ArticleGenome research2020
Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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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
24 citing papers in PubMed.
- Coupling mechanisms coordinating mRNA translation with stages of the mRNA lifecycle.RNA biology · 2025Review
- Article
- Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos.Nucleic acids research · 2025Article
- RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks.Bioinformatics (Oxford, England) · 2025Article
- SSRP1/SLC3A2 Axis in Arginine Transport: A New Target for Overcoming Immune Evasion and Tumor Progression in Peripheral T-Cell Lymphoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Study of the RNA splicing kinetics via in vivo 5-EU labeling.RNA (New York, N.Y.) · 2024Article
- Nanodynamo quantifies subcellular RNA dynamics revealing extensive coupling between steps of the RNA life cycle.Nature communications · 2024Article
- Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain.Nucleic acids research · 2024Article
- Deciphering a global source of non-genetic heterogeneity in cancer cells.Nucleic acids research · 2023Article
- bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling.RNA (New York, N.Y.) · 2023Article
- Dynamically regulated transcription factors are encoded by highly unstable mRNAs in theRNA (New York, N.Y.) · 2023Article
- Combined modelling of mRNA decay dynamics and single-molecule imaging in the Drosophila embryo uncovers a role for P-bodies in 5' to 3' degradation.PLoS biology · 2023Article
- News from around the RNA world: new avenues in RNA biology, biotechnology and therapeutics from the 2022 SIBBM meeting.Biology open · 2022Article
- False-positive IRESes fromProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver.PLoS genetics · 2022Article
- Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment.BMC bioinformatics · 2022Article
- Genetic variants associated mRNA stability in lung.BMC genomics · 2022Article
- Analysis of mRNA Dynamics Using RNA Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnover.Briefings in bioinformatics · 2021Article
- Dynamics of transcriptional and post-transcriptional regulation.Briefings in bioinformatics · 2021Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The quantification of the kinetic rates of RNA synthesis, processing, and degradation are largely based on the integrative analysis of total and nascent transcription, the latter being quantified through RNA metabolic labeling. We developed INSPEcT-, a computational method based on the mathematical modeling of premature and mature RNA expression that is able to quantify kinetic rates from steady-state or time course total RNA-seq data without requiring any information on nascent transcripts. Our approach outperforms available solutions, closely recapitulates the kinetic rates obtained through RNA metabolic labeling, improves the ability to detect changes in transcript half-lives, reduces the cost and complexity of the experiments, and can be adopted to study experimental conditions in which nascent transcription cannot be readily profiled. Finally, we applied INSPEcT- to the characterization of post-transcriptional regulation landscapes in dozens of physiological and disease conditions. This approach was included in the INSPEcT Bioconductor package, which can now unveil RNA dynamics from steady-state or time course data, with or without the profiling of nascent RNA.
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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.