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Hodgins-Davis A, et al.  (2012) Abundant gene-by-environment interactions in gene expression reaction norms to copper within Saccharomyces cerevisiae. Genome Biol Evol 4(11):1061-79

Abstract: Genetic variation for plastic phenotypes potentially contributes phenotypic variation to populations that can be selected during adaptation to novel ecological contexts. However, the basis and extent of plastic variation that manifests in diverse environments remains elusive. Here, we characterize copper reaction norms for mRNA abundance among five Saccharomyces cerevisiae strains to 1) describe population variation across the full range of ecologically relevant copper concentrations, from starvation to toxicity, and 2) to test the hypothesis that plastic networks exhibit increased population variation for gene expression. We find that although the vast majority of the variation is small in magnitude (considerably <2-fold), not just some, but most genes demonstrate variable expression across environments, across genetic backgrounds, or both. Plastically expressed genes included both genes regulated directly by copper-binding transcription factors Mac1 and Ace1 and genes indirectly responding to the downstream metabolic consequences of the copper gradient, particularly genes involved in copper, iron, and sulfur homeostasis. Copper-regulated gene networks exhibited more similar behavior within the population in environments where those networks have a large impact on fitness. Nevertheless, expression variation in genes like Cup1, important to surviving copper stress, was linked with variation in mitotic fitness and in the breadth of differential expression across the genome. By revealing a broader and deeper range of population variation, our results provide further evidence for the interconnectedness of genome-wide mRNA levels, their dependence on environmental context and genetic background, and the abundance of variation in gene expression that can contribute to future evolution.

Status: Published Type: Journal Article PubMed ID: 23019066

Topics addressed in this paper

Number of different genes curated to this paper: 106

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Topics Topics not linked to Genes Genes linked to topics (#1 - 10 )
ACO1 ADD37 AIM19 ALD6 ASE1 ATG1 BLM10 BSD2 BTN2 CAN1
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Cell Growth and Metabolism yg ball
Genomic expression study yg ball
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Topics Genes linked to topics (#11 - 20 )
CCT3 CCT8 CIA2 CRG1 CRH1 CRS5 CTR1 CTR3 CUP1-1 CUP1-2
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Topics Genes linked to topics (#21 - 30 )
CUP2 DAK2 DAL4 DAL5 DUR1,2 DUR3 ECM29 ENB1 ERG27 FCY2
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Topics Genes linked to topics (#31 - 40 )
FIT1 FRE1 FRE7 FUN19 GAC1 GDH1 GET3 GND1 GRE2 GYP7
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Topics Genes linked to topics (#41 - 50 )
HMX1 HSP10 HSP30 HSP42 HXK2 IMA1 IMA2 IMA3 IMA4 IME1
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Topics Genes linked to topics (#51 - 60 )
INN1 JID1 KEX2 KGD1 KGD2 LEU1 MAL12 MAL31 MAL32 MET5
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Topics Genes linked to topics (#61 - 70 )
MET8 NRT1 PET18 PRE3 PRE4 PRE9 PUT4 RAD54 RIM4 RIP1
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Topics Genes linked to topics (#71 - 80 )
RPN2 RPT4 RPT5 SDH4 SDS22 SDS23 SFK1 SIT1 SKN1 SKO1
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Topics Genes linked to topics (#81 - 90 )
SLT2 SOD1 SOD2 SSA3 SSU1 TCP1 THI11 THI13 THI2 THI22
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Topics Genes linked to topics (#91 - 100 )
THI5 THI7 THI72 TKL1 TOS8 TPO4 TRR1 UBP3 UBX6 UFD4
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Topics Genes linked to topics (#101 - 106 )
UGA4 UMP1 WSC4 YPS5 YPS6 ZWF1
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