Simultaneous quantification of mrna and protein in single cells reveals post-transcriptional effects of genetic variation

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25 Scopus citations


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.

Original languageEnglish (US)
Article numbere60645
Pages (from-to)1-34
Number of pages34
StatePublished - Oct 2020

Bibliographical note

Funding Information:
We thank Scott McIsaac and Leonid Kruglyak for yeast strains, Joshua Bloom for implementing the MULTIPOOL algorithm in R, and Mahlon Collins for the mCherry/GFP protein fusion flow cytometry data. We thank the University of Minnesota Genomics Center, the University of Minnesota?s Center for Mass Spectrometry and Proteomics, and the University of Minnesota?s Flow Cytometry Resource. We thank members of the Albert lab for critical feedback on the manuscript.

Publisher Copyright:
© Brion et al.


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