Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome‐wide transcriptional oscillators

Genetic and environmental factors are well‐studied influences on phenotype; however, time is a variable that is rarely considered when studying changes in cellular phenotype. Time‐resolved microarray data revealed genome‐wide transcriptional oscillation in a yeast continuous culture system with ∼ 2 and ∼ 4 h periods. We mapped the global patterns of transcriptional oscillations into a 3D map to represent different cellular phenotypes of redox cycles. This map shows the dynamic nature of gene expression in that transcripts are ordered and coupled to each other through time and concentration space. Although cells differed in oscillation periods, transcripts involved in certain processes were conserved in a deterministic way. When oscillation period lengthened, the peak to trough ratio of transcripts increased and the fraction of cells in the unbudded (G0/G1) phase of the cell division cycle increased. Decreasing the glucose level in the culture medium was one way to increase the redox cycle, possibly from changes in metabolic flux. The period may be responding to lower glucose levels by increasing the fraction of cells in G1 and reducing S‐phase gating so that cells can spend more time in catabolic processes. Our results support that gene transcripts are coordinated with metabolic functions and the cell division cycle. Time‐resolved microarray data revealed genome‐wide transcriptional oscillation in a yeast continuous culture system with ∼ 2 and ∼ 4 h periods. Transcripts are ordered and coupled to each other through time and concentration space. Gene transcripts appear to be coordinated with metabolic functions and the cell division cycle.