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

Autoři: Sheila Lutz aff001;  Christian Brion aff001;  Margaret Kliebhan aff001;  Frank W. Albert aff001
Působiště autorů: Department of Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, MN, United States of America aff001
Vyšlo v časopise: DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories. PLoS Genet 15(11): e32767. doi:10.1371/journal.pgen.1008375
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008375


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.

Klíčová slova:

Alleles – Gene expression – Genetic loci – Glucose – Guide RNA – Saccharomyces cerevisiae – Yeast


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