Global analysis of gene expression patterns in the dauer larvae of Caenorhabditis elegans

C. elegans can develop into dauer larvae when conditions are not favorable for reproduction. Upon encountering conditions permissive for reproduction, the dauer larvae recover and recommence development into an adult. The process of dauer recovery has been largely unexplored but is important for successful propagation. This study examines the transcriptional response as dauers recover and resume reproductive development.;We used nearly full-genome DNA microarrays to profile dauer recovery over a 12 hour time course. For comparison, we also profiled the feeding of starved L1 animals over a similar time course. Using stringent statistical criteria, we defined a set of 2430 genes that were differentially expressed during dauer recovery. Of these, 446 genes behaved similarly in both time courses and define a common feeding response gene group. The remaining 1984 genes were specific to dauer recovery; we subdivided these genes into five groups with similar gene expression kinetic profiles. We analyzed the gene compositions of these six gene groups. Examination of a set of genes that are transiently induced during dauer recovery suggests that execution of dauer recovery may employ a hormonal mechanism. Our dataset and analysis provide a molecular framework from which to examine all aspects of dauer biology. Furthermore, since the dauer larvae may be analogous to the infective stage of parasitic nematodes, our analysis of dauer recovery may be illuminating for the nematode infective process.;DNA microarrays are powerful high-throughput functional genomics reagents. We have constructed a nearly full-genome DNA microarray for C. elegans . These microarrays contain 21,504 spots covering 17,088 genes which corresponds to 83--87% coverage of the known predicted genes in the genome. The nearly full-genome microarrays have been used successfully for many experiments, and we anticipate continued fruitful endeavors when utilizing this reagent.;In a set of unrelated experiments, we investigated an aspect of signal transduction. Identification of the downstream targets of C. elegans mpk-1 is necessary for uncovering the mechanism by which let-60 Ras-mediated signal transduction leads to establishment and execution of cell fate. We isolated smk-4(ga136) in a genetic screen. Based on genetic characterization, smk-4( ga136) may be a novel downstream target of mpk-1.