Now that the C. elegans genome has been sequenced, the current challenge is to understand the function of the genes in the genome. Only 9 percent of genes have been studied using classical genetic or biochemical approaches, and so it is evident that we need high throughput, efficient methods to annotate gene function. One way to uncover the function of a gene is to determine when, where and under which conditions it is expressed. DNA microarrays are an extremely powerful tool to profile changes in gene expression on a global scale.The first main goal of this proposal is to use DNA microarrays containing nearly every gene in the C. elegans genome to determine which genes are expressed in the major tissues of the adult hermaphrodite. We will use a new method called mRNA tagging to identify most or all of the genes expressed in muscle cells, neurons, skin epithelia, intestinal cells and the vulval precursor cells. We will also use the full genome DNA microarrays to determine how these tissues respond to Ras activation. This global survey of gene expression in C. elegans development will provide important insight into how each of the genes may function, and will greatly speed up scientific advances in C. elegans biology.The second main goal of this proposal will test the hypothesis that the order of genes in the genome is influenced by their expression pattern. The global expression data will be used to determine whether genes expressed in the same tissue tend to be clustered together on the chromosomes. One likely explanation for gene clustering is that chromosomes in a specific tissue are divided into regions of active and inactive chromatin, so that genes expressed in a given tissue tend to cluster together because they are constrained to regions of active chromatin. To test this explanation for gene clustering, DNA microarrays will be used in chromatin immunoprecipitation experiments to identify regions of active chromatin from muscle cells, to see if gene clusters occur in regions of active chromatin.