-wide studies that require bioinformatic analysis. We also collaborate with systems biologist Stas Shvartsman, who models Zelda interactions with the patterning morphogens. Together these approaches will allow an understanding of how global factors like Zelda interact with key regulators to control robust expression of the early zygotic genome.