RNA Immunoprecipitation Sequencing

RIP-Seq maps the sites at which proteins are bound to the RNA within RNA-protein complexes (Zhao et al., 2010). In this method, RNA-protein complexes are immunoprecipitated with antibodies targeted to the protein of interest. After RNase digestion, RNA protected by protein binding is extracted and reverse-transcribed to cDNA. The locations can then be mapped back to the genome. Deep sequencing of cDNA provides single-base resolution of protein-bound RNA.


  • Maps specific protein-RNA complexes, such as polycomb-associated RNAs
  • Low background and higher resolution of binding site due to RNase digestion
  • No prior knowledge of the RNA is required
  • Genome-wide RNA screen


  • Requires antibodies to the targeted proteins
  • Nonspecific antibodies will precipitate nonspecific complexes
  • Lack of crosslinking or stabilization of the complexes may lead to false negatives
  • RNase digestion must be controlled carefully


Illumina Library prep and Array Kit Selector


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