SPELL - Nematode

Citation	Grishkevich V, Ben-Elazar S, Hashimshony T, Schott DH, Hunter CP, Yanai I. A genomic bias for genotype-environment interactions in C. elegans. Mol Syst Biol, 2012.
PubMed ID	22669615
Short Description	A genomic bias for genotype-environment interactions in C. elegans. GEO Record: GSE34650 Platform: GPL13394 Download gene-centric, log2 transformed data: WBPaper00041174.ce.mr.csv
# of Conditions	90
Full Description	The phenotype of an organism is determined by its genotype and environment. An interaction between these two arises from the differential effect of the environment on gene expression in distinct genotypes; however, the genomic properties identifying these are not well understood. Here we analyze the transcriptomes of five C. elegans strains (genotype) cultivated in five growth conditions (environment), and find that highly regulated genes, as distinguished by intergenic lengths, motif concentration, and expression levels, are particularly biased toward genotype-environment interactions. Sequencing these strains, we find that genes with expression variation across genotypes are enriched for promoter single-nucleotide polymorphisms (SNPs), as expected. However, genes with genotype-environment interactions do not significantly differ from background in terms of their promoter SNPs. Collectively, these results indicate that the highly regulated nature of particular genes predispose them for exhibiting genotype-environment interaction as a consequence of changes to upstream regulators. This observation may provide a deeper understanding into the origin of the extraordinary gene expression diversity present in even closely related species. Experimental Details: WBPaper00041174:AB2_Control_1 WBPaper00041174:CB4856_Control_1 WBPaper00041174:RC301_Control_1 WBPaper00041174:CB4857_Control_1 WBPaper00041174:N2_Control_1 WBPaper00041174:HC445_Control_1 WBPaper00041174:AB2_25C_1 WBPaper00041174:CB4856_25C_1 WBPaper00041174:RC301_25C_1 WBPaper00041174:CB4857_25C_1 WBPaper00041174:N2_25C_1 WBPaper00041174:HC445_25C_1 WBPaper00041174:AB2_High-pH-Salt_1 WBPaper00041174:CB4856_High-pH-Salt_1 WBPaper00041174:RC301_High-pH-Salt_1 WBPaper00041174:CB4857_High-pH-Salt_1 WBPaper00041174:N2_High-pH-Salt_1 WBPaper00041174:HC445_High-pH-Salt_1 WBPaper00041174:AB2_Liquid_1 WBPaper00041174:CB4856_Liquid_1 WBPaper00041174:RC301_Liquid_1 WBPaper00041174:CB4857_Liquid_1 WBPaper00041174:N2_Liquid_1 WBPaper00041174:HC445_Liquid_1 WBPaper00041174:AB2_infection_1 WBPaper00041174:CB4856_infection_1 WBPaper00041174:RC301_infection_1 WBPaper00041174:CB4857_infection_1 WBPaper00041174:N2_infection_1 WBPaper00041174:HC445_infection_1 WBPaper00041174:AB2_Control_2 WBPaper00041174:CB4856_Control_2 WBPaper00041174:RC301_Control_2 WBPaper00041174:CB4857_Control_2 WBPaper00041174:N2_Control_2 WBPaper00041174:HC445_Control_2 WBPaper00041174:AB2_25C_2 WBPaper00041174:CB4856_25C_2 WBPaper00041174:RC301_25C_2 WBPaper00041174:CB4857_25C_2 WBPaper00041174:N2_25C_2 WBPaper00041174:HC445_25C_2 WBPaper00041174:AB2_High-pH-Salt_2 WBPaper00041174:CB4856_High-pH-Salt_2 WBPaper00041174:RC301_High-pH-Salt_2 WBPaper00041174:CB4857_High-pH-Salt_2 WBPaper00041174:N2_High-pH-Salt_2 WBPaper00041174:HC445_High-pH-Salt_2 WBPaper00041174:AB2_Liquid_2 WBPaper00041174:CB4856_Liquid_2 WBPaper00041174:RC301_Liquid_2 WBPaper00041174:CB4857_Liquid_2 WBPaper00041174:N2_Liquid_2 WBPaper00041174:HC445_Liquid_2 WBPaper00041174:AB2_infection_2 WBPaper00041174:CB4856_infection_2 WBPaper00041174:RC301_infection_2 WBPaper00041174:CB4857_infection_2 WBPaper00041174:N2_infection_2 WBPaper00041174:HC445_infection_2 WBPaper00041174:AB2_Control_3 WBPaper00041174:CB4856_Control_3 WBPaper00041174:RC301_Control_3 WBPaper00041174:CB4857_Control_3 WBPaper00041174:N2_Control_3 WBPaper00041174:HC445_Control_3 WBPaper00041174:AB2_25C_3 WBPaper00041174:CB4856_25C_3 WBPaper00041174:RC301_25C_3 WBPaper00041174:CB4857_25C_3 WBPaper00041174:N2_25C_3 WBPaper00041174:HC445_25C_3 WBPaper00041174:AB2_High-pH-Salt_3 WBPaper00041174:CB4856_High-pH-Salt_3 WBPaper00041174:RC301_High-pH-Salt_3 WBPaper00041174:CB4857_High-pH-Salt_3 WBPaper00041174:N2_High-pH-Salt_3 WBPaper00041174:HC445_High-pH-Salt_3 WBPaper00041174:AB2_Liquid_3 WBPaper00041174:CB4856_Liquid_3 WBPaper00041174:RC301_Liquid_3 WBPaper00041174:CB4857_Liquid_3 WBPaper00041174:N2_Liquid_3 WBPaper00041174:HC445_Liquid_3 WBPaper00041174:AB2_infection_3 WBPaper00041174:CB4856_infection_3 WBPaper00041174:RC301_infection_3 WBPaper00041174:CB4857_infection_3 WBPaper00041174:N2_infection_3 WBPaper00041174:HC445_infection_3.
Tags	Method: microarray, Species: Caenorhabditis elegans, Topic: innate immune response, Topic: response to osmotic stress