Figure - available from: Advanced Science
This content is subject to copyright. Terms and conditions apply.
Patient plasma tDR signature reveals distinct stress responses during CPB surgery. A) About 10% total reads mapped to tRNA genes in the examined human plasma Exs samples. B) A large proportion of plasma tDRs are derived from tRNA‐Glu, tRNA‐Gly, tRNA‐Pro, and tRNA‐Val. C) Plasma tDRs are mainly 16–18 or 31–35 nts in length. D) Plasma tDRs are predominantly tRNA halves that derived from both ends of tRNA genes. E) Plasma tDRs end at position 32, 33, 72, or 74 of tRNAs. PCA analysis based on F) tDR landscapes provides better resolution to distinguish pre‐CPB from post‐CPB surgery than the one based on G) miRNA expression. H) CPB surgery‐modulated tDRs are overlapped with nutritional deprivation‐shaped and oxidative stress‐shaped extracellular tDR signatures but not hypoxia‐shaped extracellular tDR signature. I) Representative CPB surgery‐modulated tDRs that also found in GSD‐shaped extracellular tDR signatures (red), in GSD and H2O2‐regulated extracellular tDR signatures (purple), and in H2O2‐shaped extracellular tDR signatures (blue), and not found in three profiled stress‐specific extracellular tDR signatures (orange). Paired two‐tailed t‐test.
Source publication
The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints of distinct stress responses may identify novel biomarkers and key signaling pathways for different diseases. Emerging evidence shows that transfer RNA‐derived small RNAs (tDRs) play pivotal roles in stress responses. However,...
Citations
... (Cristodero et al., 2021). Similarly, in vitro experiments suggested human ANG efficiently cleaves CCA ends before anticodon cleavage, likely inducing global translation inhibition (Czech et al., 2013). However, recent studies based on next generation sequencing revealed most of the 3 0 -tiRNAs had intact CCA termini (Akiyama, Lyons, et al., 2022;G. Li et al., 2022;Su et al., 2019), implying that ANG predominantly targets anticodon loops compared to CCA termini. Therefore, at least in human cells, the impact of CCA-shortening on translation seems small. ...
... It has been recently suggested that RNase 1, another RNase A superfamily enzyme, is a main RNase responsible for ANG-independent stress-induced tiRNA production (G. Li et al., 2022). In addition, RNase L also generates tiRNA-like tDRs in response to viral infection (Donovan et al., 2017). ...
Transfer RNA (tRNA)‐derived RNAs (tDRs) are a class of small non‐coding RNAs that play important roles in different aspects of gene expression. These ubiquitous and heterogenous RNAs, which vary across different species and cell types, are proposed to regulate various biological processes. In this review, we will discuss aspects of their biogenesis, and specifically, their contribution into translational control. We will summarize diverse roles of tDRs and the molecular mechanisms underlying their functions in the regulation of protein synthesis and their impact on related events such as stress‐induced translational reprogramming.
This article is categorized under: RNA Processing > Processing of Small RNAs
Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs
... Although it is highly resistant to degradation, once cleaved by r-RNase 1 or by FBSderived RNase A, it typically does not survive as a nicked tRNA ( Fig. 2A). This implicates extracellular RNases in the degradation of tDRs (47). In contrast, tRNA Gly GCC is sensitive to initial cleavage events, but nicked tRNAs produced therefrom are intrinsically stable. ...
Nonvesicular extracellular RNAs (nv-exRNAs) constitute the majority of the extracellular RNAome, but little is known about their stability, function, and potential use as disease biomarkers. Herein, we measured the stability of several naked RNAs when incubated in human serum, urine, and cerebrospinal fluid (CSF). We identified extracellularly produced tRNA-derived small RNAs (tDRs) with half-lives of several hours in CSF. Contrary to widespread assumptions, these intrinsically stable small RNAs are full-length tRNAs containing broken phosphodiester bonds (i.e., nicked tRNAs). Standard molecular biology protocols, including phenol-based RNA extraction and heat, induce the artifactual denaturation of nicked tRNAs and the consequent in vitro production of tDRs. Broken bonds are roadblocks for reverse transcriptases, preventing amplification and/or sequencing of nicked tRNAs in their native state. To solve this, we performed enzymatic repair of nicked tRNAs purified under native conditions, harnessing the intrinsic activity of phage and bacterial tRNA repair systems. Enzymatic repair regenerated an RNase R-resistant tRNA-sized band in northern blot and enabled RT-PCR amplification of full-length tRNAs. We also separated nicked tRNAs from tDRs by chromatographic methods under native conditions, identifying nicked tRNAs inside stressed cells and in vesicle-depleted human biofluids. Dissociation of nicked tRNAs produces single-stranded tDRs that can be spontaneously taken up by human epithelial cells, positioning stable nv-exRNAs as potentially relevant players in intercellular communication pathways.
