Aging is defined by a progressive decline in the physiological functions of organisms. Mutations in genomic DNA or the impairments of protein homeostasis cause aging at the cellular levels, contributing to organismal aging (1, 2). RNA, which transmits the information from DNA to proteins during transcription and translation, likely plays a key role in aging as well. We and other research groups have reported that RNA quality control and homeostasis are critical for longevity and to delay aging (3-8). Two DEAD-box RNA helicases, HEL-1 and SACY-1 (suppressor of ACY-4 sterility), which may contribute to RNA homeostasis, are required for longevity conferred by various interventions, including reduced insulin/IGF-1 singling (IIS) in
tsRNAs, which are generated by the cleavage of tRNAs (13), are a novel class of ncRNAs. tsRNAs are categorized by the cleavage sites of tRNAs: tRNA halves, tRNA-derived RNA fragments (tRFs), and internal-tRFs (i-tRFs) (Fig. 1). tRNA halves are also known as tRNA-derived stress-induced RNAs (tiRNAs), because they are generated under stress conditions, such as starvation, oxidative stress, heat shock, or radiation (14-16); hereafter, we will refer to tRNA halves as tiRNAs, and all the other tsRNAs as tRFs. Angiogenin in mammals and Ribonuclease T2-like 1 (Rny1) in yeast cleave nucleotides in the anticodon loops of tRNAs to generate 30-40 nucleotide-long tiRNAs (16, 17). tRFs are 14-30 nucleotides in length (13, 18), and were reported to be generated by the cleavage of pseudouridine (T)- or dihydrouridine (D)-loops of tRNAs by DICER, angiogenin, and RNase T1 (19-21). Other enzymes, including angiogenin and RNase T1, are also responsible for the generation of tRFs (21). Among them 5’- or 3’-tRFs contain the ends of mature tRNAs, whereas i-tRFs contain only internal regions of mature tRNAs (22, 23). The length of i-tRFs are more variable than other types of tsRNAs, 15-36 nucleotides in length (23). Cleaved 5’-reader and 3’-trailer sequences of pre-tRNAs are considered as tRFs as well. Additionally, pre-tRNAs can be cleaved into tRFs, which are approximately 40 nucleotides in length (24). tsRNAs are not just byproducts generated from random degradation of tRNAs, because they play active roles in diverse biological processes that include gene silencing, translation, transposition, apoptosis, and intergenerational inheritance (13).
In this review, we discuss the roles of tsRNAs in organismal aging and cellular senescence. We describe studies that showed changes in tsRNA levels during aging. We discuss the roles of tsRNAs in age-related diseases, including cancer and neurodegenerative diseases. We also review studies suggesting potential aging-regulating roles of tsRNAs. Because several papers on tsRNAs employed inappropriate methods for performing gain-of- or loss-of-function experiments, here we only discussed papers that used proper methods (25). Understanding the roles of tsRNAs in the regulation of aging will provide key information about how RNAs affect organismal aging and cellular senescence, similar to what DNA and protein homeostasis does.
Studies have revealed that in multiple species including
tsRNAs are associated with age-related diseases that include cancer and neurodegenerative disorders (13). Specific tsRNAs are differentially expressed, and play important roles in several types of human cancer. Sequencing analysis identified tsRNAs that are differentially expressed in nasopharyngeal carcinoma and their potential targets that contribute to cancer (31). tsRNAs appear to directly regulate cancer progression, because overexpression of, or treatment with specific tsRNAs whose levels are increased in cancer cells, can further enhance cancer cell proliferation (32, 33). tsRNAs influence cancer metastasis, as exemplified by a study with a tRF derived from the 5’-end of tRNACys (5’-tRFCys) (34). 5’-tRFCys stabilizes the mRNAs of platelet activating factor acetylhydrolase 1b regulatory subunit (
Multiple studies have provided evidence for the key roles of tsRNAs in neurodegenerative diseases. Abnormal tRNA metabolism by mutations in cleavage and polyadenylation factor I subunit 1 (
Previous studies have established that protein synthesis greatly affects aging rates in animals (41). Overall protein synthesis is reduced in long-lived mutants, such as animals with reduced IIS or mechanistic target of rapamycin (mTOR) signaling (42, 43). Additionally, the inhibition of mRNA translation contributes to longevity in
Although the direct roles of tsRNAs in cellular senescence or organismal aging remain poorly understood, emerging evidence indicates their modulatory roles in aging. A study using multiple model organisms, including
Several studies revealed that the composition of sperm tiRNAs is altered by diet or during sperm maturation, and sperm tiRNAs contribute to epigenetic inheritance (59-61). High-fat diets, which can cause metabolic diseases, alter tiRNA fractions in mouse sperm, and the offspring of males fed with high-fat diets suffer from glucose intolerance (60). Inflammation-induced metabolic diseases in adult male mice also alter the composition of sperm tiRNAs, leading to increased body weight and glucose intolerance in their offspring (62) (Fig. 2C). Specifically, the injection of sperm tiRNAs from mice with metabolic disorders into normal mouse zygote is sufficient to cause metabolic impairments in developed animals (60, 62). These studies suggest that tsRNAs play direct roles in the transmission of paternal metabolic diseases to offspring. Obesity is accompanied by physiological changes that are similar to those observed during aging, as exemplified by the accumulation of senescent cells and DNA instability resulting from oxidative stress (63). In addition, metabolic diseases are considered as age-associated diseases (64). Therefore, these studies raise the possibility that tsRNAs inherited from sperm may accelerate aging, accompanied by metabolic defects, including obesity and insulin resistance.
