ArticleMolecular systems biology2024
Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting.
Article in Molecular systems biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- The periphery of nuclear speckles defines a spatially and temporally regulated compartment of long-lived intron-retained RNAs that resolves during mitosis.Nature cell biology · 2026Article
- Predicting human mRNA isoform levels from site-specific splicing kineticsbioRxiv : the preprint server for biology · 2026Article
- Temporal gating dictates stress-induced transcript export from the nucleus.bioRxiv : the preprint server for biology · 2026Article
- Transcriptional and functional profiles of muscarinic receptor-expressing neurons in primate lateral prefrontal and anterior cingulate cortices.Communications biology · 2026Article
- Article
- UBA2A regulates seed dormancy and the stability of chromatin-retained DOG1 messenger RNA.Journal of integrative plant biology · 2025Article
- Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances.bioRxiv : the preprint server for biology · 2025Article
- Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite.PLoS computational biology · 2025Article
- Gene-specific transcript buffering revealed by perturbation of coactivator complexes.Science advances · 2025Article
- Halfpipe: a tool for analyzing metabolic labeling RNA-seq data to quantify RNA half-lives.NAR genomics and bioinformatics · 2025Article
- Spatial omics advances for in situ RNA biology.Molecular cell · 2024Review
- Toward Mapping Spatiotemporally Resolved Transcriptomes and RNA-Protein Interactions.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
6 authors.
Funding
Abstract
Eukaryotic mRNAs are transcribed, processed, translated, and degraded in different subcellular compartments. Here, we measured mRNA flow rates between subcellular compartments in mouse embryonic stem cells. By combining metabolic RNA labeling, biochemical fractionation, mRNA sequencing, and mathematical modeling, we determined the half-lives of nuclear pre-, nuclear mature, cytosolic, and membrane-associated mRNAs from over 9000 genes. In addition, we estimated transcript elongation rates. Many matured mRNAs have long nuclear half-lives, indicating nuclear retention as the rate-limiting step in the flow of mRNAs. In contrast, mRNA transcripts coding for transcription factors show fast kinetic rates, and in particular short nuclear half-lives. Differentially localized mRNAs have distinct rate constant combinations, implying modular regulation. Membrane stability is high for membrane-localized mRNA and cytosolic stability is high for cytosol-localized mRNA. mRNAs encoding target signals for membranes have low cytosolic and high membrane half-lives with minor differences between signals. Transcripts of nuclear-encoded mitochondrial proteins have long nuclear retention and cytoplasmic kinetics that do not reflect co-translational targeting. Our data and analyses provide a useful resource to study spatiotemporal gene expression regulation.
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Registered trials
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