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

William Beckman; Ilona M Vuist; Hermannus Kempe; Pernette J Verschure

doi:10.1007/978-1-4939-7774-1_21

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.

Authors

William Beckman¹, Ilona M Vuist¹, Hermannus Kempe¹, Pernette J Verschure²

Affiliations

¹ Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
² Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands. p.j.verschure@uva.nl.

PMID: 29524147
DOI: 10.1007/978-1-4939-7774-1_21

Abstract

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

Substances

RNA, Messenger
RNA