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Related Experiment Videos

Gene-environment interaction in yeast gene expression.

Erin N Smith1, Leonid Kruglyak

  • 1Lewis-Sigler Institute for Integrative Genomics and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America.

Plos Biology
|April 18, 2008
PubMed
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Gene-environment interactions significantly impact gene expression, with local genetic variants showing stable effects and distant variants being condition-dependent. A specific gene, IRA2, was identified as a key regulator of growth-related transcripts under varying conditions.

Area of Science:

  • Genetics
  • Molecular Biology
  • Systems Biology

Background:

  • Gene-environment interactions are crucial for phenotypic variation but remain poorly understood.
  • Analyzing transcript abundance as quantitative traits offers a powerful approach to study these interactions broadly.
  • Yeast provides a tractable model system for dissecting the genetic basis of gene expression variation.

Purpose of the Study:

  • To characterize the genetic architecture of gene-environment interactions in yeast gene expression.
  • To identify specific genetic loci and regulatory variants that mediate condition-dependent gene expression.
  • To understand how environmental conditions modulate the effects of different classes of regulatory variants.

Main Methods:

  • Comparing gene expression profiles of two distinct yeast strains (BY and RM) under two different carbon source conditions (glucose and ethanol).

Related Experiment Videos

  • Expression profiling of over 100 segregants from a BY x RM cross in both growth conditions.
  • Quantitative trait loci (QTL) mapping to identify genetic linkages influencing gene expression variation.
  • Detailed characterization of a specific locus (IRA2) and its role in regulating growth-related transcripts.

    • Main Results:

    • Thousands of transcripts exhibited significant strain, condition, and strain-condition interaction effects.
    • 1,555 linkages for 1,382 transcripts showed significant gene-environment interaction.
    • Local genetic linkages (cis-acting) were generally more stable across conditions than distant linkages (trans-acting).
    • The IRA2 gene locus was identified as a major regulator of growth-related transcripts, with the RM allele showing stronger inhibition of Ras/PKA signaling.

    Conclusions:

    • Environmental conditions significantly shape the genetic basis of gene expression variation.
    • Local and distant regulatory variants exhibit distinct patterns of condition-dependence.
    • The IRA2 gene and its alleles provide a molecular example of how gene-environment interactions influence complex traits.
    • These findings offer insights into designing future studies on the genetic basis of complex traits and adaptation.