Ribo-proteomics approach to profile RNA–protein and protein–protein interaction networks

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Abstract

Characterizing protein–protein and protein–RNA interaction networks is a fundamental step to understanding the function of an RNA-binding protein. In many cases, these interactions are transient and highly dynamic. Therefore, capturing stable as well as transient interactions in living cells for the identification of protein-binding partners and the mapping of RNA-binding sequences is key to a successful establishment of the molecular interaction network. In this chapter, we will describe a method for capturing the molecular interactions in living cells using formaldehyde as a crosslinker and enriching a specific RNA–protein complex from cell extracts followed by mass spectrometry and Next-Gen sequencing analyses.

Original languageEnglish (US)
Pages (from-to)165-174
Number of pages10
JournalMethods in Molecular Biology
Volume1421
DOIs
StatePublished - Jan 1 2016

Keywords

  • Crosslinking immunoprecipitation
  • Formaldehyde crosslinking
  • Mass spectrometry
  • Next-Gen sequencing
  • RNA-binding proteins

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