MicroRNA Crosslinking and Immunoprecipitation

miR-CLIP was developed to identify mRNA targets of miRNA, using synthetic miRNAs (Imig et al., 2014). The capture probes in miR-CLIP are pre-miRNAs conjugated to psoralen and biotin that can be crosslinked with mRNA to isolate their targets from total RNA.First, a miR-CLIP capture probe needs to be designed and tested for functionality and strong binding affinity. Next, they are transfected into cells and UV-crosslinked at 254 nm and 365 nm, followed by immunoprecipitation of the crosslinked complex. The RNA is extracted and further purified by streptavidin pull-down. The isolated RNA targets can now be reverse-transcribed and processed into cDNA libraries for sequencing.


  • Identifies targets of miRNAs genome-wide
  • Capture probe miRNA sequences can be easily modified to investigate different miRNA species


  • Not yet adopted widely by the scientific community
  • Requires careful design of miRNA capture probes


Illumina Library prep and Array Kit Selector


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Tycowski K. T., Guo Y. E., Lee N., et al. Viral noncoding RNAs: more surprises. Genes Dev. 2015;29:567-584


Imig J., Brunschweiger A., Brummer A., et al. miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nat Chem Biol. 2014;advance online publication: