Gene regulation during stress response transcription in Saccharomyces Cerevisiae

DYNAMIC TRANSCRIPTOME ANALYSIS MEASURES RATES OF MRNA SYNTHESIS AND
DECAY IN YEAST To obtain rates of mRNA synthesis and decay in
yeast, we established dynamic transcriptome analysis (DTA). DTA
combines non-perturbing metabolic RNA labeling with dynamic kinetic
modeling. DTA reveals that most mRNA synthesis rates are around
several transcripts per cell and cell cycle, and most mRNA
half-lives range around a median of 11 min. DTA can monitor the
cellular response to osmotic stress with higher sensitivity and
temporal resolution than standard transcriptomics. In contrast to
monotonically increasing total mRNA levels, DTA reveals three
phases of the stress response. During the initial shock phase, mRNA
synthesis and decay rates decrease globally, resulting in mRNA
storage. During the subsequent induction phase, both rates increase
for a subset of genes, resulting in production and rapid removal of
stress-responsive mRNAs. During the recovery phase, decay rates are
largely restored, whereas synthesis rates remain altered,
apparently enabling growth at high salt concentration.
Stress-induced changes in mRNA synthesis rates are predicted from
gene occupancy with RNA polymerase II. Thus, DTA realistically
monitors the dynamics in mRNA metabolism that underlie gene
regulatory systems.