Another focus of the laboratory has been to understand the biochemical basis of combinatorial control of gene transcription by DNA binding proteins. Embryos regulate their growth and development in many ways, but control of gene transcription is essential for directing cells along particular developmental pathways. In Drosophila, a cascade of nuclear regulatory events establishes very early differences in cell fates by producing intricate patterns of gene expression. Many of these pattern-forming genes encode DNA binding proteins that regulate each others expression, and subsequently instruct the rest of the genome in a manner appropriate to each position in the organism. These regulatory proteins are conserved across the evolutionary distance separating flies and humans. This applies to both their primary structure, implying similarity in mechanism, and often their developmental function. That is, the regulatory scheme in which they function solves a common problem of developing multi-cellular organisms. Our current studies revolve around understanding specific mechanisms of two types: first, which gene products interact directly with which genes and other gene products, and second, how this impinges on transcriptional regulation and, relatedly, the stability of the epigenome.
My laboratory studies the regulation and function of two homeodomain-containing proteins. The homeodomain is a highly conserved sequence-specific DNA binding domain found in transcriptional regulators from yeast to humans. One of these, Engrailed (En), is a potent repressor of transcription that recruits the corepressor Groucho, a homolog of the TLE family of mammalian cofactors. We study interactions between En and the Pbx and Meis/PREP families of Hox protein cofactors, which serve to increase its DNA-binding specificity and thereby direct it to particular target genes. The interaction with En confers a novel activity on the Meis/PREP-Pbx complex (in Drosophila, Hth-Exd), that of transcriptional repression. Our analysis focuses on the biochemical interactions among these factors, and on the functional consequences of altering those interactions.
Even-skipped (Eve) is another homeodomain transcription factor that regulates developmental processes in a highly conserved fashion. Eve, like En, uses both Groucho-dependent and -independent mechanisms to repress transcription. The combinatorial regulation of gene expression by the homeodomain superfamily of transcription factors serves as a paradigm for understanding how cell-type specificity and intercellular signaling are integrated by DNA elements in all eukaryotic organisms.