... The main classes of small ncRNAs are miRNAs, small interfering RNAs (siRNAs), piwi-interacting RNAs (piRNAs), Y-RNAs, and tRNA-derived small RNAs (tDRs) [10,11]. Most small ncRNAs are capable of regulating gene expression either transcriptionally or epitranscriptionally [10,12]. ...
... Extracellular tDR is a newly identified small regulatory RNA species. A recent study has demonstrated that extracellular tDRs are much more dynamically regulated than intracellular tDRs and extracellular miRNAs in both cardiomyocytes and cardiac fibroblasts upon the treatments of ischemia/reperfusion-related stressors [11]. Notably, more than 3000 extracellular tDRs are significantly regulated by nutritional deprivation or ischemia, and approximately 2000 extracellular tDRs are differentially expressed upon ischemia/reoxygenation treatment mimicking ischemia/reperfusion injury in both cardiomyocytes and cardiac fibroblasts [11]. ...
... A recent study has demonstrated that extracellular tDRs are much more dynamically regulated than intracellular tDRs and extracellular miRNAs in both cardiomyocytes and cardiac fibroblasts upon the treatments of ischemia/reperfusion-related stressors [11]. Notably, more than 3000 extracellular tDRs are significantly regulated by nutritional deprivation or ischemia, and approximately 2000 extracellular tDRs are differentially expressed upon ischemia/reoxygenation treatment mimicking ischemia/reperfusion injury in both cardiomyocytes and cardiac fibroblasts [11]. Detailedly, extracellular tDR-1:32-His-GTG-1, tDR-37:72-Val-TAC-1, tDR-1:32-Pro-AGG-1-M4, tDR-2:30-Glu-CTC-1, tDR-2:30-Glu-CTC-1-D4G, tDR-1:31-Glu-TTC-4, tDR-3:31-Gly-GCC-2-M2, and tDR-40:72-Asn-GTT-1-M2 were significantly induced by ischemia/reoxygenation from both cardiomyocytes and cardiac fibroblasts, and extracellular tDR-1:36-Glu-CTC-1, tDR-1:36-Glu-CTC-1-D5G, tDR-1:36-Asp-GTC-2-M2, and tDR-42:75-Ser-GCT-3 were downregulated considerably upon cardiac ischemia/reoxygenation [11]. ...
Cardiovascular diseases (CVDs) remain the world’s leading cause of death despite the best available healthcare and therapy. Emerging as a key mediator of intercellular and inter-organ communication in CVD pathogenesis, extracellular vesicles (EVs) are a heterogeneous group of membrane-enclosed nano-sized vesicles released by virtually all cells, of which their RNA cargo, especially non-coding RNAs (ncRNA), has been increasingly recognized as a promising diagnostic and therapeutic target. Recent evidence shows that ncRNAs, such as small ncRNAs, circular RNAs, and long ncRNAs, can be selectively sorted into EVs or other non-vesicular carriers and modulate various biological processes in recipient cells. In this review, we summarize recent advances in the literature regarding the origin, extracellular carrier, and functional mechanisms of extracellular ncRNAs with a focus on small ncRNAs, circular RNAs, and long ncRNAs. The pathophysiological roles of extracellular ncRNAs in various CVDs, including atherosclerosis, ischemic heart diseases, hypertension, cardiac hypertrophy, and heart failure, are extensively discussed. We also provide an update on recent developments and challenges in using extracellular ncRNAs as biomarkers or therapeutical targets in these CVDs.
... Ribonuclease (RNase) 1 is also a member of the vertebrate secreted ribonuclease family which shows high activity against double-stranded RNA (dsRNA) 38 , where it digests RNAs to single nucleotide products. RNase 1 is ubiquitously expressed but has been found to be upregulated during oxidative stress, and has been reported to cleave tRNA indicating it may also function to generate stress-induced tRFs 39,40 . However, it has also been suggested that these tRFs may be generated extracellularly by secreted RNase 1, and the CCA tail was also found to be cleaved 40 . ...
