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Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. | Corcoran et al. Genome Biology 2011 12 R79 http genomebiology.eom 2011 12 8 R79 Genome Biology METHOD Open Access PARalyzer definition of RNA binding sites from PAR-CLIP short-read sequence data David L CorcoranH Stoyan Georgiev1 2t Neelanjan Mukherjee1 Eva Gottwein3 4 Rebecca L Skalsky5 Jack D Keene5 and Uwe Ohler1 6 Abstract Crosslinking and immunoprecipitation CLIP protocols have made it possible to identify transcriptome-wide RNA-protein interaction sites. In particular PAR-CLIP utilizes a photoactivatable nucleoside for more efficient crosslinking. We present an approach centered on the novel PARalyzer tool for mapping high-confidence sites from PAR-CLIP deep-sequencing data. We show that PARalyzer delineates sites with a high signal-to-noise ratio. Motif finding identifies the sequence preferences of RNA-binding proteins as well as seed-matches for highly expressed microRNAs when profiling Argonaute proteins. Our study describes tailored analytical methods and provides guidelines for future efforts to utilize high-throughput sequencing in RNA biology. PARalyzer is available at http www.genome.duke.edu labs ohler research PARalyzer . Background RNA binding proteins RBPs play important roles in the life cycle of a transcript from its nascence by RNA polymerase until its decay by RNases. All steps of RNA processing and function including splicing nuclear export localization stability and small RNA-mediated regulation are controlled by different RBPs and ribonucleoproteins 1 . The identification of which RBPs or ribonucleoproteins interact with which transcripts how they interact and where the interaction occurs has been the focus of many studies. Recent advancements in high-throughput genomic technologies have resulted in profiles of transcriptome-wide RNA-protein interactions in vivo. Two of the most established methods for the investigation of these interactions are RIP-Chip 2 or RIP-seq 3 4 and crosslinking and immunoprecipitation CLIP 5 . RIPChip was the .
