Recent computational developments on CLIP-seq data analysis and microRNA targeting implications

Silvia Bottini; David Pratella; Valerie Grandjean; EMANUELA REPETTO; Michele Trabucchi

doi:10.1093/bib/bbx063

journal article Open Access Jun 12, 2017

Recent computational developments on CLIP-seq data analysis and microRNA targeting implications

Silvia Bottini David Pratella Valerie Grandjean EMANUELA REPETTO Michele Trabucchi

Briefings in Bioinformatics Vol. 19 No. 6 pp. 1290-1301 · Oxford University Press (OUP)

View at Publisher Save 10.1093/bib/bbx063

Abstract

AbstractCross-Linking Immunoprecipitation associated to high-throughput sequencing (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.

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Details

Published: Jun 12, 2017
Vol/Issue: 19(6)
Pages: 1290-1301
License: View

Authors

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Silvia Bottini