The transcriptional signatures of Caenorhabditis elegans dauer larvae
Both plasticity and robustness are pervasive features of developmental programs.  The dauer in Caenorhabditis elegans is an alternative to the third larval stage of the nematode and is an example of phenotypic plasticity. The dauer is an arrested, hypometabolic state that undergoes dramatic changes in gene expression compared to conspecifics that continue development, and can be induced by several adverse environments or genetic mutations that act as independent and parallel inputs into the larval developmental program. However, given the different genetic or environmental triggers that can induce dauer, gene expression in dauer larvae could be invariant or vary depending on the larvae's route into dauer entry; this question has not been examined. Here we use RNA-sequencing to characterize gene expression in dauer larvae induced to arrest development in response to different stimuli.  By assessing the variance in the expression levels of all genes and computing the Spearman's rank-order correlation of gene expression within several Gene Ontologies (GO) and gene networks, we find that the expression patterns of most genes, except for those that act in specific defense and metabolic pathways, are strongly correlated between the different dauer larvae, suggestive of transcriptional robustness.  We speculate that the transcriptional robustness of core dauer pathways allows for the buffering of variation in the expression of genes involved in their response to the environment, allowing the different dauers to be better suited to survive in and exploit different niches. Overall design: Comparative gene expression profiling analysis of RNA-seq data for  C. elegans dauer of the following gennotypeswild-type dauers (N2; Bristol) ;daf-2 (e1370) III,daf-7(e1372) III ;ilc-17.1 (syb5296) X  ;cep-1 (cep-1oe) [unc-119 (ed4); gtIs1 [CEP-1::GFP + unc-119 (+)]