Control of Transcription by Cell Size
Figure 1
Identification of ploidy-regulated genes in yeast (Σ1278b).
(A) RNA-seq analysis of the Σ1278b haploid and tetraploid transcriptomes. Two pairs of haploid and tetraploid cultures, A and B, were processed for transcriptional profiling (using Illumina Genome Analyzer 2). Reads were mapped to the annotated Σ1278b genome. We calculated ORF expression based on the number of reads mapping inside the ORF. SC, synthetic complete medium. (B) RNA-seq read counts. More than 90% of the approximately 9 million reads in each sample were mapped to the genome. More than 60% of the mapped reads fell within annotated ORFs. The majority of remaining reads mapped to the rDNA locus and Ty elements. The processed data (with calculations for fold changes and p-values) are in Dataset S1. (C) Ploidy alters expression of only a small number of genes. Read counts for all transcripts at the two ploidies are plotted, and several differentially regulated genes are specified. The comparable expression of most transcripts between the two ploidies shows that the tetraploid cells were euploid [42]. (D) Identification of genes differentially expressed in the tetraploid. Within each pair of haploid (1n)–tetraploid (4n) RNA-seq datasets, differentially expressed candidate genes were ranked by fold change in expression. Comparison of top-ranking candidates between both pairs produced overlapping genes that were called differentially expressed (see details in Materials and Methods). Cutoffs for top-ranking candidates were selected to obtain a sufficient set of overlapping genes for GO analysis while ensuring that the overlap remained highly statistically significant by hypergeomtric test.