tRFdb

tRFdb catalogs and predicts targets of transfer RNA-derived fragments (tRFs) to support analysis of their roles in gene regulation and disease.

Key Features:

• Catalog content: Relational database of transfer RNA-derived fragments (tRFs) characterized as 14–32 nucleotides originating from mature or precursor tRNAs and distinct from stress-induced fragments generated by anti-codon loop cleavage.
• Coverage and predictions: Contains 936 distinct tRFs across eight species and predicts over 135,000 potential tRF–target interactions.
• Target prediction: Predicts tRF–mRNA interactions using RNAhybrid and IntaRNA.
• Prediction outputs: Reports binding-site locations, the specific regions involved in binding, and predicted binding free energies, with graphical representation of interactions.
• Experimental evidence: Incorporates manually curated experimental evidence supporting predicted interactions.
• Functional analysis integration: Links predicted target genes to the DAVID web server for downstream functional pathway analysis and gene ontology annotation.

Scientific Applications:

• Functional role analysis: Analysis of tRF involvement in cell-cycle progression and regulation of RNA-induced silencing complex (RISC) dynamics.
• Mechanistic studies in disease: Elucidation of molecular mechanisms in human diseases through identification of putative tRF targets and binding sites.
• Experimental prioritization and annotation: Prioritization of candidate targets for experimental validation using predicted binding energies and curated evidence, and facilitation of pathway and GO annotation via DAVID.

Methodology:

tRF–mRNA interactions were predicted using RNAhybrid and IntaRNA, reporting binding-site locations, binding regions, and binding free energies, and predicted targets were linked to DAVID for pathway and gene ontology analysis.