Detecting RNA base methylations in single cells by in situ hybridization

Rohan T. Ranasinghe*, Martin R. Challand, Kristina A. Ganzinger, Benjamin W. Lewis, Charlotte Softley, Wolfgang H. Schmied, Mathew H. Horrocks, Nadia Shivji, Jason W. Chin, James Spencer, David Klenerman

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)

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Methylated bases in tRNA, rRNA and mRNA control a variety of cellular processes, including protein synthesis, antimicrobial resistance and gene expression. Currently, bulk methods that report the average methylation state of ~104-107 cells are used to detect these modifications, obscuring potentially important biological information. Here, we use in situ hybridization of Molecular Beacons for single-cell detection of three methylations (m6 2A, m1G and m3U) that destabilize Watson-Crick base pairs. Our method - methylation-sensitive RNA fluorescence in situ hybridization - detects single methylations of rRNA, quantifies antibiotic-resistant bacteria in mixtures of cells and simultaneously detects multiple methylations using multicolor fluorescence imaging.

Original languageEnglish
Article number655
Number of pages10
JournalNature Communications
Issue number1
Publication statusPublished - 13 Mar 2018

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    Ranasinghe, R. T., Challand, M. R., Ganzinger, K. A., Lewis, B. W., Softley, C., Schmied, W. H., Horrocks, M. H., Shivji, N., Chin, J. W., Spencer, J., & Klenerman, D. (2018). Detecting RNA base methylations in single cells by in situ hybridization. Nature Communications, 9(1), [655].