ArticleGenome research2012
Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 178 papers, 2 of them syntheses that pooled it.
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Who cites it
178 citing papers in PubMed, 2 syntheses or guidelines pooled it, 313 citations in OpenAlex.
- The genetic and biochemical determinants of mRNA degradation rates in mammals.Genome biology · 2022Pooled it
- MC EMiNEM maps the interaction landscape of the Mediator.PLoS computational biology · 2012Pooled it
- Endoplasmic reticulum engagement of transcripts triggers VSG mRNA balancing in trypanosomes.PLoS pathogens · 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
- Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation.Science (New York, N.Y.) · 2026Article
- Fundamental errors in RNA velocity arising from the omission of cell growth.bioRxiv : the preprint server for biology · 2025Article
- The CCR4-NOT complex: a multifaceted sensor of molecular signals instructing eukaryotic mRNA translation and stability.Nucleic acids research · 2025Review
- RNADecayCafe, a uniformly processed atlas of RNA half-life estimates across multiple human cell lines.bioRxiv : the preprint server for biology · 2025Article
- Global changes in synthesis rates and mRNA stabilities during adaptive responses to cell wall stress in yeast.Scientific reports · 2025Article
- RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks.Bioinformatics (Oxford, England) · 2025Article
- Gene-specific transcript buffering revealed by perturbation of coactivator complexes.Science advances · 2025Article
- Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex.Molecular cell · 2025Article
- Halfpipe: a tool for analyzing metabolic labeling RNA-seq data to quantify RNA half-lives.NAR genomics and bioinformatics · 2025Article
- RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease.Journal of molecular biology · 2025Review
- Assessment of mRNA Decay and Calculation of Codon Occurrence to mRNA Stability Correlation Coefficients after 5-EU Metabolic Labeling.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Modeling of mRNA deadenylation rates reveal a complex relationship between mRNA deadenylation and decay.The EMBO journal · 2024Article
- Dyna-vivo-seq unveils cellular RNA dynamics during acute kidney injury via in vivo metabolic RNA labeling-based scRNA-seq.Nature communications · 2024Article
- Non-redundant roles for the human mRNA decapping cofactor paralogs DCP1a and DCP1b.Life science alliance · 2024Article
- RNA polymerase II transcription initiation in holo-TFIID-depleted mouse embryonic stem cells.Cell reports · 2024Article
- Article
118 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To monitor eukaryotic mRNA metabolism, we developed comparative dynamic transcriptome analysis (cDTA). cDTA provides absolute rates of mRNA synthesis and decay in Saccharomyces cerevisiae (Sc) cells with the use of Schizosaccharomyces pombe (Sp) as an internal standard. cDTA uses nonperturbing metabolic labeling that supersedes conventional methods for mRNA turnover analysis. cDTA reveals that Sc and Sp transcripts that encode orthologous proteins have similar synthesis rates, whereas decay rates are fivefold lower in Sp, resulting in similar mRNA concentrations despite the larger Sp cell volume. cDTA of Sc mutants reveals that a eukaryote can buffer mRNA levels. Impairing transcription with a point mutation in RNA polymerase (Pol) II causes decreased mRNA synthesis rates as expected, but also decreased decay rates. Impairing mRNA degradation by deleting deadenylase subunits of the Ccr4-Not complex causes decreased decay rates as expected, but also decreased synthesis rates. Extended kinetic modeling reveals mutual feedback between mRNA synthesis and degradation that may be achieved by a factor that inhibits synthesis and enhances degradation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.