Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes

Landry, Christian R.; Oh, Julia; Hartl, Daniel L.; Cavalieri, Duccio

doi:10.1016/j.gene.2005.10.042

Cited by 100 publications

(119 citation statements)

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“…Transcripts that are present at levels below the detection limit of the Affymetrix microarrays would also go undetected. Furthermore, the exact composition of the transcriptional networks may differ for different populations, and genotype-by-environment interactions may cause shifts in the transcriptional modules under different environmental conditions (Fay et al 2004;Landry et al 2006;Sambandan et al 2006;Monroy et al 2007). Nonetheless, it is clear that the transcriptional network associated with acute exposure to ethanol shifts dramatically as flies develop tolerance.…”

Section: Resultsmentioning

confidence: 99%

Alcohol Sensitivity in Drosophila: Translational Potential of Systems Genetics

et al. 2009

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Identification of risk alleles for human behavioral disorders through genomewide association studies (GWAS) has been hampered by a daunting multiple testing problem. This problem can be circumvented for some phenotypes by combining genomewide studies in model organisms with subsequent candidate gene association analyses in human populations. Here, we characterized genetic networks that underlie the response to ethanol exposure in Drosophila melanogaster by measuring ethanol knockdown time in 40 wildderived inbred Drosophila lines. We associated phenotypic variation in ethanol responses with genomewide variation in gene expression and identified modules of correlated transcripts associated with a first and second exposure to ethanol vapors as well as the induction of tolerance. We validated the computational networks and assessed their robustness by transposon-mediated disruption of focal genes within modules in a laboratory inbred strain, followed by measurements of transcript abundance of connected genes within the module. Many genes within the modules have human orthologs, which provides a stepping stone for the identification of candidate genes associated with alcohol drinking behavior in human populations. We demonstrated the potential of this translational approach by identifying seven intronic single nucleotide polymorphisms of the Malic Enzyme 1 (ME1) gene that are associated with cocktail drinking in 1687 individuals of the Framingham Offspring cohort, implicating that variation in levels of cytoplasmic malic enzyme may contribute to variation in alcohol consumption.

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Section: Resultsmentioning

confidence: 99%

Alcohol Sensitivity in Drosophila: Translational Potential of Systems Genetics

et al. 2009

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“…It has been previously shown that gene essentiality and network connectivity in yeast is correlated with sequence conservation (Carlson et al 2006). Another study in yeast also found that dispensable genes showed higher rates of G·E interaction but found no evidence for a relationship between sequence evolution and G·E interaction (Landry et al 2006). Analyses to test if genetic variation is constrained for consensus regulators await resequencing studies in wheat that would allow for the comparison of genetic variation between genes with environmentally unique or conserved expression patterns.…”

Section: Comparison Of Gene Expression Network Across Environmentsmentioning

confidence: 99%

“…The extent of G·E for a particular trait in part determines heritability and our understanding of the underlying biology. Transcriptional regulation of genes plays a large role in the response of an organism to the environment, and this modulation of gene expression is itself genetically controlled and subject to G·E interactions (Landry et al 2006;Li et al 2006;Smith and Kruglyak 2008). A number of studies have used broad transcriptional profiling in segregating or natural populations to identify genetic loci that control gene expression, commonly referred to as genetical genomics or gene expression QTL (eQTL) mapping (Jansen and Nap 2001;Brem et al 2002;Schadt et al 2003;Brem and Kruglyak 2005;Zhang et al 2011).…”

