Research Projects

Mechanisms of transcriptional repressors We are interested in understanding basic principles of transcriptional regulation using the powerful molecular genetics of Drosophila. We are pursuing complementary biochemical, molecular biological and genetic approaches to determine how transcriptional repressors control gene expression.

Currently, several projects in the laboratory focus on the activity of proteins that play key roles in developmental gene regulation, including the short-range repressors Knirps and Giant, the long-range repressor Hairy, and cofactors that associate with these DNA binding proteins. Short-range repressors interfere with activators located within 100 bp, producing a very local effect, while long-range proteins have a dominant effect, shutting down regulatory elements over a kilobase away. The mechanisms by which these proteins exert their differential effects are poorly understood.

We can measure the activity of short-range repressors by targeting them to reporter transgenes expressed in embryos. Here, we measure repression by the Giant repressor, which is expressed in two broad bands. Where Giant is expressed, expression of lacZ is repressed. In this experiment, we demonstrate that Giant requires the CtBP corepressor for full activity; a mutant lacking CtBP is only weakly repressed.

CtBP is an evolutionarily conserved corepressor with strong sequence similarities to NAD binding dehydrogenase enzymes. We are using whole fly assays to determine the structural features required for this protein to function. Misexpression of CtBP induces developmental abnormalities in eye and wing.

Cis Regulatory Grammar and Systems Biology Our work has uncovered many instances of context dependence for action of transcriptional repressors, indicating that the design of a regulatory element dictates the functional output. We are using quantitative measurements of gene expression together with mathematical models of cis element activity to develop bioinformatics tools to predict the evolution of known enhancers and the activity of novel regulatory sequences. This work is focused on understanding the particular parameters affecting short-range repressors, but can be extended more generally to other proteins to more fully describe developmental networks.

Retinoblastoma Tumor Suppressor Proteins The Retinoblastoma tumor suppressor is frequently misregulated in human cancer. Drosophila also possesses two Retinoblastoma homologs, and together with the Henry laboratory, we have undertaken biochemical and genetic studies to better understand how cofactors regulate the activity of RB proteins in a developmental context. Affinity purification of these proteins has identified a host of chromatin modifying factors associated with Drosophila RB proteins. In a novel pathway, we have additionally identified proteins that stabilize RB against premature proteolysis, possibly linking RB turnover to activity at the promoter.

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