Abstract
Trans-acting DNA variants may specifically affect mRNA or protein levels of genes located throughout the genome. However, prior work compared trans-acting loci mapped in separate studies, many of which had limited statistical power. Here, we developed a CRISPR-based system for simultaneous quantification of mRNA and protein of a given gene via dual fluorescent reporters in single, live cells of the yeast Saccharomyces cerevisiae. In large populations of recombinant cells from a cross between two genetically divergent strains, we mapped 86 trans-acting loci affecting the expression of ten genes. Less than 20% of these loci had concordant effects on mRNA and protein of the same gene. Most loci influenced protein but not mRNA of a given gene. One locus harbored a premature stop variant in the YAK1 kinase gene that had specific effects on protein or mRNA of dozens of genes. These results demonstrate complex, post-transcriptional genetic effects on gene expression.
Highlights
Phenotypic variation in genetically complex traits is shaped by DNA variants throughout the genome
Protein abundance is measured via a fluorescent green fluorescent protein (GFP) tag fused to the C-terminus of the given protein of interest (Huh et al, 2003)
After transcription of the mRNA along with this tag, the guide RNA (gRNA) is released from the mRNA by two flanking self-cleaving ribozymes (Hammerhead, Hh; and Hepatitis Delta Virus, HDV) (Gao and Zhao, 2014)
Summary
Phenotypic variation in genetically complex traits is shaped by DNA variants throughout the genome. Recreate the same conditions, subtle differences (for example, in the precise stage of cell growth, medium composition, temperature, or handling of the isolated mRNA or proteins) could influence measures of gene expression (Gallego Romero et al, 2014; Gibson et al, 2007; Hayeshi et al, 2008), potentially inflating the discrepancy between eQTLs and pQTLs. To date, no study of regulatory variation has measured mRNA and protein with high statistical power and in the same samples. The role of genetic variation on post-transcriptional processes remains unclear, especially for trans-acting variation We addressed this challenge by developing a system for quantifying mRNA and protein from the same gene simultaneously, in the same, live, single yeast cells using two fluorescent reporters. These results demonstrate considerable differences in the genetic basis of variation in mRNA vs protein abundance
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