hiCLIP sequences RNA duplexes bound to RBPs in vivo. The unique cloning and linker-adapter system in hiCLIP identifies whether the RBP-bound duplex originates from the same RNA or different RNAs.
Similar to CLIP library preparation techniques, RNA and RBPs are UV-crosslinked, partially digested, and immunoprecipitated. The signature hiCLIP cloning and linker-adapters are ligated to both strands of the duplex. The 3' end of the linker-adapter is dephosphorylated and ligated to the 5' end of the other strand. The bound proteins are removed with proteinase K. The cDNA library is prepared in a similar dashion to iCLIP for high-throughput sequencing. The cloning and linker-adapters enable the mapping of the hybrid reads to the transcriptome and distinguish whether the duplex is formed by the same RNAs or different RNAs.