Recent computational developments on CLIP-seq data analysis and microRNA targeting implications. (12th June 2017)

• Record Type: Journal Article
• Authors: Bottini, Silvia; Pratella, David; Grandjean, Valerie; Repetto, Emanuela; Trabucchi, Michele
• Is Part Of: Briefings in bioinformatics. Volume 19:Number 6(2018:Nov.)
• Page Start: 1290
• Page End: 1301
• Publication Date: 2017-06-12
• Subjects: RNA immunoprecipitation; bioinformatics workflow -- computational guideline -- large-scale analysis -- quality management -- microRNAs -- human pathologies; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbx063
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: C ross-L inking I mmunop recipitation associated to high-throughput seq uencing (CLIP-seq) is a technique used to identify RNA directly bound to RNA-binding proteins across the entire transcriptome in cell or tissue samples. Recent technological and computational advances permit the analysis of many CLIP-seq samples simultaneously, allowing us to reveal the comprehensive network of RNA–protein interaction and to integrate it to other genome-wide analyses. Therefore, the design and quality management of the CLIP-seq analyses are of critical importance to extract clean and biological meaningful information from CLIP-seq experiments. The application of CLIP-seq technique to Argonaute 2 (Ago2) protein, the main component of the microRNA (miRNA)-induced silencing complex, reveals the direct binding sites of miRNAs, thus providing insightful information about the role played by miRNA(s). In this review, we summarize and discuss the most recent computational methods for CLIP-seq analysis, and discuss their impact on Ago2/miRNA-binding site identification and prediction with a regard toward human pathologies.