Multiple epistatic DNA variants in a single gene affect gene expression in trans

Area of Science:

• Genetics
• Molecular Biology
• Systems Biology

Background:

• Trans-acting DNA variants influencing gene expression are key drivers of phenotypic diversity.
• The precise identity and mechanisms of these trans-acting variants are not well understood.
• Previous research suggested simple molecular architectures involving single causal variants.

Purpose of the Study:

• To investigate the complexity of trans-acting variants using the RAS signaling regulator gene IRA2 in Saccharomyces cerevisiae.
• To dissect causal variants to the nucleotide level and understand their interactions.
• To determine if previously observed simple molecular architectures are representative of trans-acting variation.

Main Methods:

• Systematic CRISPR-based genome engineering in yeast.
• Sensitive phenotyping strategies to analyze gene expression and growth.
• Nucleotide-level dissection of causal variants within the IRA2 gene.

Main Results:

• Identified at least seven causal nonsynonymous variants in the IRA2 gene.
• Demonstrated that variant effects are modulated by nonadditive, epistatic interactions.
• Discovered that two variants at the 5'-end only impacted gene expression and growth when combined with a third, otherwise inactive, variant.

Conclusions:

• The molecular basis of trans-acting genetic variation is potentially more complex than previously assumed.
• Epistasis and multiple interacting variants play a significant role in trans-acting effects.
• Simple models of trans-acting variation may not fully capture the genetic architecture of phenotypic diversity.