Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

• Published in: Molecular systems biology 2011-01, Vol.7 (1), p.458-n/a
• Main Authors: Miller, Christian, Schwalb, Björn, Maier, Kerstin, Schulz, Daniel, Dümcke, Sebastian, Zacher, Benedikt, Mayer, Andreas, Sydow, Jasmin, Marcinowski, Lisa, Dölken, Lars, Martin, Dietmar E, Tresch, Achim, Cramer, Patrick
• Format: Article
• Language: English
• Subjects: Baking yeast; Biology; Cell culture; Cell cycle; Cellular stress response; Chemical synthesis; Computer applications; Data acquisition; Decay; Decay rate; DNA microarrays; DNA-directed RNA polymerase; Dynamics; EMBO09; EMBO36; Environmental changes; Environmental conditions; Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation, Fungal; gene regulation; Genome, Fungal; Genomes; Growth conditions; Half-Life; Hybridization; Labelling; Logistic Models; Metabolism; Molecular biology; Molecular chains; Monitors; mRNA stability; mRNA transcription; mRNA turnover; Mutation; Nucleoside analogs; Oligonucleotide Array Sequence Analysis; Organic chemistry; Osmotic stress; Purification; Quantitative analysis; Recovery; Regulation; Ribonucleic acid; RNA; RNA polymerase; RNA polymerase II; RNA Stability; RNA, Fungal - biosynthesis; RNA, Fungal - genetics; RNA, Messenger - biosynthesis; RNA, Messenger - genetics; Saccharomyces cerevisiae; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; salt stress response; Sensitivity; Stress; Stress concentration; Stress, Physiological; Temporal resolution; Transcription factors; Transcription Factors - metabolism; Transcription, Genetic; Yeast
• ISSN: 1744-4292; 1744-4292
• DOI: 10.1038/msb.2010.112

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. Synopsis Nascent transcriptome analysis reveals dynamics of mRNA synthesis and decay in yeast. The first step in the expression of the genome is the synthesis of messenger‐RNA (mRNA). In all cells, the regulation of mRNA levels in response to changing environmental conditions is a fundamental process. Classical methods to study such changes in mRNA levels, however, fail to unravel whether such changes are due to changes in mRNA synthesis (transcription) or changes in mRNA decay, which both contribute to setting mRNA levels. Therefore, the regulation of mRNA stability and turnover is poorly understood, and new methods for a quantitative analysis of mRNA synthesis and decay are urgenlty sought. In this study, we describe a novel method termed dynamic transcriptome analysis (DTA), which can be used to determine synthesis and decay rates of mRNAs on a genome‐wide level in yeast and other eukaryotic cells. We applied DTA to the model organism Saccharomyces cerevisiae and analyzed the dynamics of the transcriptome under standard growth conditions as well as under osmotic stress conditions. DTA relies on a combination of biochemistr