Figure 5. Pairing TFs play a minimal role in transcriptional regulation of the HAS1-TDA1 locus.

(A) Mutations in S. cerevisiae HAS1pr-TDA1pr tested for transcriptional effects in S. cerevisiae x S. uvarum hybrids. Colored boxes indicate TF motifs. Wild type and mutated sequences are shown below boxes, with mutated bases in lowercase, red letters. (B) Rgt1 regulates TDA1 expression in cis. RNA-seq expression levels for S. cerevisiae (Sc) and S. uvarum (Su) copies of HAS1 and TDA1 in saturated cultures of strains shown in panel A. FPKM = fragments per kilobase per million read pairs. Bars indicate mean ± s.e.m. of biological triplicates. **p<0.01 (Student’s t-test). (C) Mutations in pairing region cause few transcriptional changes. Volcano plot of fold change vs. p-value in mutant strains compared to wild type, shown in (A). (D) RNA-seq expression levels for HAS1 and TDA1 in saturated cultures of wild type haploid S. cerevisiae and gene deletion strains. Bars indicate mean ± s.e.m. of biological triplicates. *p<0.05 (Student’s t-test).

Figure 5—figure supplement 1. Transcriptional effects of TF deletion in saturated culture and exponential growth.

(A) Volcano plots of differentially expressed genes in TF deletion strains compared to a wild-type control in saturated culture conditions, by RNA-seq. (B) Comparison of log₂ fold change from RNA-seq in saturated culture conditions to gene expression microarray ‘X scores’ (normalized, confidence-weighted log ratios) in exponential growth (Hu et al., 2007), with deleted gene highlighted in red.

Figure 5—figure supplement 2. Comparison of TF binding targets and differentially expressed genes upon TF deletion.

(A) Genes with upstream Rgt1 ChIP-seq peaks in saturated cultures are upregulated upon RGT1 deletion. Scatter plots of log₂ ChIP-seq peak fold enrichment vs. log₂ fold change in RNA expression for downstream genes, excluding the deleted TF gene, in saturated culture. (B) Genes with upstream Leu3 ChIP-seq peaks in exponential growth are downregulated upon LEU3 deletion. Same as panel A but for exponential growth, using microarray ‘X scores’ (normalized, confidence-weighted log ratios) for differential gene expression (Hu et al., 2007).