Chromatin Isolation by RNA Purification

ChIRP, also commonly referred to as ChIRP-seq, is a protocol to detect the locations on the genome where ncRNAs, such as lncRNAs, and their proteins are bound (Chu et al., 2011). In this method, samples are first crosslinked and sonicated. Biotinylated tiling oligos are hybridized to the RNAs of interest, and the complexes are captured with streptavidin magnetic beads. After treatment with RNase H, the DNA is extracted and sequenced. Deep sequencing can determine the lncRNA/protein interaction site at single-base resolution.


  • Identifies binding sites anywhere on the genome
  • Enables discovery of new binding sites
  • Allows selection of specific RNAs of interest


  • Nonspecific oligonucleotide interactions can lead to misinterpretation of binding sites
  • Chromatin can be disrupted during the preparation stage
  • The sequence of the RNA of interest must be known


Illumina Library prep and Array Kit Selector


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