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RNA regulation is key to understanding the rules that govern gene expression regulation and epigenetic changes. The systemic action of several RNA-binding proteins (RBPs) is one of the principal mechanisms of post-transcriptional gene regulation. Several experimental techniques was developed to determine RBPs binding sites were SELEX, RIP-chip and CLIP. In particular, CLIP-seq protocols combine the action of CLIP and next-generation sequencing (NGS) to derive a transcriptome-wide set of RBP binding sites. There are different CLIP-seq protocols; each one introduces experimental variations to improve the signal to noise ratio (iCLIP, PAR-CLIP and HITS-CLIP). The main challenge of these protocols is to improve the signal to noise ratio, hence to remove background and false positives.
(Reyes-Herrera and Ficarra, 2014) Computational Methods for CLIP-seq Data Processing. Bioinform Biol Insights.