ChIRP-MS: RNA-Directed Proteomic Discovery

Methods Mol Biol. 2018:1861:37-45. doi: 10.1007/978-1-4939-8766-5_3.

Abstract

Comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-ms) is a novel technique for studying endogenous ribonucleoprotein complexes. ChIRP-ms is robust across a wide range of expression level, from abundant housekeeping RNAs (e.g., spliceosomal U RNAs) to relatively lowly expressed RNAs (e.g., Xist). In vivo RNA-protein interactions are chemically cross-linked, and purified using biotinylated antisense oligonucleotides against RNA of interest. Coprecipitated proteins are gently eluted, and identified by mass-spectrometry (for discovery) or by western blotting (for validation).

Keywords: Mass-spec; RNA-binding proteins; lncRNA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Humans
  • Mass Spectrometry / methods*
  • Proteomics / methods*
  • RNA, Untranslated / metabolism
  • RNA-Binding Proteins / analysis*
  • RNA-Binding Proteins / metabolism

Substances

  • RNA, Untranslated
  • RNA-Binding Proteins