Capr: Revealing structural specificities of rna-binding protein target recognition using clip-seq data

Tsukasa Fukunaga; Haruka Ozaki; Goro Terai; Kiyoshi Asai; Wataru Iwasaki; Hisanori Kiryu

doi:10.1186/gb-2014-15-1-r16

Capr: Revealing structural specificities of rna-binding protein target recognition using clip-seq data

Tsukasa Fukunaga^*, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki, Hisanori Kiryu

^*Corresponding author for this work

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

55 Citations (Scopus)

Abstract

RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible to exhaustively identify RNA fragments that bind to RBPs. However, no efficient bioinformatics method exists to reveal the structural specificities of RBP-RNA interactions using these data. We present CapR, an efficient algorithm that calculates the probability that each RNA base position is located within each secondary structural context. Using CapR, we demonstrate that several RBPs bind to their target RNA molecules under specific structural contexts.

Original language	English
Article number	R16
Journal	Genome Biology
Volume	15
Issue number	1
DOIs	https://doi.org/10.1186/gb-2014-15-1-r16
Publication status	Published - 2014
Externally published	Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/gb-2014-15-1-r16

Cite this

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title = "Capr: Revealing structural specificities of rna-binding protein target recognition using clip-seq data",

abstract = "RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible to exhaustively identify RNA fragments that bind to RBPs. However, no efficient bioinformatics method exists to reveal the structural specificities of RBP-RNA interactions using these data. We present CapR, an efficient algorithm that calculates the probability that each RNA base position is located within each secondary structural context. Using CapR, we demonstrate that several RBPs bind to their target RNA molecules under specific structural contexts.",

author = "Tsukasa Fukunaga and Haruka Ozaki and Goro Terai and Kiyoshi Asai and Wataru Iwasaki and Hisanori Kiryu",

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AU - Terai, Goro

AU - Asai, Kiyoshi

AU - Iwasaki, Wataru

AU - Kiryu, Hisanori

N1 - Funding Information: The authors thank their research group colleagues for assistance in this research. This study was supported by JSPS KAKENHI Grant Numbers 22240031 (to KA and HK), 23710231 (to WI) and 25134701 and 25870190 (to HK). The computations were performed using the supercomputing facilities at the Human Genome Center, University of Tokyo [53]. Publisher Copyright: © 2014 Fukunaga et al.

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N2 - RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible to exhaustively identify RNA fragments that bind to RBPs. However, no efficient bioinformatics method exists to reveal the structural specificities of RBP-RNA interactions using these data. We present CapR, an efficient algorithm that calculates the probability that each RNA base position is located within each secondary structural context. Using CapR, we demonstrate that several RBPs bind to their target RNA molecules under specific structural contexts.

AB - RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible to exhaustively identify RNA fragments that bind to RBPs. However, no efficient bioinformatics method exists to reveal the structural specificities of RBP-RNA interactions using these data. We present CapR, an efficient algorithm that calculates the probability that each RNA base position is located within each secondary structural context. Using CapR, we demonstrate that several RBPs bind to their target RNA molecules under specific structural contexts.

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Capr: Revealing structural specificities of rna-binding protein target recognition using clip-seq data

Abstract

ASJC Scopus subject areas

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