Quantifying Protein-mRNA Interactions in Single Live Cells

Bin Wu, Adina R. Buxbaum, Zachary B. Katz, Young J. Yoon, Robert H. Singer

Research output: Contribution to journalArticlepeer-review

56 Scopus citations


Summary Specific binding proteins are crucial for the correct spatiotemporal expression of mRNA. To understand this process, a method is required to characterize RNA-protein interactions in single living cells with subcellular resolution. We combined endogenous single RNA and protein detection with two-photon fluorescence fluctuation analysis to measure the average number of proteins bound to mRNA at specific locations within live cells. We applied this to quantify the known binding of zipcode binding protein 1 (ZBP1) and ribosomes to β-actin mRNA within subcellular compartments of primary fibroblasts and neurons. ZBP1-mRNA binding did not occur in nuclei, contrary to previous conclusions. ZBP1 interaction with β-actin mRNA was enhanced perinuclearly in neurons compared to fibroblasts. Cytoplasmic ZBP1 and ribosome binding to the mRNA were anti-correlated depending on their location in the cell. These measurements support a mechanism whereby ZBP1 inhibits translation of localizing mRNA until its release from the mRNA peripherally, allowing ribosome binding.

Original languageEnglish (US)
Pages (from-to)211-220
Number of pages10
Issue number1
StatePublished - Jul 3 2015
Externally publishedYes


  • ZBP1
  • beta-actin mRNA
  • fluorescence fluctuation spectroscopy
  • ribosomes
  • translational regulation

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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