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Updated: Jul 9, 2025
10:24
Visualization of Endoplasmic Reticulum Localized mRNAs in Mammalian Cells
Published on: December 17, 2012
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System-wide analysis of RNA and protein subcellular localization dynamics.
Eneko Villanueva1, Tom Smith1,2, Mariavittoria Pizzinga2,3
1Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
Nature Methods
|November 30, 2023
Summary
This study introduces a new framework to track RNA and protein locations within cells, offering a comprehensive view of cellular dynamics. The findings reveal how cellular components move during stress responses, impacting cell homeostasis.
Area of Science:
- Cell Biology
- Molecular Biology
- Systems Biology
Background:
- Subcellular dynamics of RNA and proteins are crucial for cell homeostasis.
- Characterizing these dynamics at high resolution remains a significant challenge in cell biology.
Purpose of the Study:
- To develop an integrative framework for simultaneous interrogation of transcriptome and proteome dynamics at subcellular resolution.
- To provide a system-wide quantification of RNA and protein proportional distribution across cellular compartments.
Main Methods:
- Integration of Localization of RNA (LoRNA) and streamlined density-based localization of proteins by isotope tagging (dLOPIT).
- Mapping of RNA and protein localization to organelles (nucleus, endoplasmic reticulum, mitochondria) and membraneless compartments (cytosol, nucleolus, cytosolic granules).
Main Results:
- A cell-wide overview of localization dynamics for 31,839 transcripts and 5,314 proteins during the unfolded protein response.
- Demonstration that endoplasmic reticulum-localized transcripts are more efficiently recruited to cytosolic granules than cytosolic RNAs.
- Identification of the translation initiation factor eIF3d as critical for sustaining cytoskeletal function.
Conclusions:
- The developed framework offers the most comprehensive overview to date of RNA and protein subcellular localization dynamics.
- Understanding these dynamics provides insights into cellular responses to stress and maintenance of homeostasis.
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