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confidence: 99%

Systems Genetics of Environmental Response in the Mature Wheat Embryo

Munkvold

Laudencia‐Chingcuanco

Sorrells

2013

Genetics

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Quantitative phenotypic traits are influenced by genetic and environmental variables as well as the interaction between the two. Underlying genetic · environment interaction is the influence that the surrounding environment exerts on gene expression. Perturbation of gene expression by environmental factors manifests itself in alterations to gene co-expression networks and ultimately in phenotypic plasticity. Comparative gene co-expression networks have been used to uncover biological mechanisms that differentiate tissues or other biological factors. In this study, we have extended consensus and differential Weighted Gene Co-Expression Network Analysis to compare the influence of different growing environments on gene co-expression in the mature wheat (Triticum aestivum) embryo. This network approach was combined with mapping of individual gene expression QTL to examine the genetic control of environmentally static and variable gene expression. The approach is useful for gene expression experiments containing multiple environments and allowed for the identification of specific gene co-expression modules responsive to environmental factors. This procedure identified conserved coregulation of gene expression between environments related to basic developmental and cellular functions, including protein localization and catabolism, vesicle composition/trafficking, Golgi transport, and polysaccharide metabolism among others. Environmentally unique modules were found to contain genes with predicted functions in responding to abiotic and biotic environmental variables. These findings represent the first report using consensus and differential Weighted Gene Coexpression Network Analysis to characterize the influence of environment on coordinated transcriptional regulation. Q UANTITATIVE phenotypic traits are governed by genetics, environment, and interactions between the two (G·E). The extent of G·E for a particular trait in part determines heritability and our understanding of the underlying biology. Transcriptional regulation of genes plays a large role in the response of an organism to the environment, and this modulation of gene expression is itself genetically controlled and subject to G·E interactions (Landry et al. 2006;Li et al. 2006;Smith and Kruglyak 2008). A number of studies have used broad transcriptional profiling in segregating or natural populations to identify genetic loci that control gene expression, commonly referred to as genetical genomics or gene expression QTL (eQTL) mapping (Jansen and Nap 2001;Brem et al. 2002;Schadt et al. 2003;Brem and Kruglyak 2005;Zhang et al. 2011). In plants a number of studies have been conducted on a range of species including Arabidopsis thaliana, barley (Hordeum vulgare), maize (Zea mays), poplar (Populus spp.), and wheat (Triticum aestivum) (Decook et al. 2006;Jordan et al. 2007;Keurentjes et al. 2007;West et al. 2007;Potokina et al. 2008;Drost et al. 2010;Druka et al. 2010;Holloway et al. 2011;Zhang et al. 2011). Using a genetical genomics approach, gene expr...

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“…Recent studies comparing genomic expression within and between species reveal distinct patterns of variation (Fay and Wittkopp 2008). Genes with variable expression tend to be nonessential genes, genes with paralogs, and genes with upstream TATA elements (Denver et al 2005;Landry et al 2006Landry et al , 2007Tirosh et al 2006;Kvitek et al 2008). Many of these are responsive to mutation accumulation (Denver et al 2005;Rifkin et al 2005;Landry et al 2007) and, in the case of TATA-containing genes, to environmental perturbation (Basehoar et al 2004;Raser and O'Shea 2004;Blake et al 2006).…”

mentioning

confidence: 99%

“…Several studies have compared condition-specific expression variation across yeast strains responding to nutrient changes (Landry et al 2006), copper treatment (Fay et al Microarray data from this article have been deposited with the National Institutes of Health GEO Database under accession no. GSE15147.…”

mentioning

confidence: 99%

Transient Genotype-by-Environment Interactions Following Environmental Shock Provide a Source of Expression Variation for Essential Genes

Eng¹,

Kvitek

Keleş³

et al. 2010

Genetics

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Understanding complex genotype-by-environment interactions (GEIs) is crucial for understanding phenotypic variation. An important factor often overlooked in GEI studies is time. We measured the contribution of GEIs to expression variation in four nonlaboratory Saccharomyces cerevisiae strains responding dynamically to a 25°-37°heat shock. GEI was a major force explaining expression variation, affecting 55% of the genes analyzed. Importantly, almost half of these expression patterns showed GEI influence only during the transition between environments, but not in acclimated cells. This class reveals a genotype-by-environment-by-time interaction that affected expression of a large fraction of yeast genes. Strikingly, although transcripts subject to persistent GEI effects were enriched for nonessential genes with upstream TATA elements, those displaying transient GEIs were enriched for essential genes regardless of TATA regulation. Genes subject to persistent GEI influences showed relaxed constraint on acclimated gene expression compared to the average yeast gene, whereas genes restricted to transient GEIs did not. We propose that transient GEI during the transition between environments provides a previously unappreciated source of expression variation, particularly for essential genes.

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Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes

Cited by 100 publications

References 45 publications

Alcohol Sensitivity in Drosophila: Translational Potential of Systems Genetics

Alcohol Sensitivity in Drosophila: Translational Potential of Systems Genetics

Systems Genetics of Environmental Response in the Mature Wheat Embryo

Transient Genotype-by-Environment Interactions Following Environmental Shock Provide a Source of Expression Variation for Essential Genes

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