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- Title
PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks.
- Authors
Lin, Jianan; Zhang, Yuping; Frankel, Wayne N.; Ouyang, Zhengqing
- Abstract
RNA-protein interaction plays important roles in post-transcriptional regulation. Recent advancements in cross-linking and immunoprecipitation followed by sequencing (CLIP-seq) technologies make it possible to detect the binding peaks of a given RNA binding protein (RBP) at transcriptome scale. However, it is still challenging to predict the functional consequences of RBP binding peaks. In this study, we propose the Protein-RNA Association Strength (PRAS), which integrates the intensities and positions of the binding peaks of RBPs for functional mRNA targets prediction. We illustrate the superiority of PRAS over existing approaches on predicting the functional targets of two related but divergent CELF (CUGBP, ELAV-like factor) RBPs in mouse brain and muscle. We also demonstrate the potential of PRAS for wide adoption by applying it to the enhanced CLIP-seq (eCLIP) datasets of 37 RNA decay related RBPs in two human cell lines. PRAS can be utilized to investigate any RBPs with available CLIP-seq peaks. PRAS is freely available at .
- Subjects
RNA-binding proteins; NON-coding RNA; RNA-protein interactions; PHYSICAL &; theoretical chemistry
- Publication
PLoS Computational Biology, 2019, Vol 15, Issue 8, p1
- ISSN
1553-734X
- Publication type
Article
- DOI
10.1371/journal.pcbi.1007227