Measuring mRNA Decay in Budding Yeast Using Single Molecule FISH

Methods Mol Biol. 2018:1720:35-54. doi: 10.1007/978-1-4939-7540-2_4.


Cellular mRNA levels are determined by the rates of mRNA synthesis and mRNA decay. Typically, mRNA degradation kinetics are measured on a population of cells that are either chemically treated or genetically engineered to inhibit transcription. However, these manipulations can affect the mRNA decay process itself by inhibiting regulatory mechanisms that govern mRNA degradation, especially if they occur on short time-scales. Recently, single molecule fluorescent in situ hybridization (smFISH) approaches have been implemented to quantify mRNA decay rates in single, unperturbed cells. Here, we provide a step-by-step protocol that allows quantification of mRNA decay in single Saccharomyces cerevisiae using smFISH. Our approach relies on fluorescent labeling of single cytoplasmic mRNAs and nascent mRNAs found at active sites of transcription, coupled with mathematical modeling to derive mRNA half-lives. Commercially available, single-stranded smFISH DNA oligonucleotides (smFISH probes) are used to fluorescently label mRNAs followed by the quantification of cellular and nascent mRNAs using freely available spot detection algorithms. Our method enables quantification of mRNA decay of any mRNA in single, unperturbed yeast cells and can be implemented to quantify mRNA turnover in a variety of cell types as well as tissues.

Keywords: Budding yeast; Fluorescent in situ hybridization; S. cerevisiae; Single cells; Single molecule; Yeast; mRNA decay; mRNA decay rate; mRNA half-life; mRNA turnover; smFISH.

MeSH terms

  • Algorithms
  • Cytoplasm / chemistry
  • Cytoplasm / genetics
  • In Situ Hybridization, Fluorescence / methods*
  • Kinetics
  • Models, Biological
  • RNA Stability*
  • RNA, Messenger / chemistry*
  • Saccharomyces cerevisiae / chemistry*
  • Saccharomyces cerevisiae / genetics
  • Single-Cell Analysis / methods*
  • Transcription, Genetic


  • RNA, Messenger