Identification of a Xist silencing domain by Tiling CRISPR

Sci Rep. 2019 Feb 20;9(1):2408. doi: 10.1038/s41598-018-36750-0.


Despite essential roles played by long noncoding RNAs (lncRNAs) in development and disease, methods to determine lncRNA cis-elements are lacking. Here, we developed a screening method named "Tiling CRISPR" to identify lncRNA functional domains. Using this approach, we identified Xist A-Repeats as the silencing domain, an observation in agreement with published work, suggesting Tiling CRISPR feasibility. Mechanistic analysis suggested a novel function for Xist A-repeats in promoting Xist transcription. Overall, our method allows mapping of lncRNA functional domains in an unbiased and potentially high-throughput manner to facilitate the understanding of lncRNA functions.

Publication types

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

MeSH terms

  • Animals
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics
  • Humans
  • Mice
  • Mouse Embryonic Stem Cells / metabolism
  • RNA, Long Noncoding / genetics*
  • Regulatory Sequences, Ribonucleic Acid / genetics*
  • Transcription, Genetic*


  • RNA, Long Noncoding
  • Regulatory Sequences, Ribonucleic Acid
  • XIST non-coding RNA