Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in XXXX .

@entity375 @entity11510
To obtain rates of mRNA synthesis and decay in @entity375 , we established dynamic transcriptome analysis ( @entity11510 ). @entity11510 combines non-perturbing metabolic RNA labeling with dynamic kinetic modeling. @entity11510 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. @entity11510 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, @entity11510 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. @entity11510 -derived mRNA synthesis rates identified 16 stress-specific pairs/triples of cooperative transcription factors, of which seven were known. Thus, @entity11510 realistically monitors the dynamics in mRNA metabolism that underlie gene regulatory systems.
