There is much about early development that is not understood. At some point after fertilization the zygotic genome is activated, and genes that are necessary for upcoming developmental events are transcribed. Many early genes have been characterized and placed into gene networks, but how they come to be activated at the proper time, in the proper order, and in a robust manner is unclear. In the last grant period, it was revealed that the Drosophila embryo uses a simple strategy to collectively and selectively activate genes - the transcription factor Zelda (Zld) recognizes and binds a specific sequence motif (CAGGTA), and subsequently integrates gene networks into a system of coherent and incoherent feed-forward loops. In doing so, Zld drives the major reprogramming event that occurs during the maternal-to-zygotic transition (MZT), where the embryo takes over control of development from the mother. This is the first demonstration of such a regulator in any organism, thus, Zld provides a paradigm for the global coordination of gene networks in early development. Zld resembles a special class of transcription factors called pioneer factors, which are the first to engage target genes, providing competence for future activation when developmental signals come along. The goal of this proposal is to reveal the underlying mechanisms by which Zld functions to regulate zygotic genome activation (ZGA) and to provide robust temporal control to the activities of the key developmental regulators. Zld protein is initially at low levels, rises in concentration by one hour, coincident with ZGA, then decreases in the third hour. The regulation of Zld protein dynamics and how Zld times the on-off state of early genes is unclear. The hypothesis that a threshold level of Zld triggers genome activation will be tested by altering Zld concentrations and monitoring target gene activation. Whether Zld itself is regulated will be assessed, with focus on a potential role of the zld 3'UTR. The idea that Zld binding leads to local remodeling of the chromatin landscape, thus increasing accessibility of other factors, leading to increased """"""""expressivity"""""""" of target genes will be tested. Global changes in chromatin states at enhancers and transcription start sites before ZGA when the genome is inactive, after ZGA when the early set of zygotic genes are transcribed, and later when many early genes are turned off and others are activated will be examined. Importantly, comparing chromatin states in wild-type and zld mutants will reveal if Zld mediates epigenetic changes during the MZT, and if certain chromatin marks prepare genes for future transcriptional activation/repression. Genetic, genomic, and biochemical approaches will be used to test these hypotheses. Key reagents include zld mutants, zld rescue transgenes to alter Zld levels, and transcriptional reporter transgenes to assay Zld target- gene responses to changes in Zld binding sites. The experimental approaches will lead to a greater understanding of zygotic genome reprogramming from a quiescent state to a robustly active state in early development.
In recent years, Drosophila, with its genetic amenability, molecular genetic tools, and the relative ease of collecting and analyzing embryos, has been successfully developed as a model system to study gene regulatory networks in early development. The coordination of developmental processes that the embryo undergoes in the first few hours of development is regulated by the novel transcription factor Zelda. We will reveal the underlying mechanisms by which Zelda coordinates gene networks in a timely and robust manner, and the principles deduced from this project will be applicable to other temporally coordinated events and to more complex organisms.
|Sun, Yujia; Nien, Chung-Yi; Chen, Kai et al. (2015) Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation. Genome Res 25:1703-14|
|Fu, Shengbo; Nien, Chung-Yi; Liang, Hsiao-Lan et al. (2014) Co-activation of microRNAs by Zelda is essential for early Drosophila development. Development 141:2108-18|
|Foo, Sun Melody; Sun, Yujia; Lim, Bomyi et al. (2014) Zelda potentiates morphogen activity by increasing chromatin accessibility. Curr Biol 24:1341-1346|
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|Liang, Hsiao-Lan; Xu, Mu; Chuang, Yi-Chun et al. (2012) Response to the BMP gradient requires highly combinatorial inputs from multiple patterning systems in the Drosophila embryo. Development 139:1956-64|
|Nien, Chung-Yi; Liang, Hsiao-Lan; Butcher, Stephen et al. (2011) Temporal coordination of gene networks by Zelda in the early Drosophila embryo. PLoS Genet 7:e1002339|
|Struffi, Paolo; Corado, Maria; Kaplan, Leah et al. (2011) Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer. Development 138:4291-9|
|Liang, Hsiao-Lan; Nien, Chung-Yi; Liu, Hsiao-Yun et al. (2008) The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila. Nature 456:400-3|
|Yao, Li-Chin; Phin, Sopheap; Cho, Jane et al. (2008) Multiple modular promoter elements drive graded brinker expression in response to the Dpp morphogen gradient. Development 135:2183-92|
|Lin, Meng-chi; Park, Jeongsook; Kirov, Nikolai et al. (2006) Threshold response of C15 to the Dpp gradient in Drosophila is established by the cumulative effect of Smad and Zen activators and negative cues. Development 133:4805-13|
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