... Different purification approaches also influenced RNA type read distributions, but this study reported similar read counts from plasma and serum 46 . tRFs have also been detected in cell culture media 39,46,48 , one study which profiled intra-and extra-cellular tRFs generated in response to stress found that intracellular tRF species overlapped in multiple stress conditions, whereas extracellular tRFs provided distinct profiles depending on the stress type 39 . Interestingly, extracellular microRNA profiles did not vary between stress types, indicating secreted tRFs may provide more informative biomarkers than secreted microRNAs. ...
... Different purification approaches also influenced RNA type read distributions, but this study reported similar read counts from plasma and serum 46 . tRFs have also been detected in cell culture media 39,46,48 , one study which profiled intra-and extra-cellular tRFs generated in response to stress found that intracellular tRF species overlapped in multiple stress conditions, whereas extracellular tRFs provided distinct profiles depending on the stress type 39 . Interestingly, extracellular microRNA profiles did not vary between stress types, indicating secreted tRFs may provide more informative biomarkers than secreted microRNAs. ...
Transfer RNAs play a crucial role in protein translation where they bring amino acids to the ribosome to be incorporated into nascent polypeptide chains. During stress conditions tRNAs can be cleaved to generate tRNA-derived fragments. Several ribonucleases have been identified that cleave tRNA, however mutations in the stress-induced ribonuclease Angiogenin have been identified in a range of neurological disorders including Amyotrophic Lateral Sclerosis, Parkinson’s Disease, and Alzheimer’s Disease, suggesting that tRNA cleavage may be dysregulated in neurological disease. tRNA fragments have been detected in biofluids indicating they may be of use as biomarkers for neurological diseases. There is considerable variability in the methods used to quantify tRFs from size selection, adapter ligation, removal of RNA modifications, and sequence analysis approaches which can make it difficult to reconcile multiple studies. Here we review the biology of transfer RNAs and the biogenesis of tRNA-derived fragments, with a focus on the methods used to identify and quantify tRNA fragments and how different methodological approaches can influence tRNA fragment detection. We provide an overview of current literature on the identification of tRNA fragments in neurological disease models and patient samples, with a focus on circulating tRNA fragments as potential biomarkers of neurological diseases.
... (b) Table of tDRs significantly altered in SARS-CoV-2-infected patients compared to uninfected individuals with the naming conventions: tRF ID is from the original data base used in the analysis and using the former name of tRNA fragments (http://genome.bioch.virginia.edu/trfdb/ [27,28] accessed on 17 January 2022); the tDR name is a shortened name used for convenience in this manuscript; the tDRnamer is the most accurate naming convention for the tRNA-derived RNAs [29,30], http://trna.ucsc.edu/ tDRnamer/docs/ accessed on 12 November 2022; NA is not applicable for 5020a because it is too short to be identified in the tDRnamer data base (http://trna.ucsc.edu/tDRnamer/index.html) accessed on 12 November 2022. ...
The COVID-19 pandemic revealed a need for new understanding of the mechanisms regulating host–pathogen interactions during viral infection. Transfer RNA-derived RNAs (tDRs), previously called transfer RNA fragments (tRFs), have recently emerged as potential regulators of viral pathogenesis. Many predictive studies using bioinformatic approaches have been conducted providing a repertoire of potential small RNA candidates for further analyses; however, few targets have been validated to directly bind to SARS-CoV-2 sequences. In this study, we used available data sets to identify host tDR expression altered in response to SARS-CoV-2 infection. RNA-interaction-prediction tools were used to identify sequences in the SARS-CoV-2 genome where tDRs could potentially bind. We then developed luciferase assays to confirm direct regulation through a predicted region of SARS-CoV-2 by tDRs. We found that two tDRs were downregulated in both clinical and in vitro cell culture studies of SARS-CoV-2 infection. Binding sites for these two tDRs were present in the 3′ untranslated region (3′UTR) of the SARS-CoV-2 reference virus and both sites were altered in Variants of Concern (VOCs) that emerged later in the pandemic. These studies directly confirm the binding of human tDRs to a specific region of the 3′UTR of SARS-CoV-2 providing evidence for a novel mechanism for host–pathogen regulation.
... The role of tRNA and tRNA modifications in neurological disorders such as Amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) and Parkinson's disease (PD), was driven to the spotlight with the demonstration of an impact of RNA modifications on tRNA processing into tRNA-derived fragments of different size, generally referred as tsRNAs, or, for miR-like fragments as tRFs [1]. Such processing is a complex process, involving a number of different nucleases, including angiogenin (ANG), with the latter cleaving tRNA in the anticodon loop and thus generating so-called tiRNAs [2,3] while other processing steps that give rise to tiRNA-type fragments are ANG-independent [4]. For the remainder of this manuscript, we will use the term tsRNA for simplicity. ...
