A tRNA fragment, 5′-tiRNAVal, suppresses the Wnt/β-catenin signaling pathway by targeting FZD3 in breast cancer

Mo, Dongping; Jiang, Pan; Yang, Yining; Mao, Xuelian; Tan, Xiaojie; Tang, Xun; Da, Wang; Li, Bing; Wang, Xiaoming; Tang, Li; Yan, Feng

doi:10.1016/j.canlet.2019.05.007

Cited by 122 publications

(146 citation statements)

References 46 publications

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“…Third, the hg38 sequence information of tRFs is not updated in public databases. Additionally, tiRNAs and tRFs not included in tRFdb, such as 5'-tiRNAVal and tRF5-Glu, which have been reported to repress mRNA by seed pairing (18,43,44), were not considered in this version.…”

Section: Discussionmentioning

confidence: 99%

tRFTar: predicting the targets of tRNA-derived fragments

Xiao

Gao

Huang

et al. 2020

Preprint

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Background: tRNA-derived fragments (tRFs) are 14–40-nucleotide-long, small non-coding RNAs derived from specific tRNA cleavage events with key regulatory functions in many biological processes. Many studies have shown that tRFs are associated with Argonaute (AGO) complexes and inhibit gene expression in the same manner as miRNAs. However, there are currently no tools for accurately predicting tRF target genes. Methods: We used tRF-mRNA pairs identified by crosslinking, ligation, and sequencing of hybrids (CLASH) and covalent ligation of endogenous AGO-bound RNAs (CLEAR)-CLIP to assess features that may participate in tRF targeting, including the sequence context of each site and tRF-mRNA interactions. We applied genetic algorithm (GA) to select key features and support vector machine (SVM) to construct tRF prediction models. Results: We first identified features that globally influenced tRF targeting. Among these features, the most significant were the minimum free folding energy (MFE), position 8 match, number of bases paired in the tRF-mRNA duplex, and length of the tRF, which were consistent with previous findings. Our constructed model yielded an area under the receiver operating characteristic (ROC) curve (AUC) = 0.980 (0.977-0.983) in the training process and an 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' untranslated region (3'-UTR) of the human genome. Seven of nine target/nontarget 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 humans with a user-friendly interface.

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Section: Discussionmentioning

confidence: 99%

tRFTar: predicting the targets of tRNA-derived fragments

Xiao

Gao

Huang

et al. 2020

Preprint

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“…In summary, tRFs and tiRNAs have important roles in gene expression, gene translation, and the development and progression of various DT tumors (17). They affect tumor cell proliferation, migration and invasion (48,57). To date, the origin and function of tRFs and tiRNAs remain to be fully elucidated, and their roles in DT tumor progression also require further investigation.…”

Section: Summary and Future Directionsmentioning

confidence: 99%

The role of Transfer RNA-Derived Small RNAs (tsRNAs) in Digestive System Tumors

Wang¹,

Yan²,

Xu³

et al. 2020

J. Cancer

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Transfer RNA-derived small RNA(tsRNA) is a type of non-coding tRNA undergoing cleavage by specific nucleases such as Dicer. TsRNAs comprise of tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs). Based on the splicing site within the tRNA, tRFs can be classified into tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF. TiRNAs can be classified into 5′-tiRNA and 3′-tiRNA. Both tRFs and tiRNAs have important roles in carcinogenesis, especially cancer of digestive system. TRFs and tiRNAs can promote cell proliferation and cell cycle progression by regulating the expression of oncogenes, combining with RNA binding proteins such as Y-box binding protein 1 (YBX1) to prevent transcription. Despite many reviews on the basic biological function of tRFs and tiRNAs, few have described their correlation with tumors especially gastrointestinal tumor. This review focused on the relationship of tRFs and tiRNAs with the biological behavior, clinicopathological characteristics, diagnosis, treatment and prognosis of digestive system tumors, and would provide novel insights for the early detection and treatment of digestive system tumors.

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“…Although most tiRNAs are upregulated in tumor tissues and cells, there are some studies reporting that a few tiRNAs were downregulated, which may serve as novel biomarkers (Zhu et al, ) and suppress cancer progression (Mo et al, ). The previous study showed 5′‐tiRNA‐Val facilitated tumor metastasis of CRC.…”

Section: Role Of Tirnas In Cancermentioning

confidence: 99%