Single-molecule resolution fluorescent in situ hybridization (smFISH) in the yeast S. cerevisiae

Methods Mol Biol. 2013:1042:33-46. doi: 10.1007/978-1-62703-526-2_3.


Regulating gene expression is a major task for all cellular systems. RNA production and degradation plays a critical role in this process and accurately measuring cellular mRNA levels is essential to understanding gene expression regulation. Classical biochemical assays that study gene expression rely on extracting RNAs from large populations of cells, taking them out of their native context and thereby losing spatial information as well as cell-to-cell variability. In this chapter, we describe a fluorescent in situ hybridization (FISH) technique that circumvents this problem by detecting single RNAs in single cells. The technique employs multiple single-stranded short DNA probes fluorescently labeled with organic dyes that hybridize to target RNAs in fixed cells, allowing quantification and localization of RNAs at the single-cell level and at single-molecule resolution. The protocol described here has been optimized for the yeast S. cerevisiae.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Probes / chemistry
  • DNA Probes / genetics
  • Fluorescent Dyes / chemistry
  • Gene Expression Regulation, Fungal / genetics
  • In Situ Hybridization, Fluorescence / methods*
  • RNA, Messenger / biosynthesis
  • RNA, Messenger / genetics*
  • Saccharomyces cerevisiae / cytology*
  • Single-Cell Analysis / methods


  • DNA Probes
  • Fluorescent Dyes
  • RNA, Messenger