Prediction of CRISPR/Cas9 single guide RNA cleavage efficiency and specificity by attention-based convolutional neural networks

CRISPR/Cas9 is a preferred genome editing tool and has been widely adapted to ranges of disciplines, from molecular biology to gene therapy. A key prerequisite for the success of CRISPR/Cas9 is its capacity to distinguish between single guide RNAs (sgRNAs) on target and homologous off-target sites. Thus, optimized design of sgRNAs by maximizing their on-target activity and minimizing their potential off-target mutations are crucial concerns for this system. Several deep learning models have been developed for comprehensive understanding of sgRNA cleavage efficacy and specificity. Although the proposed methods yield the performance results by automatically learning a suitable representation from the input data, there is still room for the improvement of accuracy and interpretability. Here, we propose novel interpretable attention-based convolutional neural networks, namely CRISPR-ONT and CRISPR-OFFT, for the prediction of CRISPR/Cas9 sgRNA on- and off-target activities, respectively. Experimental tests on public datasets demonstrate that our models significantly yield satisfactory results in terms of accuracy and interpretability. Our findings contribute to the understanding of how RNA-guide Cas9 nucleases scan the mammalian genome. Data and source codes are available at https://github.com/Peppags/CRISPRont-CRISPRofft.