HiChIRP reveals RNA-associated chromosome conformation

Nat Methods. 2019 Jun;16(6):489-492. doi: 10.1038/s41592-019-0407-x. Epub 2019 May 27.


Modular domains of long non-coding RNAs can serve as scaffolds to bring distant regions of the linear genome into spatial proximity. Here, we present HiChIRP, a method leveraging bio-orthogonal chemistry and optimized chromosome conformation capture conditions, which enables interrogation of chromatin architecture focused around a specific RNA of interest down to approximately ten copies per cell. HiChIRP of three nuclear RNAs reveals insights into promoter interactions (7SK), telomere biology (telomerase RNA component) and inflammatory gene regulation (lincRNA-EPS).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cells, Cultured
  • Chromatin / chemistry*
  • Chromatin / genetics*
  • Chromosomes
  • Embryonic Stem Cells / cytology
  • Embryonic Stem Cells / metabolism*
  • Gene Expression Regulation*
  • Genome
  • Mice
  • Promoter Regions, Genetic
  • RNA / chemistry*
  • RNA / genetics
  • RNA, Long Noncoding / genetics*
  • Telomerase / chemistry*
  • Telomerase / genetics


  • Chromatin
  • EPS long non-coding RNA, mouse
  • RNA, Long Noncoding
  • telomerase RNA
  • RNA
  • Telomerase