Abstract
BackgroundTransfer RNA (tRNA)-derived fragments (tRFs) have been widely identified in nature, functioning in diverse biological and pathological situations. Yet, the presence of these small RNAs in Plasmodium spp. remains unknown. Systematic identification and characterization of tRFs is therefore highly needed to understand further their roles in Plasmodium parasites, particularly in the virulent Plasmodium falciparum parasite.ResultsGenome-wide small RNAs with sizes ranging from 18–30 nucleotides from P. falciparum were deep-sequenced via Illumina HiSeq 2000 technology. In-depth analysis revealed the presence of a vast number of small RNAs originating from tRNA-coding genes, responsible for 22.4% of the total reads as the second predominant group. Three P. falciparum-derived tRF types (ptRFs) were identified as 5'ptRFs, mid-ptRFs and 3'ptRFs. The majority (90%) of ptRFs were derived from tRNAs that coded eight amino acids: Pro, Phe, Asn, Gly, Cys, Gln, His and Ala. Stem-loop reverse transcription polymerase chain reaction further confirmed the presence of tRFs in the blood stages of P. falciparum. Four new motifs with an enriched G/C feature were determined at cleavage sites that might guide the generation of ptRFs.ConclusionsTo our knowledge, this is the first report of a genome-wide investigation of ptRFs from Plasmodium species. The identification of ptRFs reveals a complex small RNA system manipulated by the malaria parasite, and might promote research on the function of tRFs in the pathogenesis of Plasmodium infections.
Highlights
Transfer Ribonucleic acid (RNA)-derived fragments have been widely identified in nature, functioning in diverse biological and pathological situations
Within the same range of 18–30 nt, small RNAs in T. gondii reached peaks at 21 and 26 nt in two different strains, in correspondence to 18.92% and 18.13% of unique small RNAs, respectively [31]. This implied that the features of P. falciparum small RNAs seemed to be different from the canonical 21–23 nt miRNAs. These P. falciparum small RNAs were derived from mRNAs, ribosomal RNAs, Transfer RNA (tRNA), small nuclear RNA/small nucleolar RNAs, previously reported non-coding RNAs, as well as some unannotated RNAs (Table 1, Fig. 1b)
We found that the tRNA-derived small RNAs were abundantly presented in the library as the second predominant group, which represented 22.4% of the total reads (Fig. 1b)
Summary
Transfer RNA (tRNA)-derived fragments (tRFs) have been widely identified in nature, functioning in diverse biological and pathological situations. Other than the three major types of small RNAs including microRNAs (miRNAs), endogenous small interference RNAs (endo-siRNAs) and PiWi-interacting RNAs (piRNAs) [6, 7], the advance in deep sequencing technology has unveiled new classes of small RNAs with novel features and functions. One such class is those derived from transfer RNAs (tRNAs), commonly referred to as tRFs (tRNA-derived RNA fragments), which were once mis-annotated as miRNAs [8, 9].
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