epistatic variation

Gerke J, Lorenz K & Cohen B 2009 Genetic interactions between transcription factors cause natural variation in yeast. Science 323:498-501.

  • natural variation in the efficiency of sporulation, the program in yeast that initiates the sexual phase of the life cycle, between oak tree and vineyard strains is due to allelic variation between four nucleotide changes in three transcription factors
  • these results illustrate how genetic interactions between transcription factors are a major source of phenotypic diversity within species
  • sporulation efficiency is a highly heritable complex trait that varies among natural populations of S. cerevisiae
  • one major QTL (marker L7.9) covers a 100-kb confidence interval on chromosome 7
  • RME1, a transcription factor that suppresses sporulation in specific cell types (30), resides in this peak
  • to test whether allelic variation in RME1 produces variation in sporulation efficiency, we deleted each parental allele of RME1 in a hybrid background
  • through reciprocal hemizygosity analysis
  • the allelic contributions of RME1 from each parent were different
  • confirming that variation in RME1 affects sporulation efficiency (Fig. 2A)
  • the coding region of RME1 contains no amino acid substitutions between the oak and vineyard parents
  • a single nucleotide insertion/deletion 308 base pairs (bp) upstream of the initiation codon (fig. S2A) accounts for the effect of the RME1 locus on sporulation efficiency (Fig. 2B)
  • the vineyard strain allele [RME1(del-308A)], which has a deletion of a single adenine relative to the oak strain, also reduces sporulation efficiency in laboratory strains
  • this nucleotide change presumably increases the expression of RME1, which represses sporulation, as the RME1(del-308A) allele is expressed at higher levels than the oak allele
  • a second major QTL (L10.14) located in a 50-kb confidence interval on chromosome 10 also contained a strong candidate gene
  • IME1 is a transcriptional activator and master regulator that initiates yeast sporulation
  • reciprocal hemizygosity analysis confirmed that IME1 quantitatively controls sporulation efficiency (Fig. 2A)
  • we identified 8 polymorphisms in the coding region, both synonymous and nonsynonymous, and 39 polymorphisms in the noncoding regions of IME1 between the oak and vineyard strain
  • allele replacements demonstrated that two of these polymorphisms account for the full effect of the IME1 locus on sporulation efficiency (Fig. 2C)
  • we identified a causative nonsynonymous substitution in the vineyard strain, IME1 (L325M)
  • we also identified a noncoding IME1(A-548G) polymorphism in an 11-bp sequence that is conserved among three yeast species closely related to S. cerevisiae
  • the third major QTL affecting sporulation occurs in a 100-kb region of chromosome 13 (L13.6, fig. S1D)
  • reciprocal hemizygosity analysis of genes in this region identified RSF1 as a candidate gene affecting sporulation efficiency (Fig. 2A)
  • allele replacements (fig. S3) confirmed that a single derived polymorphism in the vineyard strain—coding for a substitution of a conserved glutamic acid with a glycine RSF1(D181G)—is responsible for the allelic effect of RSF1
  • RSF1 encodes a transcriptional activator of mitochondrial genes critical for cellular respiration
  • analysis of the allele replacement strains revealed extensive interactions among the four nucleotides
  • as all possible two-, three-, and four-way interactions are statistically significant in an analysis of variance (table S3)
  • the interactions indicate that the vineyard alleles work synergistically to reduce sporulation efficiency
  • the strongest interactions observed occurred between RME1(del-308A) and the two polymorphisms at IME1 (Fig. 4B)
  • the RSF1 vineyard allele, which causes less than a 3% change on its own, also was found to interact synergistically with the other vineyard alleles (Fig. 4C) and was responsible for 11%, 13%, and 16% drops in sporulation efficiency through its two-way interactions
  • these results illustrate mechanisms by which combinations of alleles can produce a phenotypic change larger than expected from individual effects
  • genetic interactions (epistasis) are often seen between genomic regions affecting quantitative traits
  • this study demonstrates how a small number of nucleotides can create complex, quantitative variation in phenotype
  • highlighting the importance of single nucleotides on epistasis
  • if prevalent, genetic interactions between nucleotides will be a major hurdle in the endeavor to connect genetic and phenotypic variation in humans
  • our identification of epistasis between RME1 and IME1 supports the idea that a search for epistasis should incorporate previous knowledge of functional relationships between genes and proteins