UNIT 21.25 Capture Hybridization Analysis of RNA Targets (CHART)

  1. Matthew D. Simon

Published Online: 1 JAN 2013

DOI: 10.1002/0471142727.mb2125s101

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Simon, M. D. 2013. Capture Hybridization Analysis of RNA Targets (CHART). Current Protocols in Molecular Biology. 101:21.25:21.25.1–21.25.16.

Author Information

  1. Department of Molecular Biophysics and Biochemistry and Chemical Biology Institute, Yale University, West Haven, Connecticut

Publication History

  1. Published Online: 1 JAN 2013
  2. Published Print: JAN 2013


The genome is regulated by trans-acting factors that bind to specific loci in chromatin. In addition to protein factors, it has become clear that large non-coding RNAs can also act on chromatin at sites distant from where they are transcribed. This unit describes a means of identifying the genomic targets of those large non-coding RNAs. To accomplish this, the endogenous RNA of interest (here Drosophila roX2 is used as an example) is enriched from cross-linked chromatin extracts using short biotinylated complementary oligodeoxyribonucleotides. The targets of the RNA can be determined by examining the proteins and DNA that are enriched under these conditions. This analysis can be extended genome-wide by subjecting the enriched DNA to deep sequencing. Curr. Protoc. Mol. Biol. 101:21.25.1–21.25.16. © 2013 by John Wiley & Sons, Inc.


  • CHART;
  • chromatin;
  • non-coding RNA;
  • lncRNA