In July 2025, researchers published a study titled "A hypoxia-responsive tRNA-derived small RNA confers renal protection through RNA autophagy" online in Science. The research found that the hypoxia-induced tDR derived from the 3' end of tRNA-Asp-GTC (tRNA-Asp-GTC-3'tDR) activates autophagy flux in renal cells, and its silencing blocks this flux.
Gain-of-function and loss-of-function studies in mouse kidney disease models demonstrated that tRNA-Asp-GTC-3'tDR possesses substantial renal protective functions. Mechanistically, tRNA-Asp-GTC-3'tDR assembles into a stable G-quadruplex structure and sequesters pseudouridine synthase 7 (PUS7), preventing the catalytic pseudouridylation of histone mRNA.
The resulting pseudouridylation defect directs histone mRNA to the autophagosome-lysosome pathway, triggering RNA autophagy. This tDR-induced RNA autophagy pathway is activated during kidney disease in both mice and humans, suggesting clinical relevance. Consequently, tRNA-Asp-GTC-3'tDR plays a role in regulating RNA autophagy, which helps maintain renal cellular homeostasis and protects the kidneys from injury.
Cleavage products of transfer RNA (tRNA) are known as tRNA-derived small RNAs (tsRNAs or tDRs), a class of evolutionarily conserved non-coding small RNAs that play important roles in cellular stress responses. For instance, the 5' halves of tRNA-Ala and tRNA-Cys are cleaved by endonucleases such as angiogenin at the anticodon loop and are involved in the regulation of stress granules and global translation. Two tDRs from both ends of tRNA-Asp-GTC, tRNA-Asp-GTC-3'tDR and tRNA-Asp-GTC-5'tDR, have been shown to be the most highly upregulated hypoxia-responsive tDRs in various cell types. However, their roles in regulating cellular stress responses remained unclear.
Using ultra-sensitive Northern blotting and an engineered fluorescent reporter for tRNA-Asp-GTC-3'tDR, researchers validated the biogenesis of hypoxia-induced tRNA-Asp-GTC-3'tDR in human embryonic kidney (HEK) cells and further confirmed the critical role of the endonuclease angiogenin in its biogenesis. Through overexpression (using synthetic mimics) or specific silencing (using locked nucleic acid-modified antisense oligonucleotides, ASOs), the study demonstrated that tRNA-Asp-GTC-3'tDR (but not the 5'tDR) is necessary and sufficient to drive autophagy flux in HEK cells.
Figure 1. tRNA-Asp-GTC-3'tDR induces RNA autophagy in kidney cells. (Li G, et al., 2025)
Mechanistically, the regulation of autophagy flux by tRNA-Asp-GTC-3'tDR depends heavily on its binding to the RNA-modifying enzyme pseudouridine synthase 7 (PUS7). The interaction between tRNA-Asp-GTC-3'tDR and PUS7 relies on a structural oligo-guanine motif and the binding motif of PUS7, with the former allowing for the formation of a stable intermolecular G-quadruplex (G4) structure.
The binding and sequestration of PUS7 by tRNA-Asp-GTC-3'tDR prevents the pseudouridylation of target mRNAs, particularly histone mRNAs. Pseudouridine-deficient histone mRNAs are targeted to the autophagosome-lysosome pathway for degradation, triggering RNA autophagy as a possible stress-adaptive response.
In summary, this work contributes to emerging research on the roles of tDRs in cellular homeostasis and stress response. The study found that the hypoxia-responsive tRNA-Asp-GTC-3'tDR maintains renal cell homeostasis and plays a key role in the stress response by regulating autophagy flux. tRNA-Asp-GTC-3'tDR levels are sharply elevated in mouse and human kidney diseases to enhance autophagy flux, preventing cell damage, inflammation, and fibrosis.
Mechanistically, key structural motifs in tRNA-Asp-GTC-3'tDR, including the oligo-guanine motif and the T-arm region, are essential for both tDR stability and the sequestration of the RNA-modifying enzyme PUS7. This sequestration subsequently drives RNA autophagy by preventing PUS7 from targeting histone mRNA for pseudouridylation and stabilization. Therefore, targeting tRNA-Asp-GTC-3'tDR to maintain autophagy flux in kidney disease may be a promising therapeutic strategy.
Reference
Li G, et al. A hypoxia-responsive tRNA-derived small RNA confers renal protection through RNA autophagy. Science, 2025, 389(6763): eadp5384.