tRNA-derived RNAs: Biogenesis and roles in translational control

Optimization of ACE-tRNAs function in translation for suppression of nonsense mutations

Nonsense suppressor transfer RNAs (tRNAs) or AntiCodon-Edited tRNAs (ACE-tRNAs) have long been envisioned as a therapeutic approach to overcome genetic diseases resulting from the introduction of premature termination codons (PTCs). The ACE-tRNA approach for the rescue of PTCs has been hampered by ineffective delivery through available modalities for gene therapy. Here we have screened a series of ACE-tRNA expression cassette sequence libraries containing >1800 members in an effort to optimize ACE-tRNA function and provide a roadmap for optimization in the future. By optimizing PTC suppression efficiency of ACE-tRNAs, we have decreased the amount of ACE-tRNA required by ∼16-fold for the most common cystic fibrosis-causing PTCs.

tRNA, yRNA, and rRNA fragment excisions do not involve canonical microRNA biogenesis machinery

The excision of specific tRNA-derived small RNAs (tsRNAs), yRNA-derived small RNAs (ysRNAs) and ribosomal RNA-derived small RNAs (rsRNAs) is now well established. Several reports have suggested many of these fragments function much like traditional microRNAs (miRNAs). That said, whereas the expressions of the majority of appreciably expressed miRNAs in HCT116 colon cancer cells are significantly decreased in individual knockouts (KOs) of DROSHA, DGCR8, XPO5, and DICER, on average, only 3.5% of tsRNA, ysRNA, and rsRNA expressions are impaired. Conversely, tsRNA, ysRNA, and rsRNA expressions are significantly increased in each of these KOs as compared to WT. As such, although DICER has been suggested to be involved with the expression of specific tsRNAs, ysRNAs, and rsRNAs, our study finds no evidence supporting the involvement of any of these canonical miRNA biogenesis enzymes in their expressions.

Repurposing tRNA isodecoders for non-canonical functions via tRNA cleavage

Transfer RNAs (tRNAs) are the key adaptor molecules aiding protein synthesis. Hundreds of tRNA genes are found in the human genome but the biological significance of this genetic excess is still enigmatic. The tRNA repertoires are variable between tissues and cells as well as during development. Such variations can only be partially explained by the correlation to the physiological needs in protein production, e.g. by changes in the expression of tRNA isoacceptor sets (tRNAs charged with the same amino acid but bearing different anticodons). However, changes in the expression levels of individual isodecoders (tRNAs with the same anticodon) are less understood. Besides canonical functions in mRNA translation, tRNAs are implicated in non-canonical functions unrelated to protein synthesis. tRNAs are rich source of small non-protein coding RNAs called tRNA-derived RNAs (tDRs), which include tRNA-derived stress-induced RNAs (tiRNAs) formed in response to stress. Here, we show that tiRNAs derived from isodecoders different in a single nucleotide can also differ in their activities. Specifically, we show that isodecoder sets for tRNA His-GTG , tRNA Gly-GCC and tRNA Cys-GCA are cleaved by ribonucleases to yield 5'-tiRNAs showing differential activity towards mRNA reporter translation. Our data propose a model where cleavage repurposes specific tRNA isodecoders for non-canonical functions.

Significance Statement

The human genome encodes hundreds of transfer RNA (tRNA) genes to decode 61 codons. The basis for such genetic redundancy is unclear but the increase in the number of tRNA genes goes in concert with the complexity of an organism. While changes in the expression of isoacceptor tRNA pools can reflect adaptation to demanding protein synthesis needs and/or codon usage, the variations in the expression of the individual tRNA isodecoders are documented but poorly understood. Such expression variations are hypothesized to contribute to non-canonical tRNA functions, yet physiological relevance remains ambiguous. We report here that specific tRNA isodecoders can be functionally repurposed through cleavage that produces tRNA-derived RNAs (tDRs). The repurposing employs nucleotide variations in isodecoders leading to the production of distinct sets of tDRs with variable bioactivities.

The making and breaking of tRNAs by ribonucleases

Ribonucleases (RNases) play important roles in supporting canonical and non-canonical roles of tRNAs by catalyzing the cleavage of the tRNA phosphodiester backbone. Here, we highlight how recent advances in cryo-electron microscopy (cryo-EM), protein structure prediction, reconstitution experiments, tRNA sequencing, and other studies have revealed new insight into the nucleases that process tRNA. This represents a very diverse group of nucleases that utilize distinct mechanisms to recognize and cleave tRNA during different stages of a tRNA's life cycle including biogenesis, fragmentation, surveillance, and decay. In this review, we provide a synthesis of the structure, mechanism, regulation, and modes of tRNA recognition by tRNA nucleases, along with open questions for future investigation.

Altered expression of transfer RNAs and their possible roles in brain white matter injury

Transfer RNAs (tRNAs) can regulate cell behavior and are associated with neurological disorders. Here, we aimed to investigate the expression levels of tRNAs in oligodendrocyte precursor cells (OPCs) and their possible roles in the regulation of brain white matter injury (WMI). Newborn Sprague-Dawley rats (postnatal day 5) were used to establish a model that mimicked neonatal brain WMI. RNA-array analysis was performed to examine the expression of tRNAs in OPCs. psRNAtarget software was used to predict target mRNAs of significantly altered tRNAs. Gene ontology (GO) and KEGG were used to analyze the pathways for target mRNAs. Eighty-nine tRNAs were changed after WMI (fold change absolute ≥1.5, P  < 0.01), with 31 downregulated and 58 upregulated. Among them, three significantly changed tRNAs were identified, with two being significantly increased (chr10.trna1314-ProTGG and chr2.trna2771-ProAGG) and one significantly decreased (chr10.trna11264-GlyTCC). Further, target mRNA prediction and GO/KEGG pathway analysis indicated that the target mRNAs of these tRNAs are mainly involved in G-protein coupled receptor signaling pathways and beta-alanine metabolism, which are both related to myelin formation. In summary, the expression of tRNAs in OPCs was significantly altered after brain WMI, suggesting that tRNAs may play important roles in regulating WMI. This improves the knowledge about WMI pathophysiology and may provide novel treatment targets for WMI.

Advances in methods for tRNA sequencing and quantification

In the past decade tRNA sequencing (tRNA-seq) has attracted considerable attention as an important tool for the development of novel approaches to quantify highly modified tRNA species and to propel tRNA research aimed at understanding the cellular physiology and disease and development of tRNA-based therapeutics. Many methods are available to quantify tRNA abundance while accounting for modifications and tRNA charging/acylation. Advances in both library preparation methods and bioinformatic workflows have enabled developments in next-generation sequencing (NGS) workflows. Other approaches forgo NGS applications in favor of hybridization-based approaches. In this review we provide a brief comparative overview of various tRNA quantification approaches, focusing on the advantages and disadvantages of these methods, which together facilitate reliable tRNA quantification.