DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories.

Publisher: Public Library of Science Country of Publication: United States NLM ID: 101239074 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7404 (Electronic) Linking ISSN: 15537390 NLM ISO Abbreviation: PLoS Genet Subsets: MEDLINE

Original Publication: San Francisco, CA : Public Library of Science, c2005-

Evolution, Molecular*; DNA-Binding Proteins/*genetics ; Regulatory Sequences, Nucleic Acid/*genetics ; Saccharomyces cerevisiae Proteins/*genetics ; Stearoyl-CoA Desaturase/*genetics ; Transcription Factors/*genetics; CRISPR-Cas Systems/genetics ; Fatty Acids/genetics ; Fatty Acids/metabolism ; Gene Expression Regulation, Fungal/genetics ; Green Fluorescent Proteins/genetics ; Lipid Metabolism/genetics ; Monosaccharide Transport Proteins/genetics ; Mutation, Missense/genetics ; Phenotype ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism

DNA variants that alter gene expression contribute to variation in many phenotypic traits. In particular, trans-acting variants, which are often located on different chromosomes from the genes they affect, are an important source of heritable gene expression variation. However, our knowledge about the identity and mechanism of causal trans-acting variants remains limited. Here, we developed a fine-mapping strategy called CRISPR-Swap and dissected three expression quantitative trait locus (eQTL) hotspots known to alter the expression of numerous genes in trans in the yeast Saccharomyces cerevisiae. Causal variants were identified by engineering recombinant alleles and quantifying the effects of these alleles on the expression of a green fluorescent protein-tagged gene affected by the given locus in trans. We validated the effect of each variant on the expression of multiple genes by RNA-sequencing. The three variants differed in their molecular mechanism, the type of genes they reside in, and their distribution in natural populations. While a missense leucine-to-serine variant at position 63 in the transcription factor Oaf1 (L63S) was almost exclusively present in the reference laboratory strain, the two other variants were frequent among S. cerevisiae isolates. A causal missense variant in the glucose receptor Rgt2 (V539I) occurred at a poorly conserved amino acid residue and its effect was strongly dependent on the concentration of glucose in the culture medium. A noncoding variant in the conserved fatty acid regulated (FAR) element of the OLE1 promoter influenced the expression of the fatty acid desaturase Ole1 in cis and, by modulating the level of this essential enzyme, other genes in trans. The OAF1 and OLE1 variants showed a non-additive genetic interaction, and affected cellular lipid metabolism. These results demonstrate that the molecular basis of trans-regulatory variation is diverse, highlighting the challenges in predicting which natural genetic variants affect gene expression.
Competing Interests: The authors have declared that no competing interests exist.

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R35 GM124676 United States GM NIGMS NIH HHS

0 (DNA-Binding Proteins)
0 (Fatty Acids)
0 (Monosaccharide Transport Proteins)
0 (OAF1 protein, S cerevisiae)
0 (RGT2 protein, S cerevisiae)
0 (Saccharomyces cerevisiae Proteins)
0 (Transcription Factors)
147336-22-9 (Green Fluorescent Proteins)
EC 1.14.19.1 (Stearoyl-CoA Desaturase)
EC 1.14.99.- (delta-9 fatty acid desaturase)

Date Created: 20191119 Date Completed: 20200218 Latest Revision: 20200309

20231215

PMC6886874

10.1371/journal.pgen.1008375

31738765