ArticleMolecular cell2024
Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.
Article in Molecular cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Temporal gating dictates stress-induced transcript export from the nucleus.Genes & development · 2026Article
- Pervasive noise in human pre-mRNA splice site selection.Molecular cell · 2026Article
- Modulating RNA condensates to control cell fate.Nature biotechnology · 2026Article
- Spatial mapping of RNA turnover kinetics in the mouse brain.Nature neuroscience · 2026Article
- Kinetic Control of Nuclear-encoded Mitochondrial mRNA Localization and Local Translation.bioRxiv : the preprint server for biology · 2026Article
- Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR.Genome biology · 2026Article
- Scanning transcriptomes for nonlinear, domain-level similarities using hmSEEKR.bioRxiv : the preprint server for biology · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Enhancing RNA base editing on mammalian transcripts with small nuclear RNAs.Nature chemical biology · 2026Article
- Correlated protein-RNA associations and a requirement for HNRNPU in the long-range recruitment of Polycomb Repressive Complexes by the lncRNAs Airn and Kcnq1ot1.PLoS genetics · 2026Article
- Orthrus: toward evolutionary and functional RNA foundation models.Nature methods · 2026Article
- Pan-organ poly(A) atlas reveals a post-transcriptional regulatory layer independent of RNA abundance.Nature communications · 2026Article
- Temporal gating dictates stress-induced transcript export from the nucleus.bioRxiv : the preprint server for biology · 2026Article
- Predicting Recombinant mRNA Loading into Extracellular Vesicles: Insights from CD81 Fusion Constructs.International journal of molecular sciences · 2026Article
- Circadian clock gates diurnal glucose utilization.PLoS biology · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- Translational buffering tunes gene expression in mice and humans.Genome biology · 2026Article
- Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain.bioRxiv : the preprint server for biology · 2026Article
- Article
- Multi-omic relay velocity modeling uncovers dynamic chromatin-transcription regulation across cell states.Nature communications · 2025Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
Abstract
Dissecting the regulatory mechanisms controlling mammalian transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm in human and mouse cells. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA-binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered a link between DDX3X and nuclear export. For hundreds of RNA metabolism genes, most transcripts with retained introns were degraded by the nuclear exosome, while the remaining molecules were exported with stable cytoplasmic lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, machine learning identified molecular features that predicted the diverse life cycles of mRNAs.
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