The functions of tsRNAs are also associated with cellular senescence, a major hallmark of organismal aging. Cellular damage drives cells into several fates, including cellular senescence and apoptosis (65). Noticeably tiRNAs are generated by external stress, including oxidative stress, heat shock, and radiation, which can accelerate cellular senescence. tiRNAs inhibit apoptosis by binding to cytochrome c, which elicits apoptosis in the cytosol (Fig. 3A) (66). Therefore, tiRNAs upregulated by sublethal cellular damage enhance the survival of damaged cells, possibly leading to the accumulation of senescent cells.
Transposable elements, also known as transposons, are the regions of DNA that can jump within the genome. Because transposons are inserted into genome during transposition, dysregulated transposons can negatively affect DNA integrity by increasing insertion mutations and DNA damage (67). The activation of transposable elements, including long-interspersed element-1 (LINE-1), increases during aging, and can cause cellular senescence (68). Therefore, proper suppression of transposition is important to prevent premature aging. A study revealed that 3’ terminal CCA-containing 3’-tRFs inhibit the retrotransposition of long-terminal repeat (LTR) retrotransposons (69) (Fig. 3B). Several 18 nucleotide-long 3’-tRFs compete with mature tRNAs for binding transcripts generated from retrotransposons, thereby inhibiting the jumping of LTR retrotransposons. In addition, 22 nucleotide-long 3’-tRFs contribute to downregulation of the retrotransposons by inhibiting the expression of reverse transcriptase. Thus, tRFs may prevent cellular senescence caused by transposable elements by contributing to the maintenance of genomic stability.
In this review, we have discussed the roles of tsRNAs in aging and age-related diseases. Many studies have reported the identities and the functions of various kinds of tsRNAs, thanks to advances in whole transcriptome sequencing and bioinformatic technologies. Although tsRNAs were initially regarded as byproducts of RNA metabolism, recent studies indicate that tsRNAs modulate multiple biological processes, including mRNA silencing, translation, transposition, and apoptosis. Subsequent reports have identified tsRNAs whose levels are altered during aging in a wide range of species, including
As the biology of tsRNAs is still at an early stage, numerous questions remain to be addressed for future research. The mechanisms by which tsRNA levels are altered during aging remain elusive. For example, tiRNA levels are increased during aging in
Small RNA therapeutics are emerging as promising means for targeting various diseases, including cancer (70). The majority of small RNA therapeutics utilize miRNA mimetics or anti-miRNA drugs (71). tsRNAs can potentially serve as valuable tools for small RNA therapeutics, based on their aforementioned roles in cancer and potential functions in aging. Furthermore, tsRNA-targeting drugs may have systemic effects, because of their abundance in circulating blood systems (72). Therefore, understanding the molecular actions and physiological functions of tsRNAs will help develop novel small RNA therapeutics for treating aging-related diseases or degenerative processes associated with aging.
We thank all Lee lab members for comments and discussion. This research was supported by the KAIST Key Research Institutes Project (Interdisciplinary Research Group) to S.J.V.L.
The authors have no conflicting interests.