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Technologies to measure and modulate protein subcellular localization

Nature Reviews Molecular Cell Biology (2026)Cite this article

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Abstract

How proteins localize to specific compartments, function in coordination with other biomolecules and, ultimately, contribute to diverse cellular activities are crucial questions in cell biology. Complicating the answers to these questions are multilocalizing and multifunctional proteins, whose impact on the cell depends on both spatial and temporal contexts. Therefore, contextualizing protein functions based on their subcellular localization is necessary to fully understand cell behaviours. Recent advances in instrumentation and protein labelling techniques are rapidly increasing the availability of tools, technologies and applications that measure and control protein localization and compartment-specific function. In this Review, we first discuss microscopy, mass spectrometry-based correlation profiling and proximity labelling methods that assign localizations to proteins, ranging from cellular compartments to protein–protein interactions. We next examine the available tools for manipulating protein localization and measuring the effects of these manipulations, including localization tags and bifunctional molecules. For each technology, we assess the strengths and weaknesses that ultimately determine their usefulness. We conclude with an outlook on future technological advances in the field of spatial subcellular proteomics and their potential implications for cell biology and clinical applications.

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Fig. 1: Methods for detecting protein location.
Fig. 2: Manipulating protein localization.
Fig. 3: Strategies for determining location-dependent protein function.

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Acknowledgements

The authors thank A. Sigaeva, C. Hutchings, A. Cesnik, S.-J. Tsai and K. S. Lilley for comments and feedback during the writing of the manuscript. E.L. was supported by the Wallenberg Foundation (2021.0346), Erling Persson Foundation, Göran Gustafsson Foundation, Schmidt Futures, the Bridge2AI Program (National Institutes of Health (NIH) Common Fund; OT2 OD032742), the Cancer Cell Map Initiative (National Cancer Institute (NCI) Center for Cancer Systems Biology; U54 CA274502), Stanford Institute for Human-Centered AI, Chan Zuckerberg Initiative, Phil & Penny Knight Initiative for Brain Resilience at the Wu Tsai Neurosciences Institute, Danaher and Param Hansa Philanthropies. R.T. was supported by the Life Sciences Research Foundation Fellowship (sponsored by Astellas Pharma). A.T. was supported by the Chan Zuckerberg Biohub – San Francisco and the Stanford Bio-X.

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  1. Bioengineering Department, Stanford University, Stanford, CA, USA

    William Leineweber & Emma Lundberg

  2. Department of Genetics, Stanford University, Stanford, CA, USA

    Reika Tei & Alice Ting

  3. Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden

    Anna Mäkiniemi & Emma Lundberg

  4. Chan Zuckerberg Biohub, San Francisco, CA, USA

    Alice Ting & Emma Lundberg

  5. Department of Biology, Stanford University, Stanford, CA, USA

    Alice Ting

  6. Department of Chemistry, Stanford University, Stanford, CA, USA

    Alice Ting

  7. Phil & Penny Knight Initiative for Brain Resilience at the Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA

    Alice Ting

  8. Pathology Department, Stanford University, Stanford, CA, USA

    Emma Lundberg

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W.L., R.T. and A.M. researched data for the article. E.L., W.L. and R.T. contributed substantially to discussion of the content. W.L., R.T. and A.M. wrote the article. E.M. and A.T. reviewed and/or edited the manuscript before submission.

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E.L. is an adviser for Element Biosciences, Nautilus Biotechnology, Cartography Biosciences, Genbio.ai and Pixelgen Technologies. A.T. is a scientific adviser to Third Rock Ventures. The terms of these arrangements have been reviewed and approved by Stanford University in accordance with its conflict of interest policies.

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Ensembl: https://www.ensembl.org/index.html

Human Protein Atlas: https://www.proteinatlas.org/

UniProt: https://www.uniprot.org/

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Leineweber, W., Tei, R., Mäkiniemi, A. et al. Technologies to measure and modulate protein subcellular localization. Nat Rev Mol Cell Biol (2026). https://doi.org/10.1038/s41580-026-00957-1

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