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

Abstract
Data availability
Article and author information
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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.

Data availability

Raw DNA reads from bulk segregant mapping are available via the NCBI BioProject PRJNA644804.Transcriptome sequencing data is available at GEO under accession GSE155998.Source Data files are available for Figures 4, 5, and 7.

The following data sets were generated

1. Brion C
2. Lutz S
3. Albert FW
(2020) Differential RNA abundance between S. cerevisiae yeast BY4741 strains with YAK1_WT and YAK1_Q578*
NCBI Gene Expression Omnibus, GSE155998.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE155998
1. Brion C
2. Lutz S
3. Albert FW
(2020) Simultaneous mRNA and protein quantification in single cells reveals post-transcriptional effects of genetic variation
NCBI BioProject, PRJNA644804.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA644804

The following previously published data sets were used

1. Albert FW
2. Bloom JS
3. Siegel J
4. Day L
5. Kruglyak L
(2018) Genetics of trans-regulatory variation in gene expression
Source Data 1.

https://doi.org/10.7554/eLife.35471.021
1. Albert FW
2. Bloom JS
3. Siegel J
4. Day L
5. Kruglyak L
(2018) Genetics of trans-regulatory variation in gene expression
Source Data 4.

https://doi.org/10.7554/eLife.35471.024
(2014) Genetics of single-cell protein abundance variation in large yeast populations
Supplementary Data 2.

https://www.nature.com/articles/nature12904?
(2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
Supplementary Table 1.

https://www.nature.com/articles/nature04785?

Article and author information

Author details

Christian Brion

Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States

Competing interests
The authors declare that no competing interests exist.
Sheila M Lutz

Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-6729-4598
Frank Wolfgang Albert

Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States

For correspondence
falbert@umn.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1380-8063

Funding

National Institute of General Medical Sciences (R35-GM124676)

Frank Wolfgang Albert

Alfred P. Sloan Foundation (FG-2018- 10408)

Frank Wolfgang Albert

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.