MS2-MBP-Based Affinity Purification of Nucleus- or Cytoplasm-Localized lncRNA-Protein Complexes Formed In Vivo

Methods Mol Biol. 2023:2666:231-245. doi: 10.1007/978-1-0716-3191-1_17.

Abstract

With recent emergence of huge number of long noncoding RNAs (lncRNAs), purification of lncRNA-protein (lncRNP) complexes is fundamental to understand the role of lncRNA and its biological function. However, lncRNP purification is still a daunting challenge. Here we describe a protocol to purify lncRNP formed in vivo with MS2-MBP-based affinity purification. Inducible lncRNA tagged with MS2 RNA hairpins is introduced into cells of interest, and RNP on tagged lncRNA is formed in vivo. MS2-MBP fusion protein is expressed in Escherichia coli and purified with amylose resin and HiTrap heparin column. The MS2 part of MS2-MBP fusion protein binds to the hairpins, and MBP part binds to amylose resin. We also describe a protocol to separate the nucleus and the cytoplasm so that lncRNP localized in the nucleus or cytoplasm can be individually purified. The amount of lncRNP purified is well sufficient for mass spectrometry analysis.

Keywords: Affinity purification; LncRNP; MS2 RNA hairpin; MS2-MBP fusion protein.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amylose
  • Cell Nucleus / metabolism
  • Chromatography, Affinity / methods
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Indicators and Reagents
  • Maltose-Binding Proteins
  • RNA, Long Noncoding* / metabolism
  • Recombinant Fusion Proteins / genetics

Substances

  • RNA, Long Noncoding
  • Amylose
  • Indicators and Reagents
  • Recombinant Fusion Proteins
  • Maltose-Binding Proteins