Background: The tRNA-derived fragments (tRFs) are 14–40 nucleotides, small non-coding RNAs from specific tRNA cleavages, and they have key regulatory functions in many biological processes. Many studies showed that tRFs are associated with Argonaute complexes and inhibit gene expression in the same manner as miRNAs. However, there are currently no tools to accurately predict tRF target genes.
Methods: We used tRF-mRNA pairs identified by crosslinking, ligation, and sequencing of hybrids (CLASH) and covalent ligation of endogenous Argonaute-bound RNAs (CLEAR)-CLIP to assess features that may participate in tRF targeting, including sequence context of each individual site and tRF-mRNA interactions. We applied genetic algorithm (GA) to select key features and support vector machine (SVM) to construct tRF predicting models.
Results: We first identified features that globally influenced tRF targeting. Among them, the most significant ones were minimum free folding energy (MFE), position 8 match, number of bases paired in tRF-mRNA duplex, and length of tRF, which were consistent with previous findings. We built the model with the area under the receiver operating characteristic (ROC) curve (AUC) = 0.980 (0.977-0.983) in the training process and AUC = 0.847 (0.83-0.861) in the test process. The model was applied to all the sites with perfect Watson-Crick complementarity to the seed in the 3'-UTR of human genome. Seven of nine target / non-target genes of tRFs confirmed by reporter assay were predicted.
Conclusions: Predictions can be obtained online, tRFTar, freely available at http://trftar.cmuzhenninglab.org:3838/tar/, which is the first tool to predict targets of tRFs in human with a user-friendly interface.