Document Type

Article

Publication Date

8-19-2019

Keywords

JGM

JAX Source

PLoS Comput Biol 2019 Aug 19; 15(8):e1007227

Volume

15

Issue

8

First Page

1007227

Last Page

1007227

ISSN

1553-7358

PMID

31425505

DOI

https://doi.org/10.1371/journal.pcbi.1007227

Grant

CA034196,GM124998, Pharmaceutical Research and Manufacturers of America Foundation

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 http://ouyanglab.jax.org/pras/.

Comments

Open access under the terms of the Creative Commons Attribution License.

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