Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments

Nat Methods. 2018 Dec;15(12):1074-1082. doi: 10.1038/s41592-018-0220-y. Epub 2018 Nov 26.


Methods for the systematic study of subcellular RNA localization are limited, and their development has lagged behind that of proteomic tools. We combined APEX2-mediated proximity biotinylation of proteins with photoactivatable ribonucleoside-enhanced crosslinking to simultaneously profile the proteome and the transcriptome bound by RNA-binding proteins in any given subcellular compartment. Our approach is fractionation independent and allows study of the localization of RNA processing intermediates, as well as the identification of regulatory RNA cis-acting elements occupied by proteins, in a cellular-compartment-specific manner. We used our method, Proximity-CLIP, to profile RNA and protein in the nucleus, in the cytoplasm, and at cell-cell interfaces. Among other insights, we observed frequent transcriptional readthrough continuing for several kilobases downstream of the canonical cleavage and polyadenylation site and a differential RBP occupancy pattern for mRNAs in the nucleus and cytoplasm. We observed that mRNAs localized to cell-cell interfaces often encoded regulatory proteins and contained protein-occupied CUG sequence elements in their 3' untranslated region.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Binding Sites
  • Cross-Linking Reagents / chemistry
  • Gene Expression Regulation*
  • HEK293 Cells
  • Humans
  • Isotope Labeling
  • Protein Binding
  • Proteomics / methods*
  • RNA / genetics
  • RNA / metabolism*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • Transcriptome*


  • Cross-Linking Reagents
  • RNA-Binding Proteins
  • RNA