Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets

Abstract

tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequencing libraries of immunoprecipitated Argonaute proteins (AGO-IP) and bioinformatics approaches, we identified the Arabidopsis thaliana AGO-IP tRFs. Moreover, using three degradome deep sequencing libraries, we identified four putative tRF targets. The expression pattern of tRFs, based on deep sequencing data, was also analyzed under abiotic and biotic stresses. The results obtained here represent a useful starting point for future studies on tRFs in plants.

Figure 1

tRNA-derived RNA fragments (tRFs) from Arabidopsis thaliana associated with AGO. A) Schematic representation of ArgTCG tRNA showing the 5' tRF in green, the 3' CCA tRF in red and the anti-codon in yellow. The D and TΨC loops are also shown. B) tRF class diversity of AGO-associated tRFs and unassociated ones. C) Length diversity of AGO-associated tRFs and unassociated ones. D) tRF length diversity of AGO1, 2, 4 and 7 IP deep sequencing libraries. E) Logo representation of the first 20 nucleotides of tRNAs, AGO1-IP tRFs, AGO2-IP tRFs, AGO4-IP tRFs, AGO7-IP tRFs and the A. thaliana microRNAs (miRBase v. 18). The black arrowheads indicate the first nucleotide at the 5' end. F) Expression pattern of AlaAGC, ArgCCT, ArgTCG and GlyTCC 5' tRFs in control (untreated), drought (40-50% relative water content), cold (5°C for 24 hours), and salt (200 mM of NaCl for 5 hours) conditions. The expression patterns are shown in reads per million, where the tRF frequency was divided by the total number of reads and multiplied by one million. G) Expression pattern of AlaAGC, ArgCCT, ArgTCG and GlyTCC 5' tRFs in biotic stress. The expression patterns are also shown in reads per million. The leaves were inoculated with mock solution (10 mM MgCl₂) or Pseudomonas syringae (2 x 107 cfu/ml). The inoculated leaves were collected 14 hours after inoculation.