Abstract
BackgroundDevelopment of sequencing technologies and supporting computation enable discovery of small RNA molecules that previously escaped detection or were ignored due to low count numbers. While the focus in the analysis of small RNA libraries has been primarily on microRNAs (miRNAs), recent studies have reported findings of fragments of transfer RNAs (tRFs) across a range of organisms.ResultsHere we describe Drosophila melanogaster tRFs, which appear to have a number of structural and functional features similar to those of miRNAs but are less abundant. As is the case with miRNAs, (i) tRFs seem to have distinct isoforms preferentially originating from 5’ or 3’ end of a precursor molecule (in this case, tRNA), (ii) ends of tRFs appear to contain short “seed” sequences matching conserved regions across 12 Drosophila genomes, preferentially in 3’ UTRs but also in introns and exons; (iii) tRFs display specific isoform loading into Ago1 and Ago2 and thus likely function in RISC complexes; (iii) levels of loading in Ago1 and Ago2 differ considerably; and (iv) both tRF expression and loading appear to be age-dependent, indicating potential regulatory changes from young to adult organisms.ConclusionsWe found that Drosophila tRF reads mapped to both nuclear and mitochondrial tRNA genes for all 20 amino acids, while previous studies have usually reported fragments from only a few tRNAs. These tRFs show a number of similarities with miRNAs, including seed sequences. Based on complementarity with conserved Drosophila regions we identified such seed sequences and their possible targets with matches in the 3’UTR regions. Strikingly, the potential target genes of the most abundant tRFs show significant Gene Ontology enrichment in development and neuronal function. The latter suggests that involvement of tRFs in the RNA interfering pathway may play a role in brain activity or brain changes with age.ReviewersThis article was reviewed by Eugene Koonin, Neil Smalheiser and Alexander Kel.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-015-0081-6) contains supplementary material, which is available to authorized users.
Highlights
Development of sequencing technologies and supporting computation enable discovery of small RNA molecules that previously escaped detection or were ignored due to low count numbers
We investigated whether Transfer RNA fragment (tRF)-Transfer RNAs (tRNAs) alignments displayed similar patterns to miRNAs in the read distributions
We found that tRF reads, which were more abundant in the Ago2 libraries, mapped to >100 nuclear and mitochondrial Drosophila tRNA genes covering the whole spectrum of 20 amino acids
Summary
Development of sequencing technologies and supporting computation enable discovery of small RNA molecules that previously escaped detection or were ignored due to low count numbers. Previous studies have demonstrated regulatory function of these tRFs by postulating that they bind and repress mRNAs in a fashion similar to microRNAs (miRNAs) or Karaiskos et al Biology Direct (2015) 10:51 even compete with miRNAs [2, 5, 7, 9, 12,13,14]. It is unclear if they act like plant miRNAs that are fully complementary to their targets, or like animal miRNAs that have a specific pairing “seed” region. One of them has suggested a traditional miRNA-like silencing based on complementarity of the 5' seed sequence of a tRF to a short sub-sequence within a 3’ UTR of a transcript [10]; another has shown that the last 8–10 nucleotides (nts) on the 3’ end of the tRF in the 5’ portion of the full tRNA are responsible for mRNA repression [15]
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