ArticleNature methods2024
System-wide analysis of RNA and protein subcellular localization dynamics.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Directed evolution of Lantern enables rapid RNA and protein proximity labeling.Nature chemical biology · 2026Article
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- Elongationless start-stop elements are stress-resilient translation gates that are more repressive than uTranslons.Nucleic acids research · 2026Article
- Technologies to measure and modulate protein subcellular localization.Nature reviews. Molecular cell biology · 2026Review
- Subcellular localization as a driver of protein function.Nature reviews. Molecular cell biology · 2026Review
- RNA-binding proteins and ribonucleoproteins as determinants of immunity.Nature reviews. Immunology · 2026Review
- Stress Granule Sequestration of CCR4-NOT Promotes Poly(A) Lengthening of Stress-Survival Transcripts.bioRxiv : the preprint server for biology · 2026Article
- Review
- Recent Advances in Proximity Labeling-Based Subcellular Proteomic Mapping.Molecular & cellular proteomics : MCP · 2026Review
- Integrative profiling of condensation-prone RNAs during early development.Cell genomics · 2026Article
- Proteomic analysis of mitochondria-ER contacts reveals key proteins involved in metabolic regulation in hepatocytes.Cell communication and signaling : CCS · 2026Article
- Spatially regulated mRNA translation enables functional membrane protein integration in synthetic cells.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- FracFixR: a compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data.Bioinformatics (Oxford, England) · 2026Article
- A network-guided penalized regression with application to proteomics data.Bioinformatics advances · 2026Article
- Photocatalytic labelling-enabled subcellular-resolved RNA profiling and synchronous multi-omics investigation.Nature chemistry · 2025Article
- Systematic discovery of subcellular RNA patterns in the gut epithelium.Genome biology · 2025Article
- A molecular cartographer's toolkit for mapping RNA's uncharted realms.Cell reports · 2025Review
- TAS-seq enables subcellular single-stranded adenosine profiling by signal peptide-assisted adenosine deamination.Cell reports methods · 2025Article
- Identification of candidate proteins influencing spermatogenesis in Shandong black cattle via integrated multiomics analysis.BMC genomics · 2025Article
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12 authors.
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Abstract
Although the subcellular dynamics of RNA and proteins are key determinants of cell homeostasis, their characterization is still challenging. Here we present an integrative framework to simultaneously interrogate the dynamics of the transcriptome and proteome at subcellular resolution by combining two methods: localization of RNA (LoRNA) and a streamlined density-based localization of proteins by isotope tagging (dLOPIT) to map RNA and protein to organelles (nucleus, endoplasmic reticulum and mitochondria) and membraneless compartments (cytosol, nucleolus and cytosolic granules). Interrogating all RNA subcellular locations at once enables system-wide quantification of the proportional distribution of RNA. We obtain a cell-wide overview of localization dynamics for 31,839 transcripts and 5,314 proteins during the unfolded protein response, revealing that endoplasmic reticulum-localized transcripts are more efficiently recruited to cytosolic granules than cytosolic RNAs, and that the translation initiation factor eIF3d is key to sustaining cytoskeletal function. Overall, we provide the most comprehensive overview so far of RNA and protein subcellular localization dynamics.
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