Gradients of cell signaling molecules and regulatoryfactorsare pervasivelyused in a variety of patterning process in metazoan development. Examples include the Sonic Hedgehog gradient that specifies different neuronal cell types in the neural tube of vertebrateembryos,and the Dpp gradient that patterns the developing wing imaginal disk in Drosophila larvae. The Toll-Dorsal signaling pathway represents one of the most thoroughly characterized gradient systemsin animal development. The proposed study represents a continuationof our efforts to determine how the Dorsal regulatorygradient produces multiple thresholds of gene expression and tissue differentiation in the early Drosophila embryo. The research plan includes 3 specific aims, First, we will examine the activitiesof Dorsal target genes that were identified in recent whole-genome microarray assays. Among the newly identified genes that will be tested is Eiger, the major TNF homolog in the Drosophila genome, and Mes4, which encodes a tissue-specific subunit of the CACAAT-box binding protein complex, NF-Y. Second, we will use a combination of bioinformatics methods and transgenic assays to determine how the Dorsal gradient regulates the expression of different target genes in a concentration-dependent manner. Particular efforts will focus on defining a""""""""cis- regulatory code"""""""", whereby coordinately regulated target enhancers share a characteristic combination of factor binding sites, including binding sites for Dorsal and additional,mainlyunknown regulatory factors. Third, we will determine whether immunity genes that are induced upon infection or injury share a similar organization of cis-regulatory elements. Particular efforts will focus on genes that are activated by the Dorsal-related immunity genes, Dif and Relish, and the GATA transcriptionfactor, Serpent.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Method to Extend Research in Time (MERIT) Award (R37)
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Special Emphasis Panel (NSS)
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Hoodbhoy, Tanya
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University of California Berkeley
Schools of Arts and Sciences
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Esposito, Emilia; Lim, Bomyi; Guessous, Ghita et al. (2016) Mitosis-associated repression in development. Genes Dev 30:1503-8
Fukaya, Takashi; Lim, Bomyi; Levine, Michael (2016) Enhancer Control of Transcriptional Bursting. Cell 166:358-68
Farley, Emma K; Olson, Katrina M; Zhang, Wei et al. (2015) Suboptimization of developmental enhancers. Science 350:325-8
Levine, Michael; Cattoglio, Claudia; Tjian, Robert (2014) Looping back to leap forward: transcription enters a new era. Cell 157:13-25
Boettiger, Alistair Nicol; Levine, Michael (2013) Rapid transcription fosters coordinate snail expression in the Drosophila embryo. Cell Rep 3:8-15
Lagha, Mounia; Bothma, Jacques P; Esposito, Emilia et al. (2013) Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo. Cell 153:976-87
Bothma, Jacques P; Magliocco, Joe; Levine, Michael (2011) The snail repressor inhibits release, not elongation, of paused Pol II in the Drosophila embryo. Curr Biol 21:1571-7
Papatsenko, Dmitri; Levine, Michael (2011) The Drosophila gap gene network is composed of two parallel toggle switches. PLoS One 6:e21145
Papatsenko, Dmitri; Levine, Michael; Goltsev, Yury (2011) Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles. PLoS Biol 9:e1000584
Hendrix, David; Levine, Michael; Shi, Weiyang (2010) miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data. Genome Biol 11:R39

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