How are key genes in our DNA regulated? How is their expression coordinated in the proper spaceand time during embryonic development? These questions have enormous implications in ourcomprehension of the developmental program in animals and humans. Despite this fact, our currentunderstanding of regulation of gene expression at the molecular level remains somewhatsuperficial. It has been shown that the transcription of critical developmental genes is controlled ina variety of ways by specific regions of neighboring non?coding genomic DNA sequences. Thesedistinct cis?regulatory modules (CRMs), which include transcriptional enhancers, insulators, andsilencers, have been found to regulate gene expression in all the model eukaryotic systemsstudied so far. In some cases, specific transcription factors have been found to bind at sequences inthe CRMs and to regulate their activity. However, the molecular mechanisms that determine wheretranscription factors bind within most CRM sequences and how this binding regulates CRM functionremain unclear.The Hox genes of the Drosophila bithorax complex are critical genes that determine the animal bodyplan during embryonic development. The expression of Hox genes spatially and temporally in thedeveloping embryo is controlled by CRMs. Our initial studies show that sequences at the CRMs ofthe Drosophila bithorax complex are rapidly evolving within the Drosophila genus. This is in sharpcontrast to the Hox genes, which are conserved across all bilaterian animals. The large set ofknown enhancer CRMs at the Drosophila bithorax complex, and the rapid evolution of the sequencesat these CRMs across different Drosophila species, provide an exciting opportunity to study therelationship between sequences at the CRMs, transcription factor binding and cis?regulatoryfunction.The ultimate goal of this proposal is to elucidate the molecular mechanisms which controlfunctional activity of the enhancer CRMs at the sequence level. Our proposed studies will alsoprovide insight into the evolution of cis?regulatory function across different species. The long termscientific goal of the PI is to fully investigate the molecular mechanisms by which the regulatoryregions achieve coordinated control of gene expression across the entire bithorax complex. Themajor focus of this proposal will be on the bioinformatic identification and functionalcharacterization of specific transcription factor binding sites within known CRMs of the Drosophilabithorax complex. Further experiments to test conserved sub?regions of known CRMs for functionalactivity and to investigate the functional compatibility of CRM sub?regions from distantly relatedDrosophila species will shed light on the evolution of CRM architecture and functional activity.
The issue of gene regulation is at the heart of our understanding of development and disease.Carefully timed and spatially controlled expression of key developmental genes; many of which aretranscription factors that regulate the expression of downstream genes; serves as the critical basis fornormal development. The early patterns of Hox gene expression in the embryo initiate a cascade ofregulatory events at the molecular level that has profound consequences for later development.Currently our understanding of the mechanisms of cis?regulation for the Hox genes is still verysuperficial. Our preliminary studies have led us to investigate the function of cis?regulatory modulesand how transcription factors act at the regulatory sequence level to control the expression ofHox genes at the Drosophila bithorax complex. The conservation of many of these keydevelopmental genes and mechanisms of gene regulation across all animals promises that thesestudies will be informative for studies in organisms beyond Drosophila.
