Developmental regulation of nuclear domains

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SUMMARY In metazoan embryos, maternal and zygotic factors collaborate to establish gene regulatory domains, regions of the nucleus in which participating genes are coordinately regulated, and these domains are maintained throughout development. To successfully establish domains, transcription factors must effectively locate the appropriate region of the nucleus, perform the correct function within the context of the domain, and contribute to the active maintenance of the domain as the zygote develops. Our overall goal is to determine how nuclear domains are regulated throughout development. Defining the signals that direct domain targeting will allow us to further decipher the cis regulatory code: how proteins interact with cognate sequences in a cell, leading to differentiation and disease. We will pursue this goal using the Drosophila histone locus, a highly repetitive region composed of over 100 tandem gene arrays that attract both general and unique transcription factors, forming the histone locus body (HLB) domain. We recently described some of the earliest interactions between histone locus cis sequences and transcription factors that initiate domain formation, but how transcription factors collaborate to establish and maintain a domain is not well defined. In addition, DNA sequence is not sufficient to determine transcription factor function within a domain. Rather, factors must integrate multiple sources of information outside of sequence, including genomic context, chromatin cues such as histone marks, and three dimensional locus organization, to perform correct context-specific functions. It is challenging to capture the steps that lead to nuclear domain initiation for three reasons: 1) Many key events take place in the very early embryo which has few cells and therefore little biological material with which to work; 2) Maternally deposited transcription factors are loaded into the egg and are difficult to deplete; and 3) It is not possible to use reporter transgenes before activation of the zygotic genome. However, by using an ectopic histone gene array, which is still targeted for domain formation, we can manipulate signals residing in the locus that lead to transcription factor recruitment. In my new laboratory, we are using this system, the extensive repertoire of genetic tools in Drosophila melanogaster, and creative approaches to overcome these challenges and address important gaps in our understanding of nuclear domain formation during embryogenesis. We will define the epigenetic mechanisms that initiate nuclear domains and determine how transcription factors integrate multiple levels of genomic information to perform domain-specific functions. Our work is significant because our observations will provide insight into the regulation and organization of other repetitive regions, such as the ribosomal RNA genes, as well as for non-genic regions such as telomeres and centromeres.