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Nucleic Acids Res
2021 Jan 08;49D1:D254-D260. doi: 10.1093/nar/gkaa831.
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tRFtarget: a database for transfer RNA-derived fragment targets.
Li N
,
Shan N
,
Lu L
,
Wang Z
.
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Transfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs and play important roles in biological and physiological processes. Prediction of tRF target genes and binding sites is crucial in understanding the biological functions of tRFs in the molecular mechanisms of human diseases. We developed a publicly accessible web-based database, tRFtarget (http://trftarget.net), for tRF target prediction. It contains the computationally predicted interactions between tRFs and mRNA transcripts using the two state-of-the-art prediction tools RNAhybrid and IntaRNA, including location of the binding sites on the target, the binding region, and free energy of the binding stability with graphic illustration. tRFtarget covers 936 tRFs and 135 thousand predicted targets in eight species. It allows researchers to search either target genes by tRF IDs or tRFs by gene symbols/transcript names. We also integrated the manually curated experimental evidence of the predicted interactions into the database. Furthermore, we provided a convenient link to the DAVID® web server to perform downstream functional pathway analysis and gene ontology annotation on the predicted target genes. This database provides useful information for the scientific community to experimentally validate tRF target genes and facilitate the investigation of the molecular functions and mechanisms of tRFs.
Figure 1. Illustration of the five categories of tRFs. tRF-1 or tsRNA is generated from the 3′ end of the precursor tRNA, whereas tRF-3, tRF-5, tiR and tRF-2 are derived from different parts of the mature tRNA. tRF, transfer RNA-derived fragment. tsRNA, tRNA-derived small RNA. tiR, stress-induced tRNA. ANG, angiogenin.
Figure 2. Flow diagram of constructing tRFtarget database. tRFtarget can be retrieved through web service. tRF, transfer RNA-derived fragment.
Table 1. Summary statistics of tRFtarget database
Figure 3. Illustration of the interaction structures of tRF-3–mRNA chimeras from CLASH and the corresponding binding sites in tRFtarget. The interaction structures of tRF-3–mRNA chimeras were inferred by mfold RNA Folding Form using default settings, and the reads of the chimeras and the delta G values (dG) given by mfold are shown at the right. The binding sites in tRFtarget are shown below the mfold prediction. The transcript names are shown at the left, and the prediction algorithms and free energy (FE) are shown at the right. Black represents non-interaction sequences; blue represents interaction sequences of tRFs, green and red represent paired and non-paired bases of mRNA, respectively. CLASH, cross-linking, ligation and sequencing of hybrids.
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