The eCLIP-seq method
Enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq) was developed to provide a robust and reproducible framework to identify RNA binding protein targets.
Increased efficiency, decreased PCR duplication
eCLIP-seq builds upon previous CLIP-seq methods to improve library preparation efficiency by nearly one thousand-fold, increasing experimental success rates and decreasing wasted sequencing due to PCR duplication.
Transcriptome-wide identification of RNA targets
eCLIP-seq identifies binding sites throughout RNAs, including binding to intronic and exonic positions and coding sequence and 3′ and 5′ untranslated regions, non-coding RNAs including lincRNAs and microRNAs, and retrotransposons and other RNA transcripts.
Reverse transcription often terminates at the protein-RNA crosslink site. By performing adapter ligation at the cDNA step, eCLIP can be used to identify binding sites and binding motifs with single-nucleotide resolution, depending on the target protein.