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

David L. Corcoran, Stoyan Georgiev, Neelanjan Mukherjee, Eva Gottwein, Rebecca Skalsky, Jack D. Keene, Uwe Ohler

Research output: Contribution to journalArticle

204 Citations (Scopus)

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.

Original languageEnglish (US)
Article numberR79
JournalGenome Biology
Volume12
Issue number8
DOIs
StatePublished - Aug 18 2011
Externally publishedYes

Fingerprint

photosynthetically active radiation
crosslinking
Immunoprecipitation
RNA
High-Throughput Nucleotide Sequencing
binding sites
Binding Sites
protein
Argonaute Proteins
RNA-Binding Proteins
Signal-To-Noise Ratio
MicroRNAs
Transcriptome
Nucleosides
signal-to-noise ratio
RNA-binding proteins
nucleosides
analytical method
Seeds
microRNA

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Corcoran, D. L., Georgiev, S., Mukherjee, N., Gottwein, E., Skalsky, R., Keene, J. D., & Ohler, U. (2011). PARalyzer: Definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biology, 12(8), [R79]. https://doi.org/10.1186/gb-2011-12-8-r79

PARalyzer : Definition of RNA binding sites from PAR-CLIP short-read sequence data. / Corcoran, David L.; Georgiev, Stoyan; Mukherjee, Neelanjan; Gottwein, Eva; Skalsky, Rebecca; Keene, Jack D.; Ohler, Uwe.

In: Genome Biology, Vol. 12, No. 8, R79, 18.08.2011.

Research output: Contribution to journalArticle

Corcoran, DL, Georgiev, S, Mukherjee, N, Gottwein, E, Skalsky, R, Keene, JD & Ohler, U 2011, 'PARalyzer: Definition of RNA binding sites from PAR-CLIP short-read sequence data', Genome Biology, vol. 12, no. 8, R79. https://doi.org/10.1186/gb-2011-12-8-r79
Corcoran, David L. ; Georgiev, Stoyan ; Mukherjee, Neelanjan ; Gottwein, Eva ; Skalsky, Rebecca ; Keene, Jack D. ; Ohler, Uwe. / PARalyzer : Definition of RNA binding sites from PAR-CLIP short-read sequence data. In: Genome Biology. 2011 ; Vol. 12, No. 8.
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