Serial interactome capture of the human cell nucleus

Nat Commun. 2016 Apr 4;7:11212. doi: 10.1038/ncomms11212.

Abstract

Novel RNA-guided cellular functions are paralleled by an increasing number of RNA-binding proteins (RBPs). Here we present 'serial RNA interactome capture' (serIC), a multiple purification procedure of ultraviolet-crosslinked poly(A)-RNA-protein complexes that enables global RBP detection with high specificity. We apply serIC to the nuclei of proliferating K562 cells to obtain the first human nuclear RNA interactome. The domain composition of the 382 identified nuclear RBPs markedly differs from previous IC experiments, including few factors without known RNA-binding domains that are in good agreement with computationally predicted RNA binding. serIC extends the number of DNA-RNA-binding proteins (DRBPs), and reveals a network of RBPs involved in p53 signalling and double-strand break repair. serIC is an effective tool to couple global RBP capture with additional selection or labelling steps for specific detection of highly purified RBPs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Nucleus / genetics
  • Cell Nucleus / metabolism*
  • Cell Nucleus / radiation effects
  • DNA / genetics
  • DNA / metabolism*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Gene Expression Regulation
  • Gene Regulatory Networks
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • K562 Cells
  • Protein Interaction Mapping
  • RNA, Guide / genetics
  • RNA, Guide / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • Signal Transduction
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Ultraviolet Rays

Substances

  • DNA-Binding Proteins
  • RNA, Guide
  • RNA, Messenger
  • RNA-Binding Proteins
  • Transcription Factors
  • DNA