ArticleBioinformatics (Oxford, England)2018
Dissecting newly transcribed and old RNA using GRAND-SLAM.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- Spatial mapping of RNA turnover kinetics in the mouse brain.Nature neuroscience · 2026Article
- Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR.Genome biology · 2026Article
- Ageing alters cysteine oxidation-regulated redox signalling in skeletal muscle: Integrative omics and AI-based structural predictions.Experimental physiology · 2026Article
- Cleavage of the RNA polymerase II general transcription factor TFIIB tunes transcription during stress.Genes & development · 2026Article
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- Nascent transcriptome of embryonic genome activation reveals a regulatory axis linking transcriptional priming to early lineage specification in mouse embryos.Nucleic acids research · 2026Article
- Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain.bioRxiv : the preprint server for biology · 2026Article
- A convenient single-cell assay for the newly synthesized transcriptome reveals FLI1 regulon downregulation during T cell activation.Cell reports methods · 2026Article
- Exonuclease ISG20 inhibits human cytomegalovirus replication by inducing an innate immune defense signature.PLoS pathogens · 2026Article
- Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm.Nature cell biology · 2026Article
- Viral entry shapes HCMV latency establishment.Nature communications · 2025Article
- SARS-CoV-2 nonstructural protein 1 suppresses host transcription by reducing RNA polymerase II levels.iScience · 2025Article
- Fundamental errors in RNA velocity arising from the omission of cell growth.bioRxiv : the preprint server for biology · 2025Article
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- mNature structural & molecular biology · 2025Article
- mRNA turnover dynamics are affected by cell differentiation and loss of the cytosine methyltransferase Nsun2.Nucleic acids research · 2025Article
- Single-cell RNA-seq using UltraMarathonRT expands the known transcriptome.bioRxiv : the preprint server for biology · 2025Article
- The CGG triplet repeat binding protein 1 counteracts R-loop induced transcription-replication stress.EMBO reports · 2025Article
- RNA-mediated condensation of TFE3 oncofusions facilitates transcriptional hub formation to promote translocation renal cell carcinoma.Nature communications · 2025Article
- scIVNL-seq resolves in vivo single-cell RNA dynamics of immune cells during Salmonella infection.Nature communications · 2025Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: Global quantification of total RNA is used to investigate steady state levels of gene expression. However, being able to differentiate pre-existing RNA (that has been synthesized prior to a defined point in time) and newly transcribed RNA can provide invaluable information e.g. to estimate RNA half-lives or identify fast and complex regulatory processes. Recently, new techniques based on metabolic labeling and RNA-seq have emerged that allow to quantify new and old RNA: Nucleoside analogs are incorporated into newly transcribed RNA and are made detectable as point mutations in mapped reads. However, relatively infrequent incorporation events and significant sequencing error rates make the differentiation between old and new RNA a highly challenging task. We developed a statistical approach termed GRAND-SLAM that, for the first time, allows to estimate the proportion of old and new RNA in such an experiment. Uncertainty in the estimates is quantified in a Bayesian framework. Simulation experiments show our approach to be unbiased and highly accurate. Furthermore, we analyze how uncertainty in the proportion translates into uncertainty in estimating RNA half-lives and give guidelines for planning experiments. Finally, we demonstrate that our estimates of RNA half-lives compare favorably to other experimental approaches and that biological processes affecting RNA half-lives can be investigated with greater power than offered by any other method. GRAND-SLAM is freely available for non-commercial use at http://software.erhard-lab.de; R scripts to generate all figures are available at zenodo (doi: 10.5281/zenodo.1162340).
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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.