ArticleMolecular systems biology2011
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast.
Article in Molecular systems biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 236 papers, 1 of them a synthesis that pooled it.
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Who cites it
236 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The genetic and biochemical determinants of mRNA degradation rates in mammals.Genome biology · 2022Pooled it
- Twenty-Five Years of the Environmental Stress Response and the Enduring Power of Yeast in Stress Biology.Yeast (Chichester, England) · 2026Review
- Chimeras of GROWTH-REGULATING FACTOR and GRF-INTERACTING FACTOR enhance leaf-based regeneration and transformation efficiency in tomato.Journal of experimental botany · 2026Article
- Transcription initiation drives dosage compensation establishment and maintenance in maleScience advances · 2026Article
- Nucleotide resolution 4-thiouridine sequencing by SNU-Seq and sf4sU-Seq reveals the transcriptional responsiveness of an epigenetically primed human genome.Nucleic acids research · 2026Article
- Glc7/PP1 triggers Paf1 complex dissociation from RNA polymerase II to enable transcription termination.Genes & development · 2026Article
- Nonsense-mediated mRNA decay factors target short poly(A)-tailed mRNAs lacking a premature termination codon.Nature communications · 2026Article
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- Programmed Double-stranded RNA Formation Enables Meiotic Stage Transitions.bioRxiv : the preprint server for biology · 2026Article
- MYC drives left-handed Z-DNA formation to shape gene expression.Nature communications · 2025Article
- The patterns of alternative TSS usage explain the highly heterogeneous landscape of 5'UTR lengths in eukaryotes.NAR genomics and bioinformatics · 2025Article
- Glc7/PP1 triggers Paf1 complex dissociation from RNA polymerase II to enable transcription termination.bioRxiv : the preprint server for biology · 2025Article
- Regulatory Mechanisms of miRNA Turnover: Insights into ZSWIM8-Mediated Target-Directed MicroRNA Degradation.Biomedicines · 2025Review
- Timing is everything: transcription bursting in development.Genes & development · 2025Review
- Global changes in synthesis rates and mRNA stabilities during adaptive responses to cell wall stress in yeast.Scientific reports · 2025Article
- Decay drives RNA abundance regulation using three distinct regulatory mechanisms.bioRxiv : the preprint server for biology · 2025Article
- Transient power-law behaviour following induction distinguishes between competing models of stochastic gene expression.Nature communications · 2025Article
- Transcriptional heterogeneity shapes stress-adaptive responses in yeast.Nature communications · 2025Article
- Article
- Halfpipe: a tool for analyzing metabolic labeling RNA-seq data to quantify RNA half-lives.NAR genomics and bioinformatics · 2025Article
176 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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