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 language | English (US) |
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Article number | R79 |
Journal | Genome biology |
Volume | 12 |
Issue number | 8 |
DOIs | |
State | Published - Aug 18 2011 |
Funding
We thank Thomas Tuschl, Markus Hafner and Bryan Cullen for their insightful and helpful feedback in regards to the analysis of the PAR-CLIP data as well as their assistance in editing the manuscript. The authors acknowledge support from the National Science Foundation (MCB-0822033) and the National Institutes of Health (R01 DA030086, K99 CA137860, T32 CA009111).
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Genetics
- Cell Biology