Capturing RNA-protein interaction via CRUIS

Nucleic Acids Res. 2020 May 21;48(9):e52. doi: 10.1093/nar/gkaa143.


No RNA is completely naked from birth to death. RNAs function with and are regulated by a range of proteins that bind to them. Therefore, the development of innovative methods for studying RNA-protein interactions is very important. Here, we developed a new tool, the CRISPR-based RNA-United Interacting System (CRUIS), which captures RNA-protein interactions in living cells by combining the power of CRISPR and PUP-IT, a novel proximity targeting system. In CRUIS, dCas13a is used as a tracker to target specific RNAs, while proximity enzyme PafA is fused to dCas13a to label the surrounding RNA-binding proteins, which are then identified by mass spectrometry. To identify the efficiency of CRUIS, we employed NORAD (Noncoding RNA activated by DNA damage) as a target, and the results show that a similar interactome profile of NORAD can be obtained as by using CLIP (crosslinking and immunoprecipitation)-based methods. Importantly, several novel NORAD RNA-binding proteins were also identified by CRUIS. The use of CRUIS facilitates the study of RNA-protein interactions in their natural environment, and provides new insights into RNA biology.

MeSH terms

  • CRISPR-Associated Proteins*
  • CRISPR-Cas Systems
  • HEK293 Cells
  • Humans
  • Immunoprecipitation
  • Mass Spectrometry
  • RNA / metabolism
  • RNA-Binding Proteins / metabolism*
  • Ribonucleases*


  • CRISPR-Associated Proteins
  • RNA-Binding Proteins
  • RNA
  • Ribonucleases