Methylation of RNA is normally monitored in purified cell lysates using next-generation sequencing, gel electrophoresis, or mass spectrometry as readouts. These bulk methods require the RNA from ~104 to 107 cells to be pooled to generate sufficient material for analysis. Here we describe a method—methylation-sensitive RNA in situ hybridization (MR-FISH)—that assays rRNA methylation in bacteria on a cell-by-cell basis, using methylation-sensitive hybridization probes and fluorescence microscopy. We outline step-by-step protocols for designing probes, in situ hybridization, and analysis of data using freely available code.

Springer Nature
Methods Mol. Biol.
Physics of Cellular Interactions

Ganzinger, K., Challand, M., Spencer, J., Klenerman, D., & Ranasinghe, R. (2019). Imaging rRNA methylation in bacteria by MR-FISH. In Methods Mol. Biol. (Vol. 2038, pp. 89–107). doi:10.1007/978-1-4939-9674-2_7