Quantification of mRNA Turnover in Living Cells: A Pipeline for TREAT Data Analysis

Methods Mol Biol. 2019;2038:75-88. doi: 10.1007/978-1-4939-9674-2_6.


mRNA turnover plays an important role in the regulation of post-transcriptional gene expression. While many protein factors involved in mRNA degradation have been identified, we still lack a basic understanding of the principles that regulate the spatiotemporal dynamics of mRNA turnover within single cells. To overcome this limitation, we have developed the TREAT biosensor, which allows for discrimination of intact reporter transcripts and stabilized decay intermediates using single RNA imaging. Here, we present an image analysis pipeline that performs semiautomated detection and tracking of individual mRNA particles. It colocalizes tracks and applies the colocalization information to quantify the number of intact transcripts and degradation intermediates. Based on the analysis of control data, the workflow further determines detection efficiencies and uses them to correct RNA particle numbers.

Keywords: Fluorescence microscopy; Live cell imaging; MS2/PP7 stem-loops; Single-molecule; TREAT; mRNA turnover.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biosensing Techniques*
  • Gene Expression Regulation
  • HeLa Cells
  • Humans
  • Microscopy, Fluorescence*
  • Molecular Imaging / methods*
  • RNA Stability
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Single Molecule Imaging / methods*
  • Time Factors


  • RNA, Messenger