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Can we observe changes in mRNA "state"? Overview of methods to study mRNA interactions with regulatory proteins

C Zurla1, J Jung1, P J Santangelo1

  • 1Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, UA Whitaker Blgd, Atlanta, GA 30332, USA. philip.santangelo@bme.gatech.edu.

The Analyst
|November 26, 2015
PubMed

Insights

RNA binding proteins (RBPs) control gene expression post-transcriptionally, impacting immunity, stress, and cancer. A new method using FMTRIPs, PLA, and RCA detects RNA-protein interactions in situ with high sensitivity.

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Cancer Research

Background:

  • RNA binding proteins (RBPs) are key regulators of RNA metabolism, influencing processes like editing, localization, and degradation.
  • Post-transcriptional regulation by RBPs is critical for immune and stress responses, and dysregulation is implicated in cancer.
  • Understanding RBP-RNA interactions is vital for deciphering tumorigenesis mechanisms.

Purpose of the Study:

  • To review mRNAs and RBPs involved in tumorigenesis.
  • To discuss current methodologies for detecting RNA-protein interactions.
  • To introduce a novel assay for detecting native RNA-protein interactions in situ.

Main Methods:

  • Review of literature on RBPs, mRNAs, and cancer.
  • Description of existing RNA interaction detection techniques.
  • Detailed explanation of a novel method combining peptide-modified RNA imaging probes (FMTRIPs) with proximity ligation assay (PLA) and rolling circle amplification (RCA).

Main Results:

  • The novel FMTRIPs-PLA-RCA assay enables sequence-specific detection of native RNA.
  • The method achieves single-RNA sensitivity for detection.
  • Proximity ligation assay (PLA) allows for in situ quantification and localization of protein-mRNA interactions with single-interaction sensitivity.

Conclusions:

  • The developed assay offers a sensitive and specific approach for studying RNA-protein interactions in their native context.
  • This method has significant potential for advancing cancer research by enabling detailed analysis of RBP-mRNA dynamics in tumorigenesis.
  • The technique provides a powerful tool for localizing and quantifying protein-mRNA interactions within cells.

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