This research proposal outlines methods for identification of mechanisms governing transcription in the fly immune system. Using in vitro oligonucleotide selection, we collected binding data for several transcription factors that mediate the immune response. This information was used to identify clustered binding sites in the Drosophila genome, some of which activate reporter gene expression in response to infection in transgenic flies and in tissue culture. Interestingly, these enhancers share patterns of regulatory elements which may underlie a cis-regulatory code for the immune system. One goal of this proposal is to alter the observed patterns and determine what parameters govern enhancer function. A second goal is to characterize transcription factors that mediate the immune response, and connect their mechanism of activation/synergy with the layout of their target enhancers. Once the rules governing enhancer function have been derived, a third goal would be to use bioinformatics to identify new immunity enhancers that conform to those rules. In this manner we hope to begin annotating the Drosophila genome for enhancers.
