Fig. 4: Effects of mutations in RAP1 and GCR1 binding sites have greater environmental variance than TATA box mutations for gene expression but not fitness.
a, Schematic of the S. cerevisiae TDH3 promoter showing locations of binding sites for the transcription factors RAP1 (yellow) and GCR1 (blue and red) as well as the location of the TATA box (grey) and transcription start site (arrow) for TDH3. b, Variance in effects of mutations on gene expression in the four environments tested (normalized to the reference allele in each environment) for PTDH3 alleles with a mutation only in either a RAP1 or GCR1 binding site (TFBS) or with a mutation(s) only in the TATA box (TATA). In each box plot, the centre line indicates the median effect size for the group, the bounds of the box indicate the interquartile range, and upper and lower whiskers extend from the bounds of the box to the largest and smallest values within 1.5× the interquartile range of the data. c, The same information is shown as in b but for variance in the effects of the promoter alleles on fitness rather than expression in the four environments. d, Mean relative effects of each of the 14 PTDH3 mutant alleles shown in b and c on gene expression and fitness in each of the four environments. Error bars indicate the 95% confidence interval for each genotype in each environment, calculated from four to eight replicates for gene expression and four replicates for fitness. In all panels, the colour of each point indicates whether the strain carried any mutations in the RAP1 binding site (yellow), GCR1 binding site (blue or red) or TATA box (grey).
