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Deciphering molecular interactions by proximity labeling

Nature Methods volume 18, pages 133–143 (2021)Cite this article

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Abstract

Many biological processes are executed and regulated through the molecular interactions of proteins and nucleic acids. Proximity labeling (PL) is a technology for tagging the endogenous interaction partners of specific protein ‘baits’, via genetic fusion to promiscuous enzymes that catalyze the generation of diffusible reactive species in living cells. Tagged molecules that interact with baits can then be enriched and identified by mass spectrometry or nucleic acid sequencing. Here we review the development of PL technologies and highlight studies that have applied PL to the discovery and analysis of molecular interactions. In particular, we focus on the use of PL for mapping protein–protein, protein–RNA and protein–DNA interactions in living cells and organisms.

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Fig. 1: Peroxidase- and biotin ligase-based proximity labeling methods for PPI mapping.
Fig. 2: PL-based methods to investigate protein–nucleic acid interactions.

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Acknowledgements

This work was supported by the NIH (R01-DK121409 to A.Y.T.) and Stanford Wu Tsai Neurosciences Institute. K.F.C. was supported by NIH Training Grant 2T32CA009302-41 and the Blavatnik Graduate Fellowship. P.E.C. was supported by the NSF Graduate Research Fellowship. A.Y.T. is an investigator of the Chan Zuckerberg Biohub.

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Author notes

  1. These authors contributed equally: Wei Qin, Kelvin F. Cho, Peter E. Cavanagh.

Authors and Affiliations

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

    Wei Qin, Kelvin F. Cho & Alice Y. Ting

  2. Cancer Biology Program, Stanford University, Stanford, CA, USA

    Kelvin F. Cho

  3. Department of Biochemistry, Stanford University, Stanford, CA, USA

    Peter E. Cavanagh

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

    Alice Y. Ting

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

    Alice Y. Ting

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

    Alice Y. Ting

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  1. Wei Qin
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Correspondence to Alice Y. Ting.

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Qin, W., Cho, K.F., Cavanagh, P.E. et al. Deciphering molecular interactions by proximity labeling. Nat Methods 18, 133–143 (2021). https://doi.org/10.1038/s41592-020-01010-5

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