RBPvsMIR: A Computational Pipeline to Identify Competing miRNAs and RNA-Binding Protein Pairs Regulating the Shared...

Gene post-transcription regulation involves several critical regulators such as microRNAs (miRNAs) and RNA-binding proteins (RBPs). Accumulated experimental evidences have shown that miRNAs and RBPs can competitively regulate the shared targeting transcripts. Although this establishes a novel post-transcription regulation mechanism, there are currently no computational tools to scan for the possible competing miRNA and RBP pairs. Here, we developed a novel computational pipeline-RBPvsMIR-that enables us to statistically evaluate the competing relationship between miRNAs and RBPs. RBPvsMIR first combines with previously successful miRNAs and RBP motifs discovery applications to search for overlapping or adjacent binding sites along a given RNA sequence. Then a permutation test is performed to select the miRNA and RBP pairs with the significantly enriched binding sites. As an example, we used RBPvsMIR to identify 235 competing RBP-miRNA pairs for long non-coding RNA (lncRNA) MALAT1. Wet lab experiments verified that splicing factor SRSF2 competes with miR-383, miR-502 and miR-101 to regulate MALAT1 in esophageal squamous carcinoma cells. Our study also revealed the global mutual exclusive pattern for miRNAs and RBP to regulate human lncRNAs. In addition, we provided a convenient web server (http://bmc.med.stu.edu.cn/RBPvsMIR), which should accelerate the exploration of competing miRNAs and RBP pairs regulating the shared targeting transcripts.