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

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

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

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

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

Research output: Contribution to journal › Article › peer-review

271 Scopus citations

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)
Article number	R79
Journal	Genome biology
Volume	12
Issue number	8
DOIs	https://doi.org/10.1186/gb-2011-12-8-r79
State	Published - Aug 18 2011
Externally published	Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/gb-2011-12-8-r79

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@article{7528242b991a4d558df0f558323d2a77,

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.",

author = "Corcoran, {David L.} and Stoyan Georgiev and Neelanjan Mukherjee and Eva Gottwein and Skalsky, {Rebecca L.} and Keene, {Jack D.} and Uwe Ohler",

note = "Funding Information: 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).",

year = "2011",

month = aug,

day = "18",

doi = "10.1186/gb-2011-12-8-r79",

language = "English (US)",

volume = "12",

journal = "Genome biology",

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T2 - Definition of RNA binding sites from PAR-CLIP short-read sequence data

AU - Corcoran, David L.

AU - Georgiev, Stoyan

AU - Mukherjee, Neelanjan

AU - Gottwein, Eva

AU - Skalsky, Rebecca L.

AU - Keene, Jack D.

AU - Ohler, Uwe

N1 - Funding Information: 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).

PY - 2011/8/18

Y1 - 2011/8/18

N2 - 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.

AB - 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.

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JO - Genome biology

JF - Genome biology

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ER -

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

Abstract

ASJC Scopus subject areas

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