Bioinformatic Application of Fluorescence-Based In Vivo RNA Regional Accessibility Data to Identify Novel sRNA Targets

  • Emily K. Bowman
  • Mia K. Mihailovic
  • Bridget Li
  • Lydia M. ContrerasEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2113)


Data from fluorescence-based methods that measure in vivo hybridization efficacy of unique RNA regions can be used to infer regulatory activity and to identify novel RNA: RNA interactions. Here, we document the step-by-step analysis of fluorescence data collected using an in vivo regional RNA structural sensing system (iRS3) for the purpose of identifying potential functional sites that are likely to be involved in regulatory interactions. We also detail a step-by-step protocol that couples this in vivo accessibility data with computational mRNA target predictions to inform the selection of potentially true targets from long lists of thermodynamic predictions.

Key words

Regional RNA accessibility RNA hybridization efficacy Identification of RNA-binding sites RNA-RNA interactions In vivo fluorescence-based assays Electrophoretic mobility shift assay Target networks 



This work is supported by the Welch Foundation (Grant F-1756 to LMC) and the National Science Foundation (Grant MCB 1716777 to LMC and DGE-1610403 to MKM).


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Emily K. Bowman
    • 1
  • Mia K. Mihailovic
    • 1
  • Bridget Li
    • 1
  • Lydia M. Contreras
    • 1
    Email author
  1. 1.Institute for Cellular and Molecular BiologyThe University of Texas at AustinAustinUSA

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