Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene-environment interaction in yeast gene expression

ABSTRACT: This study is a quantitative trait linkage mapping study targeted at gene-environment interaction. A family of yeast derived from BY4716 and RM11-1a was grown in two carbon sources (glucose and ethanol) and expression profiled. The analysis revealed how the influence of genetic factors changes in different conditions. Abstract: The effects of genetic variants on phenotypic traits often depend on environmental and physiological conditions, but such gene–environment interactions are poorly understood. Recently developed approaches that treat transcript abundances of thousands of genes as quantitative traits offer the opportunity to broadly characterize the architecture of gene–environment interactions. We examined the genetic and molecular basis of variation in gene expression between two yeast strains (BY and RM) grown in two different conditions (glucose and ethanol carbon sources). We observed that most transcripts vary by strain and condition, with 2,996, 3,448, and 2,037 transcripts showing significant strain, condition, and strain–condition interaction effects, respectively. We expression profiled over 100 segregants derived from a cross between RM and BY in both growth conditions, and identified 1,555 linkages for 1,382 transcripts that show significant gene–environment interaction. At the locus level, local linkages, which usually correspond to polymorphisms in cis-regulatory elements, tend to be more stable across conditions, such that they are more likely to show the same effect or the same direction of effect across conditions. Distant linkages, which usually correspond to polymorphisms influencing trans-acting factors, are more condition-dependent, and often show effects in different directions in the two conditions. We characterized a locus that influences expression of many growth- related transcripts, and showed that the majority of the variation is explained by polymorphism in the gene IRA2. The RM allele of IRA2 appears to inhibit Ras/PKA signaling more strongly than the BY allele, and has undergone a change in selective pressure. Our results provide a broad overview of the genetic architecture of gene–environment interactions, as well as a detailed molecular example, and lead to key insights into how the effects of different classes of regulatory variants are modulated by the environment. These observations will guide the design of studies aimed at understanding the genetic basis of complex traits. Keywords: QTL This data set includes 24 parental arrays (6 of each parent in each condition, 218 segregant arrays (109 in both conditions), and 4 allele replacement arrays (IRA2 replacements in both backgrounds in both conditions). All arrays are from an unique biological sample, and many are randomized for dye (no dye-swaps on the same RNA sample). For the 24 parental arrays, there are three of each strain*condition*dye combination. The segregant arrays were randomized for dye. The replacement arrays are all of the Cy5 = experimental, Cy3 = reference type. All arrays are hybridized to a common reference consisting of an equal portions of RNA samples. from BY and RM grown in glucose and ethanol. Analysis was performed using default settings in Agilent Feature Extractor software versions 8.0-9.5. Spots were excluded if their intensity was below 350 or if they were flagged as non-uniformity outliers. Transcripts were considered good if they were present in all parental arrays (for the parental analysis) or 80% of all arrays in each condition for the segregant analysis.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Erin Smith

PROVIDER: E-GEOD-9376 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Technological advances now make gene expression analysis feasible in any sequenced organism, and new sequencing methods have greatly accelerated genome sequencing. Here we show that important insights into gene function are possible by comparing gene expression response to genetic and environmental perturbations between related species. We present a gene expression compendium designed for maximal gene expression variation in the sensu stricto yeast Saccharomyces bayanus. While many aspects of gene expression are conserved over the 20 million years of evolution separating S. bayanus from the model yeast S. cerevisiae, we observe regulatory changes, including in galactose metabolism and sporulation. The expression data also allows us to predict the biological roles of genes unique to S. bayanus, leading us to propose a role in oxidative stress response for a group of genes, and also to identify a regulatory network specific to this yeast. This dataset contains 53 experiments as follows: (experiment: number of datasets (number of arrays)) growth at different temperatures: 1 (3) heat shock: 4 (18) ammonium: 1 (6) cadmium: 1 (4) copper: 1 (6) lead: 1 (6) nickel: 1 (5) sulfite toxicity: 1 (6) zinc: 1 (6) ethanol toxicity: 1 (6) sorbitol: 1 (6) bleach: 1 (6) hydrogen peroxide: 3 (17) 2-deoxyglucose: 1 (6) hydroxyurea: 1 (6) lovastatin: 1 (4) MG-132: 1 (5) MMS: 1 (6) rapamycin: 1 (6) tunicamycin: 1 (6) zeocin: 1 (6) chronological aging: 3 (13) diauxic shift: 1 (6) galactose: 5 (38) glycerol: 1 (4) sucrose: 1 (4) auxotroph starvation: 1 (11) nutrient limited chemostat growth: 3 (7) mating type and ploidy: 1 (3) alpha factor: 1 (8) cell cycle: 1 (30) sporulation: 3 (18) strain backgrounds: 1 (4) cross progeny: 1 (22) Tn7 insertions: 1 (27) 555.11 and 670.20 knockout tetrads: 2 (8) Timecourse datasets: heat shock, ammonium, cadmium, copper, lead, nickel, sulfite toxicity, zinc, ethanol toxicity, sorbitol, bleach, hydrogen peroxide, 2-deoxyglucose, hydroxyurea, lovastatin, MG-132, MMS, rapamycin, tunicamycin, zeocin, chronological aging, diauxic shift, galactose, glycerol, sucrose, auxotroph starvation, alpha factor, cell cycle, sporulation Single timepoint datasets: growth at different temperatures, strain backgrounds, cross progeny, Tn7 insertions, nutrient limited chemostat growth, mating type and ploidy, 555.11 and 670.20 knockout tetrads Almost all samples were hybridized versus a common reference prepared from a mixture of RNA from Mat a, Matx, and Mata/x cells sampled in both exponential and stationary phase. Additionally, RNA from stress conditions was included: hydrogen peroxide treatment sampled at 10, 30 and 45 minutes, and heat shock from 25 to 37 degrees sampled at 10 and 30 minutes. Samples from the following datasets were not hybridized versus the common reference (reference used in parenthesis and in array annotations): cell cycle (asynchronous culture), constant temperatures (log phase culture), mating type and ploidy (log phase culture), diauxic shift (log phase culture), and strain backgrounds (log phase culture). Replicates and dye swaps were not used.

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Gene-environment interaction in yeast gene expression

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