Identification of Functional piRNAs Using a Convolutional Neural Network

Piwi-interacting RNAs (piRNAs) are a distinct sub-class of small non-coding RNAs that are mainly responsible for germline stem cell maintenance, gene stability, and maintaining genome integrity by repression of transposable elements. piRNAs are also expressed aberrantly and associated with various kinds of cancers. To identify piRNAs and their role in guiding target mRNA deadenylation, the currently available computational methods require urgent improvements in performance. To facilitate this, we propose a robust predictor based on a lightweight and simplified deep learning architecture using a convolutional neural network (CNN) to extract significant features from raw RNA sequences without the need for more customized features. The proposed model's performance is comprehensively evaluated using k-fold cross-validation on a benchmark dataset. The proposed model significantly outperforms existing computational methods in the prediction of piRNAs and their role in target mRNA deadenylation. In addition, a user-friendly and publicly-accessible web server is available at http://nsclbio.jbnu.ac.kr/tools/2S-piRCNN/.