title: Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast.
abstract: 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. DTA-derived mRNA synthesis rates identified 16 stress-specific pairs/triples of cooperative transcription factors, of which seven were known. Thus, DTA realistically monitors the dynamics in mRNA metabolism that underlie gene regulatory systems.
authors.affiliation: Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, Munich, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Miller
authors.forename: Björn
authors.initials: B
authors.lastname: Schwalb
authors.forename: Kerstin
authors.initials: K
authors.lastname: Maier
authors.forename: Daniel
authors.initials: D
authors.lastname: Schulz
authors.forename: Sebastian
authors.initials: S
authors.lastname: Dümcke
authors.forename: Benedikt
authors.initials: B
authors.lastname: Zacher
authors.forename: Andreas
authors.initials: A
authors.lastname: Mayer
authors.forename: Jasmin
authors.initials: J
authors.lastname: Sydow
authors.forename: Lisa
authors.initials: L
authors.lastname: Marcinowski
authors.forename: Lars
authors.initials: L
authors.lastname: Dölken
authors.forename: Dietmar E
authors.initials: DE
authors.lastname: Martin
authors.forename: Achim
authors.initials: A
authors.lastname: Tresch
authors.forename: Patrick
authors.initials: P
authors.lastname: Cramer
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D006207:Half-Life; D016015:Logistic Models; D020411:Oligonucleotide Array Sequence Analysis; D020871:RNA Stability; D012331:RNA, Fungal / Q000096:biosynthesis / Q000235:genetics; D012333:RNA, Messenger / Q000096:biosynthesis* / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D013312:Stress, Physiological; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D012331:RNA, Fungal; D012333:RNA, Messenger; D014157:Transcription Factors