The molecular basis of enhancer-promoter choice. Jia Ling, Theresa Apoznanski, Stephen Small. Department of Biology, New York University, New York, NY.

   In Drosophila, AP patterning is mainly controlled by the maternally deposited TF, Bicoid (Bcd) and its target genes. Upon binding to an enhancer, Bcd is thought to interact with a target genes core promoter, forming a complex by recruiting basal transcription factors. It is intriguing that when an enhancer is located close to two genes or promoters, it usually makes a choice to activate one, not both. For instance, one of the gap genes, hunchback (hb) has a Bcd-dependent enhancer P2 activating zygotic transcription from its proximal promoter, and another enhancer activating maternal transcription from a distal promoter. Our lab identified a new Bcd-dependent enhancer 4 kb upstream of the proximal promoter and next to the distal promoter. A series of reporter genes suggests that the second Bcd-dependent enhancer actually skips over its nearest basal promoter to activate the more distally located one. This leads to the hypothesis that enhancer-promoter interactions are specific, and that only certain enhancer-promoter pairs can activate transcription. Consistent with this, data have shown that an occupied enhancer does not necessarily correlate with gene activation. We are interested in the molecular basis of enhancer-promoter choice. We are focusing on the enhancer-promoter pairs of hb, performing a series of tests, such as mutating or adding motifs, and eliminating cooperative TF bindings. The chromosome conformation capture (3C) technique will be used to identify the DNA sequences involved in enhancer-promoter interaction. We also compared expression patterns of 32 Bcd-dependent enhancer lines with nearby genes endogenous patterns and created a dataset of positive and negative promoters for motif searching. Taken together, hopefully we will find factors contributing to enhancer-promoter choice.