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PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

Authors

  • D.L. Corcoran
  • S. Georgiev
  • N. Mukherjee
  • E. Gottwein
  • R.L. Skalsky
  • J.D. Keene
  • U. Ohler

Journal

  • Genome Biology

Citation

  • Genome Biol 12 (8): R79

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/.


DOI

doi:10.1186/gb-2011-12-8-r79