CRISPR-assisted detection of RNA-protein interactions in living cells

Nat Methods. 2020 Jul;17(7):685-688. doi: 10.1038/s41592-020-0866-0. Epub 2020 Jun 22.


We have developed CRISPR-assisted RNA-protein interaction detection method (CARPID), which leverages CRISPR-CasRx-based RNA targeting and proximity labeling to identify binding proteins of specific long non-coding RNAs (lncRNAs) in the native cellular context. We applied CARPID to the nuclear lncRNA XIST, and it captured a list of known interacting proteins and multiple previously uncharacterized binding proteins. We generalized CARPID to explore binders of the lncRNAs DANCR and MALAT1, revealing the method's wide applicability in identifying RNA-binding proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • DNA-Binding Proteins / metabolism
  • HEK293 Cells
  • Humans
  • RNA, Long Noncoding / metabolism*
  • RNA-Binding Proteins / metabolism*
  • TATA-Binding Protein Associated Factors / metabolism
  • Transcription Factors / metabolism


  • DNA-Binding Proteins
  • RNA, Long Noncoding
  • RNA-Binding Proteins
  • SMARCA1 protein, human
  • TAF15 protein, human
  • TATA-Binding Protein Associated Factors
  • Transcription Factors
  • XIST non-coding RNA