Abstract
Recent studies point to the existence of poorly characterized small regulatory RNAs generated from mRNAs, rRNAs and tRNAs. To explore the subcellular location of tRNA-derived small RNAs, 0–1 and 7–8 h Drosophila embryos were fractionated on sucrose density gradients. Analysis of 12,553,921 deep-sequencing reads from unfractionated and fractionated Drosophila embryos has revealed that tRFs, which are detected mainly from the 5’ends of tRNAs, co-sediment with the non-polysomal fractions. Interestingly, the expression levels of a subset of tRFs change temporally following the maternal-to-zygotic transition in embryos. We detected non-polysomal association of tRFs in S2 cells as well. Differential tRF expression pattern points to developmental significance at the organismal level. These results suggest that tRFs are associated primarily with the non-polysomal complexes in Drosophila embryos and S2 cells.
Highlights
Transfer RNAs are well-known for their role in protein synthesis [1]. tRNAs are involved in priming reverse transcription in viruses, inducing gene expression under amino acid starvation and regulating splicing and apoptosis [2,3,4]
We demonstrate for the first time that tRNA-derived fragments (tRFs)-5s are temporally and selectively expressed in 0–1 and 7–8 h Drosophila embryos under physiological conditions
TRF biogenesis and expression levels are likely to be modulated during early development in Drosophila
Summary
Transfer RNAs (tRNAs) are well-known for their role in protein synthesis [1]. tRNAs are involved in priming reverse transcription in viruses, inducing gene expression under amino acid starvation and regulating splicing and apoptosis [2,3,4]. No change, under stress, in the amount of the full-length tRNA levels suggest that the cleavage is a general response, not a regulatory mechanism. The studies to understand the role of tRFs in gene regulation mainly dealt with miRNA-like functions. TRF-1001, which induces cell proliferation in a human prostate cancer cell line, apparently functions through a mechanism different from miRNA/siRNA pathways [12]. 5’ ends of a subset of tRNAs, suggesting temporal but selective expression under physiological conditions. Based on their length and cleavage site, tRFs appear to be different from sitRNA fragments. TRFs are primarily associated with mRNP and 60S fractions, cytoplasmically localizing away from the actively translating polyribosomes
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