Saccharomyces cerevisiae strain:FY4 Transcriptome or Gene expression. Saccharomyces cerevisiae strain:FY4

Regulation of cell growth rate is essential for maintaining cellular homeostasis and survival in diverse conditions. Changes in cell growth rate are accompanied by changes in total cellular RNA content, potentially confounding transcriptome measurements in conditions and cell types in which growth rate is not constant. Here, we studied a eukaryotic model of growth rate-related gene expression changes, introducing SPike in-assisted Absolute RNA Quantification (SPARQ), a method for measuring absolute transcript abundances using RNA-seq that does not assume a constant transcriptome size across samples. Variation in cell growth rate resulted in co-directional changes in absolute abundance of virtually every transcript, with significant coordinated responses among functionally related transcripts. We find increases in both RNA degradation and synthesis rates with increased growth rate result in increased absolute transcript abundance. We propose that ribosome abundance links environmental conditions to transcriptome amplification via nutrient-responsive signaling pathways.