Proteins that bind to RNA, known as RNA-binding proteins or RPBs, have a wide variety of roles in regulating genes, and thus represent important potential drug targets for diseases such as neurological disorders and cancers. Recent techniques, including CLIP-seq, enable measuring the positions and binding intensity of RBPs. In an important next step, a Jackson Laboratory (JAX) research team led by Zhengqing Ouyang has developed a new computational analysis tool, Protein-RNA Association Strength (PRAS), to enable researchers to predict the functional consequences of RBP binding peaks.
In a paper published in PLoS Computational Biology, Ouyang and colleagues used PRAS to predict the functional targets of two RBPs related to seizures and myotonic dystrophy, respectively, in mouse brain and muscle. They also applied the tool to the ENCODE eCLIP datasets of 37 RBPs related to RNA decay in two human cancer cell lines.
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Funding for the research was provided by the Pharmaceutical Research and Manufacturers of America Foundation, the National Institute of General Medical Sciences grant R35GM124998, the National Institute of Neurological Disorders and Stroke grant R01NS091118, and the University of Connecticut Faculty Research Excellence Program Award.
Lin et al.: PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks. PLoS Computational Biology, August 19, 2019, https://doi.org/10.1371/journal.pcbi.1007227