394V Poster Online - Virtual Posters
Tuesday June 07, 11:00 AM - 3:00 PM

Authors:
Mahlon Collins ¹; Gemechu Mekonnen ^1,2; Randi Avery ¹; Frank Albert ¹

Affiliations:
1) University of Minnesota, Minneapolis, MN; 2) Johns Hopkins University, Baltimore, MD

Keywords:
Complex traits

DNA sequence differences that influence gene expression are a key mechanistic link between individual genetic differences and variation in cellular and organismal traits. Many genetic effects on gene expression specifically affect protein levels and understanding the molecular basis of these effects remains an outstanding challenge. Protein-specific effects on gene expression may arise through variants that alter the activity of the cell's primary pathway for targeted protein degradation, the ubiquitin-proteasome system (UPS).

To explore this possibility, we developed a statistically powerful method for mapping quantitative trait loci (QTLs) for UPS activity using the yeast Saccharomyces cerevisiae. We applied this approach to 22 UPS substrates that engage multiple UPS pathways and diverse molecular mechanisms of substrate recognition and processing, including the full set of degradation signals for the UPS N-end Rule. We identified 167 UPS activity QTLs, most of which were specific to individual UPS pathways or substrates, demonstrating a highly complex genetic basis of variation in UPS activity.

Resolving four QTLs to their causal nucleotides using CRISPR-Cas9 genome engineering revealed the molecular basis of genetic effects on UPS activity. Specifically, pathway-specific influences on UPS activity resulted from regulatory and missense variants in ubiquitin system genes whose products process (NTA1), recognize (UBR1, DOA10), and ubiquitinate (UBC6) substrate proteins. Evolutionary and population genetic analysis showed that causal variants that decrease UPS activity tend to be derived and at low (< 5%) population frequency, suggesting that they reduce organismal fitness.

To understand how causal variants for UPS activity influence gene expression, we tested the effect of a derived, cis-acting causal variant in the UBR1 promoter on genome-wide protein and RNA levels. The causal UBR1 variant altered the abundance of 36 proteins without affecting levels of the corresponding mRNA transcripts, implicating genetic influences on the UPS as a prominent source of protein-specific variant effects on gene expression.

Our results define the complex genetic architecture of UPS activity, demonstrate how variation in ubiquitin system genes influences UPS protein degradation, and establish a framework for understanding how genetic effects on the UPS contribute to variation in cellular and organismal traits.