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

被引:23
作者
Bottini, Silvia [1 ]
Pratella, David [2 ]
Grandjean, Valerie [1 ]
Repetto, Emanuela [1 ]
Trabucchi, Michele [1 ]
机构
[1] INSERM, Paris, France
[2] Univ Cote Azur, Nice, France
关键词
RNA immunoprecipitation; bioinformatics workflow; computational guideline; large-scale analysis; quality management; microRNAs; human pathologies; RNA-BINDING PROTEIN; TRANSCRIPTOME-WIDE IDENTIFICATION; SINGLE-NUCLEOTIDE RESOLUTION; HITS-CLIP; NONCODING RNA; WEB SERVER; INTERACTION NETWORKS; SITE IDENTIFICATION; INTERACTION-MODEL; PAR-CLIP;
D O I
10.1093/bib/bbx063
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Cross-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.
引用
收藏
页码:1290 / 1301
页数:12
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