Abstract
BackgroundIn a deep sequencing analysis of small RNAs prepared from a living fossil, the tadpole shrimp Triops cancriformis, a 32-nt small RNA was specifically detected in the adult stage. A nucleotide sequence comparison between the 32-nt small RNA and predicted tRNA sequences in the draft nuclear genomic DNA showed that the small RNA was derived from tRNAGly(GCC). To determine the overall features of the tRNA-derived fragments (tRFs) of T. cancriformis, the small RNA sequences in each of the six developmental stages (egg, 1st − 4th instar larvae, and adult) were compared with the mitochondrial and nuclear tRNA sequences.ResultsWe found that the tRFs were derived from mitochondrial and nuclear tRNAs corresponding to 16 and 39 anticodons, respectively. The total read number of nuclear tRFs was approximately 400 times larger than the number of mitochondrial tRFs. Interestingly, the main regions in each parental tRNA from which these tRFs were derived differed, depending on the parental anticodon. Mitochondrial tRFSer(GCU)s were abundantly produced from the 5’ half regions of the parental tRNA, whereas mitochondrial tRFVal(UAC)s were mainly produced from the 3’ end regions. Highly abundant nuclear tRFs, tRFGly(GCC)s, tRFGly(CCC)s, tRFGlu(CUC)s, and tRFLys(CUU)s were derived from the 5’ half regions of the parental tRNAs. Further analysis of the tRF read counts in the individual developmental stages suggested that the expression of mitochondrial and nuclear tRFs differed during the six stages. Based on these data, we precisely summarized the positions of the tRFs in their parental tRNAs and their expression changes during development.ConclusionsOur results reveal the entire dynamics of the tRFs from both the nuclear and mitochondrial genomes of T. cancriformis and indicate that the majority of tRFs in the cell are derived from nuclear tRNAs. This study provides the first examples of developmentally expressed mitochondrial tRFs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0245-5) contains supplementary material, which is available to authorized users.
Highlights
In a deep sequencing analysis of small RNAs prepared from a living fossil, the tadpole shrimp Triops cancriformis, a 32-nt small RNA was detected in the adult stage
This study provides the first examples of developmentally expressed mitochondrial transfer RNA (tRNA)-derived fragment (tRF)
A nucleotide sequence comparison of the 32-nt small RNA reads and predicted tRNA sequences in the nuclear genomic DNA contig sequences revealed that 84.6 % of the 32-nt small RNAs were derived from tRNAGly(GCC)
Summary
In a deep sequencing analysis of small RNAs prepared from a living fossil, the tadpole shrimp Triops cancriformis, a 32-nt small RNA was detected in the adult stage. It is well known that transfer RNAs (tRNAs) are noncoding short RNAs of 70–100 nucleotides (nt) and are involved in the translation process as adapter molecules between the amino acids and the corresponding codons in the template mRNAs. In the last 10 years, several groups, including our own, have reported that particular tRNA genes, especially in the Archaea and primitive Eukaryota, are disrupted in unique ways: multiple-intron-. (d) some tRFs are bound to Argonaute/Piwi proteins, well-known components of the RNA-induced silencing complex [11, 17, 19]. The tRFs have their own specific functions (including in RNA silencing), other than as parts of adapter molecules in translation
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