* Correspondence: BiomedicalResearch Center, University of Texas Southwestern MedicalCenter, Suite NC8.512 6000 Harry Hines Blvd, Dallas, TX 75390, USA 2Harold C. PAR-CLIP introduces a distinct spectrum of substitutions (T-to-C for 4SU and G-to-A for 6SG). For example, HITS-CLIP utilizes UV cross-linking of proteins with RNA, which introduces either insertions, deletions, or substitutions, depending on the RBPs. This cross-linking process usually introduces mutations in sequence tags at RBP binding sites. PAR-CLIP introduces photoactivatable ribonucleoside analogs, such as 4-thiouridine (4SU) and 6-thioguanosine (6SG), into the RNA of cultured cells to enhance cross-linking efficiency. To increase detection sensitivity, photoactivatable-ribonucleoside-enhanced CLIP (PAR-CLIP) was also developed. For example, high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) was used to identify approximately 30 to 60 nucleotide regions around the peaks of CLIP read clusters that represent binding sites of RNA-binding proteins (RBPs). Recent technological developments, especially the technique of crosslinking immuno-precipitation coupled with high-throughput sequencing (CLIP-seq), have provided powerful tools for studying the roles of RNA regulation in the control of gene expression and the generation of phenotypic complexity. RNA's diversity in sequence and structure endows it with crucial roles in cell biology. PIPE-CLIP provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools. Here, we present PIPE-CLIP, a Galaxy framework-based comprehensive online pipeline for reliable analysis of data generated by three types of CLIP-seq protocol: HITS-CLIP, PAR-CLIP and iCLIP. However, there are few tools available to analyze CLIP-seq data, thus creating a bottleneck to the implementation of this methodology. PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysisīeibei Chen1, Jonghyun Yun1, Min Soo Kim1,2, Joshua T Mendell2,3 and Yang Xie1,2*ĬLIP-seq is widely used to study genome-wide interactions between RNA-binding proteins and RNAs.
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