Capture Hybridization Analysis of RNA Targets

CHART maps genomic binding sites of ncRNAs by isolating and sequencing the DNA regions where the crosslinked RNA-DNA-protein complexes are bound (Simon et al., 2011). CHART differs from other crosslinked-complex purification techniques, such as ChIRP, due to the use of biotinylated 24 nt oligonucleotides (C-oligos) that are highly sensitive and unique to the ncRNA of interest (Kashi et al., 2015). An RNase H mapping assay is used to design the 24 nt sequence of the C-oligos. First, nuclei samples are crosslinked and fragmented. Next, C-oligos are hybridized to the complex and bound to streptavidin beads. The mixture is washed and the complex eluted. The DNA is isolated and sequenced, and the proteins involved in the complex are isolated and analyzed by Western blots.


  • Maps genomic binding sites of lncRNAs
  • Simultaneously identifies proteins associated with the lncRNA complex


  • Needs large amount of nuclei (1 x 10^9 cells)


Illumina Library prep and Array Kit Selector


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