ArticleRNA (New York, N.Y.)2018
DRUID: a pipeline for transcriptome-wide measurements of mRNA stability.
Article in RNA (New York, N.Y.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
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Who cites it
33 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The genetic and biochemical determinants of mRNA degradation rates in mammals.Genome biology · 2022Pooled it
- CTCF aligns single-cell TAD-like domain boundaries and stabilizes long-range active chromatin clusters.Science advances · 2026Article
- Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR.Genome biology · 2026Article
- Regulation of mRNA decay and translation during the mammalian cell cycle.RNA (New York, N.Y.) · 2026Review
- Global stabilization of the transcriptome in mitotic cells.The EMBO journal · 2026Article
- RNADecayCafe, a uniformly processed atlas of RNA half-life estimates across multiple human cell lines.bioRxiv : the preprint server for biology · 2025Article
- Global inhibition of deadenylation stabilizes the transcriptome in mitotic cells.bioRxiv : the preprint server for biology · 2025Article
- Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos.Nucleic acids research · 2025Article
- tRNA modifications tune mCell · 2025Article
- 3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network.Science advances · 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
- Coordination of rhythmic RNA synthesis and degradation orchestrates 24-hour and 12-hour RNA expression patterns in mouse fibroblasts.bioRxiv : the preprint server for biology · 2023Article
- Low RNA stability signifies increased post-transcriptional regulation of cell identity genes.Nucleic acids research · 2023Article
- bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling.RNA (New York, N.Y.) · 2023Article
- A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3' UTR structure to RNA metabolism.Nucleic acids research · 2023Article
- Intron dynamics reveal principles of gene regulation during the maternal-to-zygotic transition.RNA (New York, N.Y.) · 2023Article
- Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry.Nucleic acids research · 2022Article
- Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver.PLoS genetics · 2022Article
- Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms.Nucleic acids research · 2022Article
- Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment.BMC bioinformatics · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Control of messenger RNA (mRNA) stability is an important aspect of gene regulation. The gold standard for measuring mRNA stability transcriptome-wide uses metabolic labeling, biochemical isolation of labeled RNA populations, and high-throughput sequencing. However, difficult normalization procedures have inhibited widespread adoption of this approach. Here, we present DRUID (for determination of rates using intron dynamics), a new computational pipeline that is robust, easy to use, and freely available. Our pipeline uses endogenous introns to normalize time course data and yields reproducible half-lives, even with data sets that were otherwise unusable. DRUID can handle data sets from a variety of organisms, spanning yeast to humans, and we even applied it retroactively on published data sets. We anticipate that DRUID will allow broad application of metabolic labeling for studies of transcript stability.
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