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Updated: Feb 14, 2026

Analysis of Single-cell Gene Transcription by RNA Fluorescent In Situ Hybridization FISH
Published on: October 7, 2012
Detecting RNA base methylations in single cells by in situ hybridization
Rohan T Ranasinghe1, Martin R Challand2,3, Kristina A Ganzinger4,5
1Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. rr360@cam.ac.uk.
None:
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 (m62A, 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.
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