title: PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.
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/.
authors.affiliation: Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Corcoran
authors.forename: Stoyan
authors.initials: S
authors.lastname: Georgiev
authors.forename: Neelanjan
authors.initials: N
authors.lastname: Mukherjee
authors.forename: Eva
authors.initials: E
authors.lastname: Gottwein
authors.forename: Rebecca L
authors.initials: RL
authors.lastname: Skalsky
authors.forename: Jack D
authors.initials: JD
authors.lastname: Keene
authors.forename: Uwe
authors.initials: U
authors.lastname: Ohler
mesh_terms: D060565:Argonaute Proteins / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics*; D030541:Databases, Genetic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D047468:Immunoprecipitation / Q000295:instrumentation / Q000379:methods*; D016014:Linear Models; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D012313:RNA / Q000302:isolation & purification* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D059629:Signal-To-Noise Ratio; D059467:Transcriptome
chemical_list: D060565:Argonaute Proteins; D035683:MicroRNAs; D012313:RNA