... ANG cleavage is mainly discussed here, but other concomitant pathways have been described. For instance, Dicer cleaves tRNAs into miR-like fragments (tRFs) [63,64] and another Dicer-and ANG-independent pathways have been reported [2,7,65]. These multiple and overlapping tRNA cleavage pathways create an impressive number of tRNA-derived small RNAs, thus appealing for more detailed characterization. ...
Modification of tRNA is an integral part of the epitranscriptome with a particularly pronounced potential to generate diversity in RNA expression. Eukaryotic tRNA contains modifications in up to 20% of their nucleotides, but not all sites are always fully modified. Combinations and permutations of partially modified sites in tRNAs can generate a plethora of tRNA isoforms, termed modivariants. Here, we investigate the stoichiometry of incompletely modified sites in tRNAs from human cell lines for their information content. Using a panel of RNA modification mapping methods, we assess the stoichiometry of sites that contain the modifications 5-methylcytidine (m⁵C), 2’-O-ribose methylation (Nm), 3-methylcytidine (m³C), 7-methylguanosine (m⁷G), and Dihydrouridine (D). We discovered that up to 75% of sites can be incompletely modified and that the differential modification status of a cellular tRNA population holds information that allows to discriminate e.g. different cell lines. As a further aspect, we investigated potential causal connectivity between tRNA modification and its processing into tRNA fragments (tiRNAs and tRFs). Upon exposure of cultured living cells to cell-penetrating angiogenin, the modification patterns of the corresponding RNA populations was changed. Importantly, we also found that tsRNAs were significantly less modified than their parent tRNAs at numerous sites, suggesting that tsRNAs might derive chiefly from hypomodified tRNAs.
... Using RNH1 knockout cells, we showed that the net amount of sodium arsenite-induced tiRNAs is largely dependent on the dissociation of RNH1 from all the RNase A superfamily enzymes (including ANG) expressed in the cell [27]. A recent study suggested that RNase 1, one of RNase A superfamily enzymes, is mainly responsible for ANG-independent tiRNA production [28]. Therefore, both intracellular levels of RNase A superfamily enzymes and stress-induced dissociation of RNH1 from the RNases determine the amount of tiRNA production. ...
Under stress conditions, transfer RNAs (tRNAs) are cleaved by stress-responsive RNases such as angiogenin, generating tRNA-derived RNAs called tiRNAs. As tiRNAs contribute to cytoprotection through inhibition of translation and prevention of apoptosis, the regulation of tiRNA production is critical for cellular stress response. Here, we show that RTCB ligase complex (RTCB-LC), an RNA ligase complex involved in endoplasmic reticulum (ER) stress response and precursor tRNA splicing, negatively regulates stress-induced tiRNA production. Knockdown of RTCB significantly increased stress-induced tiRNA production, suggesting that RTCB-LC negatively regulates tiRNA production. Gel-purified tiRNAs were repaired to full-length tRNAs by RtcB in vitro, suggesting that RTCB-LC can generate full length tRNAs from tiRNAs. As RTCB-LC is inhibited under oxidative stress, we further investigated whether tiRNA production is promoted through the inhibition of RTCB-LC under oxidative stress. Although hydrogen peroxide (H2O2) itself did not induce tiRNA production, it rapidly boosted tiRNA production under the condition where stress-responsive RNases are activated. We propose a model of stress-induced tiRNA production consisting of two factors, a trigger and booster. This RTCB-LC-mediated boosting mechanism may contribute to the effective stress response in the cell.
... Multiple RNases produce tiRNAs by binding with tsRNA, and ANG is mainly involved in the production of certain 3′ tiRNAs. Notably, a recent study reported that RNases, including ANG and RNASE1, not only regulate tsRNA biogenesis but also tsRNA degradation [14]. Dicer generates both tRF-3b and tRF-3a, with the former produced by cleaving the T-loop between the 54th and 55th nucleotides and the latter produced by cleaving between the 58th and 59th nucleotides [15]. ...
... Regulated by nutritional deprivation [14] tDR-1:33-Pro-AGG-1-M5 and tDR-42:74-Ser-GCT-1 Nutritional deprivation Downregulated ...
