A bioinformatics pipeline for processing CLIP-seq data of RNA-binding proteins and its application

UV cross-linking immunoprecipitation followed by high-throughput sequencing (CLIP-seq) has emerged to be a powerful tool in dissecting mechanisms of RNA-binding proteins (RBP). Based on a recently developed eCLIP method by Yeo lab at UCSD, we performed target identifications and motif analyses on several RNA-binding proteins and established a bioinformatic pipeline for CLIP-seq data of RNA-binding proteins. By integrating the analysis software and scripts from different sources and analyzing RNA-binding protein PUMILIO1(PUM1) CLIP-seq data from a human cancer cell line, we identified 1189 RNA targets and found that PUM1 preferentially bound to the 3′ untranslated region (3′ UTR) and transcription termination sites (TTS) of its target mRNAs. The motif UGUAHAUA (H stands for A/U/C) is consistent with the canonical motif sequence of PUM1 for target recognition. Hence PUM1 may be involved in the proliferation and differentiation of cancer cells by regulating target gene expression at the post-transcriptional level via binding to the 3′ UTR.