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Fluorescent In Situ Detection of RNA–Protein Interactions in Intact Cells by RNA-PLA

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RNA-Protein Complexes and Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2666))

Abstract

RNA–protein proximity ligation assay (RNA-PLA) enables the detection of specific RNA–protein interactions in fixed cells. In RNA-PLA, bridging and ligation of a circular DNA template occurs if the target RNA and protein are within 40 nanometers of each other. The resulting circular template is amplified by rolling circle amplification and abundantly recognized by fluorescent antisense DNA oligonucleotides. This strategy therefore enables localization of RNA–protein interactions in situ with high specificity and sensitivity. Here, we describe the use of RNA-PLA to detect interactions between a nuclear viral RNA and a host RNA-binding protein in Epstein-Barr virus (EBV)-infected B cells.

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Acknowledgments

We would like to thank members of the Xie laboratory for helpful discussion. Initial data in this manuscript were acquired in the laboratory of Daniel DiMaio, and in the laboratory of Joan Steitz at Yale University, with the support of a grant from the National Institute of Health (P01-CA16038). The Xie lab is supported by the National Institute of Health (R35-GM128753 to M.X.).

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Correspondence to Mingyi Xie .

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Li, T., Zhang, W., Xie, M. (2023). Fluorescent In Situ Detection of RNA–Protein Interactions in Intact Cells by RNA-PLA. In: Lin, RJ. (eds) RNA-Protein Complexes and Interactions. Methods in Molecular Biology, vol 2666. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3191-1_13

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  • DOI: https://doi.org/10.1007/978-1-0716-3191-1_13

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3190-4

  • Online ISBN: 978-1-0716-3191-1

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