... Regulated by nutritional deprivation [14] tDR Regulated by oxidative stress [14] tDR-1: 30-Glu-CTC-1 and tDR-2: 31-Glu-CTC-1 ...
tRNA-derived small RNAs (tsRNAs) are non-coding RNAs with diverse functions in various diseases. Although research on tsRNAs has focused on their roles in cancer, such as gene expression regulation to influence cancer progression and realize clinical effects, a growing number of studies are investigating the association of tsRNAs with cardiovascular diseases (CVDs), including atherosclerosis, myocardial infarction, and pulmonary hypertension. tsRNA expression varies across these diseases and could be regulated by epigenetics, tsRNA structure, and tRNA-binding proteins. tsRNAs play key roles in CVD progression, including the regulation of protein synthesis, and the different mechanisms underlying these functional roles of tsRNAs have been elucidated. Furthermore, tsRNAs are potential diagnostic biomarkers and therapeutic targets in CVDs. In this review, we summarize the biogenesis, classification, and regulation of tsRNAs and their potential application for CVD diagnosis and therapy. We also highlight the current challenges and provide perspectives for further investigation.
Graphical abstract
... The biogenesis of tsRNAs is the cleavage of either pre-tRNA or mature tRNAs by a variety of specific endoribonucleases including angiogenin (ANG), RNA enzyme Z (RNase Z), and Dicer (Yamasaki et al., 2009). Recently, RNase1 has been indicated to involve the degradation of 1,342 tsRNAs in response to H 2 O 2 treatment, though it has little relation with biogenesis of tsRNAs (Li et al., 2022b). Based on the different cleaving region within pre-/mature tRNA, tsRNAs can be classified into tRFs and tiRNAs (Zuo et al., 2021). ...
The role of tRNAs is best known as adapter components of translational machinery. According to the central dogma of molecular biology, DNA is transcribed to RNA and in turn is translated into proteins, in which tRNA outstands by its role of the cellular courier. Recent studies have led to the revision of the canonical function of transfer RNAs (tRNAs), which indicates that tRNAs also serve as a source for short non-coding RNAs called tRNA-derived small RNAs (tsRNAs). tsRNAs play key roles in cellular processes by modulating complicated regulatory networks beyond translation and are widely involved in multiple diseases. Herein, the biogenesis and classification of tsRNAs were firstly clarified. tsRNAs are generated from pre-tRNAs or mature tRNAs and are classified into tRNA-derived fragments (tRFs) and tRNA halves (tiRNA). The tRFs include five types according to the incision loci: tRF-1, tRF-2, tRF-3, tRF-5 and i-tRF which contain 3′ tiRNA and 5′ tiRNA. The functions of tsRNAs and their regulation mechanisms involved in disease processes are systematically summarized as well. The mechanisms can elaborate on the specific regulation of tsRNAs. In conclusion, the current research suggests that tsRNAs are promising targets for modulating pathological processes, such as breast cancer, ischemic stroke, respiratory syncytial virus, osteoporosis and so on, and maintain vital clinical implications in diagnosis and therapeutics of various diseases.
... Small RNA transcriptome data revealed a significant expression of 5'-end fragments (tRF-5s) in isoproterenol-induced hypertrophic rat hearts indicating that tRF-5s may play a role in cardiac hypertrophy [58]. Recent other emerging efforts have showcased the dynamic changes in the generation of tDRs with cellular stressors in cardiomyocytes and cardiac fibroblasts [59], but their function is yet to be elucidated. Undoubtedly high throughput specialized sequencing with advanced bioinformatics tools will aid to identify other tDRs involved in CR in near future and development of novel tools to study their function will aid in understanding their role in CR. ...
Regulatory RNAs or non-coding RNAs (ncRNAs) are a group of RNA molecules that do not encode proteins. Multiple studies have demonstrated that ncRNAs are not only critical for physiological processes like cellular proliferation, apoptosis, differentiation, and metabolism, but also play a significant role in the pathogenesis of different diseases. Cardiac remodeling is a complex process comprising of a variety of cellular processes that underlie the mechanistic underpinnings of diverse cardiovascular diseases. An expanding number of recent studies have implicated ncRNAs as important players in cardiac remodeling. In this review, we provide an update on the current knowledge on the role of small non-coding RNAs (including microRNAs, PIWI-interacting RNAs, and tRNA derived small RNAs), long non-coding RNAs and circular RNAs in cardiac remodeling. These studies have uncovered novel potential new pathways to target for therapeutics.
