ArticleNucleic acids research2009
Conserved principles of mammalian transcriptional regulation revealed by RNA half-life.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 152 papers, 1 of them a synthesis that pooled it.
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Who cites it
152 citing papers in PubMed, 1 synthesis or guideline pooled it, 236 citations in OpenAlex.
- The genetic and biochemical determinants of mRNA degradation rates in mammals.Genome biology · 2022Pooled it
- Spatial mapping of RNA turnover kinetics in the mouse brain.Nature neuroscience · 2026Article
- Half-Life as a Therapeutic Design Axis: Targeting Short-Lived lncRNAs With Antisense Oligonucleotides.IUBMB life · 2026Review
- The Kinetic Intron Hypothesis.bioRxiv : the preprint server for biology · 2026Article
- Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain.bioRxiv : the preprint server for biology · 2026Article
- Microarrays and the Dawn of Omics Data Analysis.Advances in experimental medicine and biology · 2026Review
- mRNA turnover dynamics are affected by cell differentiation and loss of the cytosine methyltransferase Nsun2.Nucleic acids research · 2025Article
- Codon Composition in Human Oocytes Reveals Age-Associated Defects in mRNA Decay.International journal of molecular sciences · 2025Article
- The advantage of periodic over constant signalling in microRNA-mediated regulation.Nucleic acids research · 2025Article
- Programmable RNA Nanostructures Enable Nanopore Detection of Cotranscriptionally Introduced RNA Modifications.Nano letters · 2025Article
- The Hill-Type Equation Reveals the Regulatory Principle of Target Protein Expression Led by p53 Pulsing.FASEB bioAdvances · 2025Article
- Punishment-Induced Suppression of Methamphetamine Self-Administration Is Accompanied by the Activation of the CPEB4/GLD2 Polyadenylation Complex of the Translational Machinery.International journal of molecular sciences · 2025Article
- A theoretical systems chronopharmacology approach for COVID-19: Modeling circadian regulation of lung infection and potential precision therapies.CPT: pharmacometrics & systems pharmacology · 2025Article
- Technologies for Targeted RNA Degradation and Induced RNA Decay.Chemical reviews · 2024Review
- Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting.Molecular systems biology · 2024Article
- A spectrum of nonsense-mediated mRNA decay efficiency along the degree of mutational constraint.Communications biology · 2024Article
- Impacts of the feedback loop between sense-antisense RNAs in regulating circadian rhythms.NPJ systems biology and applications · 2024Article
- Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.Molecular cell · 2024Article
- Coordination of rhythmic RNA synthesis and degradation orchestrates 24- and 12-h RNA expression patterns in mouse fibroblasts.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Subcellular RNA distribution and its change during human embryonic stem cell differentiation.Stem cell reports · 2024Article
92 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA levels in a cell are regulated by the relative rates of RNA synthesis and decay. We recently developed a new approach for measuring both RNA synthesis and decay in a single experimental setting by biosynthetic labeling of newly transcribed RNA. Here, we show that this provides measurements of RNA half-lives from microarray data with a so far unreached accuracy. Based on such measurements of RNA half-lives for human B-cells and mouse fibroblasts, we identified conserved regulatory principles for a large number of biological processes. We show that different regulatory patterns between functionally similar proteins are characterized by differences in the half-life of the corresponding transcripts and can be identified by measuring RNA half-life. We identify more than 100 protein families which show such differential regulatory patterns in both species. Additionally, we provide strong evidence that the activity of protein complexes consisting of subunits with overall long transcript half-lives can be regulated by transcriptional regulation of individual key subunits with short-lived transcripts. Based on this observation, we predict more than 100 key regulatory subunits for human complexes of which 28% could be confirmed in mice (P < 10(-9)). Therefore, this atlas of transcript half-lives provides new fundamental insights into many cellular processes.
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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.