ArticleNucleic acids research2020
Transcriptome-wide organization of subcellular microenvironments revealed by ATLAS-Seq.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- The RNA-binding protein HNRNPA2B1 regulates neurite RNA abundance and motor-dependent cargo transport.Molecular biology of the cell · 2025Article
- Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts.Genome research · 2025Article
- Analyzing RNA Localization Using the RNA Proximity Labeling Method OINC-seq.Bio-protocol · 2025Article
- Quantification of subcellular RNA localization through direct detection of RNA oxidation.Nucleic acids research · 2025Article
- Quantification of subcellular RNA localization through direct detection of RNA oxidation.bioRxiv : the preprint server for biology · 2024Article
- Spatial omics advances for in situ RNA biology.Molecular cell · 2024Review
- Intracellular spatial transcriptomic analysis toolkit (InSTAnT).Nature communications · 2024Article
- System-wide analysis of RNA and protein subcellular localization dynamics.Nature methods · 2024Article
- Transcriptome-scale methods for uncovering subcellular RNA localization mechanisms.Biochimica et biophysica acta. Molecular cell research · 2022Review
- Subcellular Transcriptomics and Proteomics: A Comparative Methods Review.Molecular & cellular proteomics : MCP · 2022Review
- Advances in spatial transcriptomic data analysis.Genome research · 2021Review
- The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.Frontiers in molecular biosciences · 2021Review
- Subcellular proteomics.Nature reviews. Methods primers · 2021Article
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2 authors.
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Abstract
Subcellular organization of RNAs and proteins is critical for cell function, but we still lack global maps and conceptual frameworks for how these molecules are localized in cells and tissues. Here, we introduce ATLAS-Seq, which generates transcriptomes and proteomes from detergent-free tissue lysates fractionated across a sucrose gradient. Proteomic analysis of fractions confirmed separation of subcellular compartments. Unexpectedly, RNAs tended to co-sediment with other RNAs in similar protein complexes, cellular compartments, or with similar biological functions. With the exception of those encoding secreted proteins, most RNAs sedimented differently than their encoded protein counterparts. To identify RNA binding proteins potentially driving these patterns, we correlated their sedimentation profiles to all RNAs, confirming known interactions and predicting new associations. Hundreds of alternative RNA isoforms exhibited distinct sedimentation patterns across the gradient, despite sharing most of their coding sequence. These observations suggest that transcriptomes can be organized into networks of co-segregating mRNAs encoding functionally related proteins and provide insights into the establishment and maintenance of subcellular organization.
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