Regulation of La/SSB-dependent viral gene expression by pre-tRNA 3′ trailer-derived tRNA fragments

Abstract

tRNA-derived RNA fragments (tRFs) have emerged as a new class of functional RNAs implicated in cancer, metabolic and neurological disorders, and viral infection. Yet our understanding of their biogenesis and functions remains limited. In the present study, through analysis of small RNA profile we have identified a distinct set of tRFs derived from pre-tRNA 3′ trailers in the hepatocellular carcinoma cell line Huh7. Among those tRFs, tRF_U3_1, which is a 19-nucleotide-long chr10.tRNA2-Ser(TGA)-derived trailer, was expressed most abundantly in both Huh7 and cancerous liver tissues, being present primarily in the cytoplasm. We show that genetic loss of tRF_U3_1 does not affect cell growth and it is not involved in Ago2-mediated gene silencing. Using La/SSB knockout Huh7 cell lines, we demonstrate that this nuclear-cytoplasmic shuttling protein directly binds to the 3′ U-tail of tRF_U3_1 and other abundantly expressed trailers and plays a critical role in their stable cytoplasmic accumulation. The pre-tRNA trailer-derived tRFs capable of sequestering the limiting amounts of La/SSB in the cytoplasm rendered cells resistant to various RNA viruses, which usurp La/SSB with RNA chaperone activity for their gene expression. Collectively, our results establish the trailer-derived tRF-La/SSB interface, regulating viral gene expression.

On the expanding roles of tRNA fragments in modulating cell behavior

“…Additionally, Kay and colleagues showed that the RNase Z/ELAC2 produces 3′ trailer tRFs in human cell lines ( 31 ). With regard to localization, the presence of ELAC2 in the cytoplasm and the production of 3′ trailer tRFs in the cytoplasm is supported by the work of Dutta and colleagues ( 2 ) and Oh and colleagues ( 32 ). However, it is not clear how pre-tRNA molecules are exported to the cytoplasm.…”

tRNA-derived RNA fragments in cancer: current status and future perspectives

“…Another mechanism for gene silencing by tRFs is through competitive binding of target proteins with mRNAs. For example, unlike the above mechanism of tRF in viral infections, a chr10.tRNA2-Ser(TGA)-derived 1-tRF, tRF_U3_1, can bind directly to La/SSB protein and inhibit La/SSB-dependent viral gene expression [46]. This means that tRFs may have involvement in multiple different mechanisms within the same disease.…”

“…In hepatocellular carcinomas (HCC), tRF_U3_1 is more abundant in the HCC cell line Huh7 and cancerous liver tissues compared to primary hepatocytes and normal liver tissues, which can inhibit viral gene expression and its precursors [46]. Whether the inhibition of viral gene expression by tRF_U3_1 has an impact on HCC still requires verification.…”

“… [ 74 ] Hepatocellular carcinomas tRF_U3_1 Upregulate in the HCC cell line and tissues Inhibit viral gene expression and its precursors. [ 46 ] Ovarian cancer tRF-03357 Oncogene Promote the cell proliferation, migration, and invasion of high-grade serous ovarian cancer partly by downregulating HMBOX1. [ 75 ] Urinary bladder carcinomas One tRF Isolated from conditioned medium of human urinary bladder carcinoma cells Inhibit the growth of endothelial cells.…”

Action mechanisms and research methods of tRNA-derived small RNAs

“…42 It has been reported that, originating from the pre-tRNA tail region, tRF regulates viral gene expression by isolating La/SSB in the cytoplasm. 43 Some researchers conducted Ago-immunoprecipitation (Ago-IP) tRF analysis and, using bioinformatics methods, found that tRF-5 mainly exists in multiple Ago-IPs in addition to Ago2-IP, while Ago2-IP has the strongest interaction with tRF-3. 44 Since only Ago2 in mammals contains a slicer domain, Daugaard et al speculated that the interaction of Ago2-tRF-3 might suppress the antisense reporter genes by directly cutting the target transcripts.…”