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

By David L. Corcoran, Stoyan Georgiev, Neelanjan Mukherjee, E. Gottwein, Rebecca L. Skalsky, Jack D. Keene, Uwe Ohler. Genome Biology, 2011

361 citations recorded by the source corpus.

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/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b7e4e451ef8c49bafbe167bbb9525ea140146aff

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In Molecular Biology

Citations in the corpus

Revealing protein–lncRNA interaction (2015, methodology): “PARalyzer [67], Piranha [68], wavClusteR [69], RIPSeeker [70], MiClip [71], PIPE-CLIP [72] and the Pyicoclip module of the Pyicoteo toolkit (previously called Pyicos) [73].”
YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs (2017, methodology): “PAR-CLIP peaks were called using PARalyzer v.1.5 (Corcoran et al., 2011) with default parameters.”
N6-methyladenosine Modulates Messenger RNA Translation Efficiency (2015, neutral): “1 (Corcoran et al., 2011) with default settings.”
Expanded identification and characterization of mammalian circular RNAs (2014, methodology): “Using data from high-throughput in vivo crosslinking experiments, which identified clusters of AGO2crosslinking sites that indicated AGO2 binding [24-26], we compared the density of AGO2-crosslinking clusters within exons that can form circRNAs to the density within their neighboring linear exons.”
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data (2013, neutral): “1 (23), other CLIP-identiﬁed binding sites clusters/peaks were used directly.”
A census of human RNA-binding proteins (2014, methodology): “To extract the binding regions, sequence reads were grouped by PARalyzer, which identifies regions with locally enriched T>C conversions in PAR-CLIP reads over background mismatch errors (Corcoran et al., 2011).”
m6A-dependent regulation of messenger RNA stability (2013, neutral): “1 with default settings 39 ; (4) for ribosome profiling, only genes with RPKM>1 were used for analysis and the change fold was calculated as log 2 (siYTHDF2/ siControl); (5) for mRNA lifetime profiling: RKPM were converted to attomole by linear-fitting of the RNA spike-in.”
RBPmap: a web server for mapping binding sites of RNA-binding proteins (2014, methodology): “The PAR-CLIP data was sorted using the PARalyzer tool (35), employing the standard protocol for ranking PAR-CLIP data based on the percent of C to T conversion centered at the anchor site and further normalized for RNA abundance.”