Establishment of Active Chromatin Domains

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Chromatin domains form within the nucleus during early development to precisely co-regulate nearby genes during the maternal to zygotic transition. Prior to zygotic genome activation, the entire genome is very open and only a few key early transcription factors are bound. Yet, many essential active and repressive chromatin domains are present right after zygotic genome activation. Little is understood about how embryos rapidly establish the critical active chromatin domains that are essential for the function of the zygotic genome. Here are several key questions about active chromatin domains that we will address in this proposal: 1) How are different effector complexes specifically targeted to active chromatin domains by similar cis-elements such that the proper domain forms at the correct genomic location? 2) How does competition between transcription factors that recognize similar cis-elements regulate the formation of active chromatin domains during development? 3) How is the three-dimensional architecture of active chromatin domains established? There are many essential chromatin domains that mediate coordinate gene activation throughout the genome including the rDNA locus, the histone locus and the dosage compensated male X-chromosome, all of which must be properly activated in the developing embryo. My research program has initially focused on two of these essential chromatin domains of coordinate gene activation in Drosophila: 1) the dosage compensated X-chromosome that balances gene dosage between sexes and 2) the histone locus body (HLB) that coordinately regulates histone gene expression. Drosophila is an ideal organism with which to study the formation of chromatin domains early in development due to their rapid and synchronized early development and the large number of genetic and biochemical tools and genomic data sets available. While many cis and trans acting factors that regulate chromatin domains have been identified, little is known about the molecular mechanisms that drive their formation at specific genomic loci during early development. Defining how the chromatin domains on the active male X-chromosome and the HLB are established and maintained over developmental time will reveal key principles by which active chromatin domains form. Using steady-state measurements, we have recently discovered that a single transcription factor, CLAMP, regulates formation of both the dosage compensated X-chromosome and the HLB active chromatin domains, providing us an entry point for revealing new insights into the dynamic process of chromatin domain formation. The significance of our work is that we will define how active chromatin domains form over developmental time and will seek to identify common underlying mechanisms that drive formation of two very different domains at specific genomic loci.