Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets

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.

Dynamics of tRNA fragments and their targets in aging mammalian brain

“…In the present study, we analyzed available RNA sequencing libraries produced from the brains of rats of different ages 26 and identified numerous tRFs, which showed consistent changes in their abundance patterns with age. We also confirmed in rat brains our previous findings on possible targeting mode of Drosophila tRFs and the functional enrichment of their targets in neuronal and developmental functions 23 . Potential targets of tRFs with clearly defined seeds showed higher levels of down-regulation with age compared to the rest of the brain transcriptome and to the targets of miRNAs upregulated with age.…”

“…A search for a near-perfect complementarity of tRF sequences against transcripts yielded very few results, both in the 12 Drosophila genomes 23 and in the present study, further suggesting a targeting mode similar to animal miRNAs. Assuming such an animal-like miRNA targeting mechanism for tRFs, we further investigated the targeting mechanism of tRFs and adjusted our computational pipeline, used previously to find targets in 12 Drosophila genomes 23 , to perform the tRF seed search in mammalian genomes.…”

“…Assuming such an animal-like miRNA targeting mechanism for tRFs, we further investigated the targeting mechanism of tRFs and adjusted our computational pipeline, used previously to find targets in 12 Drosophila genomes 23 , to perform the tRF seed search in mammalian genomes. This pipeline functions similarly to the approach used to identify such seed sequences for miRNAs 34 .…”

“…Yet another study has shown that the last 8–10 nts on the 3’ end of the tRF are responsible for mRNA repression 22 . In our lab, using a computational approach similar to detection of miRNA seeds, we have found potential seed regions on both a 5'-and a 3' tRF end 23 . Adding to this similarity, we have also reported age-related changes of tRF abundance in Drosophila melanogaster 23 , comparable to those detected for miRNA in the same organism 20 .…”

“…In our lab, using a computational approach similar to detection of miRNA seeds, we have found potential seed regions on both a 5'-and a 3' tRF end 23 . Adding to this similarity, we have also reported age-related changes of tRF abundance in Drosophila melanogaster 23 , comparable to those detected for miRNA in the same organism 20 . Such changes with age were also detected in tRFs of Caenorhabditis elegans 24 .…”