Fig. 6.

Schistosomula release tRNA-derived small RNAs (tsRNA). Reads were mapped against the S. mansoni tRNA database depleted of mitochondrial and pseudo-tRNAs available from geneDB (34) and, using an in-house script, were characterized as 5′ or 3′ tsRNAs. (a) Secondary structure of smtRNA-SeC depicting characteristic cloverleaf shape composed of D-, anticodon, variable and T-loops. Below, the coverage of RNA-seq reads mapping to smtRNA-SeC (85 nucleotides) are quantified to give an example of how 5′ and 3′ tsRNAs were identified for all tsRNAs (using our processing criteria, no full-length tRNAs were identified in our study). Dashed and solid lines represent the reads mapping to smtRNA-SeC and illustrate the sequential steps (Filter 1 and Filter 2) employed by our in-house script as outlined in the Materials and methods. The arrow represents Position 35 (U in bold), which is the terminal nucleotide (initiating from the 5′ end) used to define 5′ tsRNAs (which happens to be in the anticodon loop for smtRNA-SeC). To define 3′ tsRNAs, a maximal length of 50 nt (also represented by the black arrow) initiating from the 3′ tRNA end was used. Clear read peaks can be visualized mapping to both 5′ and 3′ ends of tRNA-SeC. (b) Bar chart represents the tsRNAs (log₂ normalized read counts) found in EV-enriched (black bars) or EV-depleted (grey bars) supernatant fractions. G1–G6 represent tsRNA groups displaying specific associations (see text for details). (c) Stacked histogram representation of 3′ tsRNAs derived from precursor tRNAs (lacking the 3′ CCA trinucleotide motif; white or light grey bars, EV-enriched and EV-depleted samples, respectively) or mature tRNAs (containing the 3′ CCA trinucleotide motif; black or dark grey bars, EV-enriched and EV-depleted samples, respectively).