AbstractEmerging evidence suggests that PIWI-interacting RNAs (piRNAs) are one of the most influential small non-coding RNAs (ncRNAs) that regulate RNA silencing. piRNA and PIWI proteins have been confirmed for disease diagnosis and treatment as novel biomarkers due to its abnormal expression in various cancers. However, the current research is not strong enough to further clarify the functions of piRNA in cancer and its underlying mechanism. Therefore, how to provide large-scale and serious piRNA candidates for biological research has grown up to be a pressing issue. The main motivation of this work is tantamount to fill the gap in research on large-scale prediction of disease-related piRNAs. In this study, a novel computational model based on the structural perturbation method is proposed, called SPRDA. In detail, the duplex network is constructed based on the piRNA similarity network and disease similarity network extracted from piRNA sequence information, Gaussian interaction profile kernel similarity information and gene-disease association information. The structural perturbation method is then used to predict the potential associations on the duplex network, which is more predictive than other network structures in terms of structural consistency. In the five-fold cross-validation, SPRDA shows high performance on the benchmark dataset piRDisease, with an AUC of 0.9529. Furthermore, the predictive performance of SPRDA for 10 diseases shows the robustness of the proposed method. Overall, the proposed approach can provide unique insights into the pathogenesis of the disease and will advance the field of oncology diagnosis and treatment.

Argonaute proteins are widespread in prokaryotes and eukaryotes. Most prokaryotic Argonaute proteins (pAgos) use 5'P-gDNA to target complementary DNA. However, more and more studies on the properties of pAgos make their functions more diversified.Previously reported pAgos only possess several forms of high activity in all eight cleavage patterns, which limits their practical applications. Here, we described a unique pAgo from Marinitoga hydrogenitolerans (MhAgo) with eight cleavage activities. MhAgo can utilize all four types of guides (5'OH-gDNA, 5'P-gDNA, 5'OH-gRNA, and 5'P-gRNA) for ssDNA and RNA cleavage. Further studies demonstrated that MhAgo had high activities with 16-21 nt guides and no obvious preferences for the 5'-end nucleotides of 5'OH-guides. Unexpectedly, MhAgo had different preferences for the 5'-end nucleotides of 5'P-guides depending on the types of targets. Although the specificity of MhAgo was related to the types of guides, single mismatches in the central and 3'-supplementary regions of guides greatly reduced the cleavage efficiency. Additionally, the electrophoretic mobility shift assay (EMSA) demonstrated MhAgo had the weakest affinity for 5'P-gRNA:tRNA duplex, which was consistent with its cleavage efficiency. In conclusion, MhAgo is highly active under a wide range of conditions and can be used for programmable endonucleolytic cleavage of both ssDNA and RNA substrates. The abundant biochemical characteristics of MhAgo broaden our understanding of pAgos and expand the potential application in nucleic acids manipulations.