The function and design of cis-acting enhancer elements regulated by short-range transcriptional repressors: Grammar studies from Drosophila melanogaster

Given that the DNA of (most) all cells in an animal is identical, how do different cells acquire the unique morphologies and functional properties to create the diverse tissues and organs in multicellular organisms? With better understanding of the nature of genes and the process of gene regulation, the central role of transcriptional regulation in directing development is becoming evident. These exquisitely orchestrated gene regulatory programs are encoded in the DNA sequence of cis-regulatory control elements, whose features are only now becoming apparent. Morphological diversity has its origins in reshaped developmental processes, and these changes often reflect alterations in genetic regulatory programs and in particular the transcriptional cis-regulatory regions. Thus, evolution of diversity is directly related to the evolution of these cis-regulatory regions or enhancers. To understand this aspect of evolution, we must first understand the structure-function relationships that apply to developmental cis-regulatory enhancers. The studies described herein highlight general principles of the design and function of cis-acting enhancer elements that are involved in the control of complex patterns of gene expression and should in turn facilitate our understanding of the regulatory logic underlying morphological complexity and diversity.; Cis-regulatory enhancer elements are thought to function as information processing centers that integrate the negative and positive transcriptional inputs incident on them, in a computer-like fashion, resolving the multiple inputs into a single output that instructs the basal transcriptional machinery to either turn the linked gene on or off. In this type of computational model for gene regulation by an enhancer, the basal transcriptional machinery plays a passive role by simply responding to signals generated by the enhancer. In contrast, the ‘Information Display’ or ‘Billboard’ model for enhancer function proposed in this study, demonstrates that instead of integrating multiple inputs, the enhancer is capable of simultaneously displaying contrasting information that is interpreted by multiple successive or simultaneous interactions with the basal promoter. Thus, the basal transcriptional machinery plays an active role in processing regulatory information presented by the cis-element.; Key structural features of the internal organization of an enhancer control its ability to convert positional information specified by the transcription factors that bind it into differential gene activity. Although many functional analyses have indicated the presence of functional constraints, no work has been carried out to systematically define the spatial constraints between transcription factor binding sites within enhancers that are required for their proper function. The experiments described here take a first step towards systematically deducing the ‘grammar’ rules for an important class of transcriptional regulators, the short-range repressors. These rules define the internal organization of a functional module regulated by them.; These studies described here have important ramifications for the biochemistry and evolution of cis-regulatory elements, and should facilitate the development of more sophisticated computational algorithms for the identification of cis-regulatory elements and for the interpretation of their biological function.