Novel strategies and questions to define gene function have emerged with the entire genome sequence of a few model organisms available or near completion. Recent examples include large-scale gene knock-out analyses, studies of simultaneous expression profiles for every gene of a genome, and the systematic identification of protein-protein interactions. The long-term goal of the investigators' laboratory is to decipher regulatory networks involved in the development of multicellular organisms. In particular, the investigators use genomic information and """"""""functional genomics"""""""" tools to participate in the identification of cross-talks between regulatory pathways. Specifically, they are generating a comprehensive protein-protein interaction database for the nematode C. elegans. The investigators have recently developed a novel version of the two-hybrid system which solves most of the common problems of the method, including the relatively high number of false positives. Current versions of the two-hybrid system often fail to provide a clear link between interaction and function. To address this, they have developed a """"""""reverse two-hybrid system"""""""" that efficiently generates protein-protein interaction defective alleles. Such alleles can be used to assess the functional significance of potential interactions. The investigators' project includes the identification of potential physical interactions using an automated version of the two-hybrid system. In addition, it includes the development of systems to systematically relate potential physical interactions to relevant functional interactions. The investigators plan to involve the worm genetics community in this project by releasing the information and the reagents into a database already widely used, ACeDB (a C. elegans database). In return, they will request from C. elegans geneticists a summary of the functional data which will be reintroduced back into the database, thereby constantly improving its quality. To generate such a comprehensive worm IST database, they favor a systematic approach that includes a priority for subsets of gene products with immediate biological interest. Here they describe a project to apply these strategies to the worm genes already associated with a phenotype, i.e. genes in which a loss-of-function mutation has already been identified and shown to be associated with a testable phenotype. This work should help in developing the tools and the strategies needed to generate and interpret a comprehensive human-protein interaction database.
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