Cell-to-Cell Transcription Variability as Measured by Single-Molecule RNA FISH to Detect Epigenetic State Switching

Methods Mol Biol. 2018;1767:385-393. doi: 10.1007/978-1-4939-7774-1_21.


Single-molecule RNA fluorescent in situ hybridization (smRNA FISH) allows for the visualization, localization, and quantification of RNA transcripts within individual cells and tissues using custom-designed fluorescently labeled oligonucleotide probes. Here we describe a protocol for the preparation, imaging, and analysis of a smRNA FISH experiment that can be applied to any RNA of choice. We also provide insights as to how this powerful tool can be used to study epigenetic regulation, for example, following the epigenetic editing of genes.

Keywords: Epigenetics; Fixation; Fluorescence microscopy; Hybridization; Image analysis; Permeabilization; RNA FISH.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Epigenesis, Genetic*
  • HEK293 Cells
  • Humans
  • In Situ Hybridization, Fluorescence / methods*
  • Microscopy, Fluorescence / methods
  • RNA / genetics*
  • RNA, Messenger / genetics*
  • Single-Cell Analysis / methods
  • Transcription, Genetic


  • RNA, Messenger
  • RNA