ArticleProceedings of the National Academy of Sciences of the United States of America2007
Microarray analysis of newly synthesized RNA in cells and animals.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
38 citing papers in PubMed, 65 citations in OpenAlex.
- Multiple strategies to resolve the conflict between replication and transcription in mammalian cells.Nucleic acids research · 2026Article
- Microarrays and the Dawn of Omics Data Analysis.Advances in experimental medicine and biology · 2026Review
- Three-way junction structure-mediated reverse transcription-free exponential amplification reaction for pathogen RNA detection.Analytical and bioanalytical chemistry · 2024Article
- Genome-wide Mapping of 5'-monophosphorylated Ends of Mammalian Nascent RNA Transcripts.Bio-protocol · 2023Article
- Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry.bioRxiv : the preprint server for biology · 2023Article
- Profiling transcription factor activity dynamics using intronic reads in time-series transcriptome data.PLoS computational biology · 2022Article
- Interrogating the transcriptome with metabolically incorporated ribonucleosides.Molecular omics · 2021Review
- A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnover.Briefings in bioinformatics · 2021Article
- Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data.BMC biology · 2021Article
- Nascent RNA analyses: tracking transcription and its regulation.Nature reviews. Genetics · 2019Review
- Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine.Wiley interdisciplinary reviews. RNA · 2019Review
- Saccharomyces cerevisiae Metabolic Labeling with 4-thiouracil and the Quantification of Newly Synthesized mRNA As a Proxy for RNA Polymerase II Activity.Journal of visualized experiments : JoVE · 2018Article
- Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development.Nature communications · 2018Article
- EC-tagging allows cell type-specific RNA analysis.Nucleic acids research · 2017Article
- Capturing in vivo RNA transcriptional dynamics from the malaria parasiteGenome research · 2017Article
- Basonuclin-1 modulates epithelial plasticity and TGF-β1-induced loss of epithelial cell integrity.Oncogene · 2015Article
- Temporally and spatially restricted gene expression profiling.Current genomics · 2014Article
- Applying thiouracil tagging to mouse transcriptome analysis.Nature protocols · 2014Article
- SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample.PloS one · 2014Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 7 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current methods to analyze gene expression measure steady-state levels of mRNA. To specifically analyze mRNA transcription, we have developed a technique that can be applied in vivo in intact cells and animals. Our method makes use of the cellular pyrimidine salvage pathway and is based on affinity-chromatographic isolation of thiolated mRNA. When combined with data on mRNA steady-state levels, this method is able to assess the relative contributions of mRNA synthesis and degradation/stabilization. It overcomes limitations associated with currently available methods such as mechanistic intervention that disrupts cellular physiology, or the inability to apply the techniques in vivo. Our method was first tested in serum response of cultured fibroblast cells and then applied to the study of renal ischemia reperfusion injury, demonstrating its applicability for whole organs in vivo. Combined with data on mRNA steady-state levels, this method provided a detailed analysis of regulatory mechanisms of mRNA expression and the relative contributions of RNA synthesis and turnover within distinct pathways, and identification of genes expressed at low abundance at the transcriptional level.
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What OpenQuestion holds
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.