Figure 1.

Overview of experimental design. (A) We replaced the wild-type allele of the RPO21 (also known as RPB1) gene with the temperature-sensitive rpb1-1 allele in both the BY4716 (BY) and the RM11-1a (RM) strains of S. cerevisiae (Nonet et al. 1987). We mated these two haploid strains to produce a diploid hybrid and grew the diploid to mid-log phase at the permissive temperature of 24°C. We rapidly shifted the temperature of the culture to 37°C, halting transcription. Immediately following the temperature shift, and at 6, 12, 18, 24, and 42 min after the shift, we isolated mRNA and performed RNA-seq. (B) By quantifying the relative levels of the BY and RM alleles for each gene, we estimated p_BY, the proportion of transcripts derived from BY, at each time point. Under the null hypothesis (H₀; dashed line) of no allele-specific differences in mRNA decay rates, p_BY remains constant. Under the alternative hypothesis (H_A; solid line) of allelic differences in mRNA decay, we expect p_BY to change as a function of time. For the gene represented by the solid line in the example pictured, p_BY decreases significantly over time, indicating that the BY allele is decaying more quickly than the RM allele of this gene.