? One of the next major goals of the Human Genome Project is to identify the function of all the genes it encodes. Arguably the greatest challenge lies in determining the in vivo functions for large sets of genes and how they orchestrate the complex processes of the cell, and animal models can play a significant role in guiding in vivo functional annotation of the human genome. C. elegans is well established as an important model system in which to study the molecular genetics of cell biology and animal development and has also become a leading model for functional genomic research; the early embryo in particular is an excellent system in which to study basic cell biological and developmental processes. RNA interference (RNAi) is a rapid reverse genetics approach to identify the in vivo functions of genes, and several large-scale RNAi scans in C. elegans have so far led to the identification of over 1,500 genes required for embryogenesis. By systematically annotating the functions of such genes in detail using time-lapse microscopy of early embryogenesis, specific cellular roles for over 200 genes have been discovered; however, it is estimated that at least an additional 1000 genes essential for embryonic development remain to be identified. The next step now required is to provide a systematic, detailed functional characterization of all the genes that play a role in this system - a """"""""phenotypic map"""""""" of in vivo functions to lay the foundation for integrative systems biology approaches. ? ? The goal of this project is to use RNAi to produce a high-resolution phenotypic map of early embryogenesis in C. elegans: a detailed functional description of all the genes required for basic cellular, subcellular, and developmental processes in the early embryo. To accomplish this goal, single-gene RNAi of all approximately 12,000 validated ORFs cloned by the ORFeome project will be performed to assay embryonic lethality and carry out systematic detailed phenotypic analysis of early embryogenesis using DIC optics. An online database, RNAiDB, will be used for all aspects of this study: data collection, scoring, analysis, and distribution. Phenotype-based bioinformatic analysis will be performed, including gene clustering based on phenotypic data and integration with other types of functional genomics data, to identify groups of genes with similar functions and to extend functional annotations, for unknown proteins in particular. The results of these analyses will be used to select groups of genes for further study using a set of subcellular markers to assay specific processes (e.g. chromosome segregation, cytoskeletal organization, cell polarity and cell fate). These secondary studies will be used both to test hypotheses generated from earlier phenotypic and bioinformatic analyses, as well as to generate more in-depth data on the functions of particular gene sets. Since many of these basic functions are carried out by highly conserved proteins, the data gathered in this project will be immediately useful to guide the functional annotation of the human and other genomes. ? ?
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