Transfer RNA-derived Small RNAs Research Articles

Genome-wide analysis of hippocampal transfer RNA-derived small RNAs identifies new potential therapeutic targets of Bushen Tiansui formula against Alzheimer’s disease

ObjectiveBushen Tiansui formula (BSTSF), a traditional Chinese medicine prescription, has been widely used to treat Alzheimer’s disease (AD). However, the mechanisms underlying its effects remain largely unknown. In this study, a rat AD model was used to study the effects of BSTSF on cognitive performance and expression of transfer RNA-derived small RNAs (tsRNAs) in the hippocampus, to determine whether treatment of AD with BSTSF could regulate the expression of tsRNAs, a novel small non-coding RNA. MethodsTo generate a validated AD model, oligomeric amyloid-β1-42 (Aβ1-42) was injected intracerebroventricularly into rats. The Morris water maze (MWM) test was used to evaluate rat cognitive performance, and tsRNA-sequencing was conducted to examine tsRNA expression in the rat hippocampus. Potential targets were validated by quantitative real-time polymerase chain reaction (qRT-PCR). Bioinformatic analyses were conducted to investigate the biological function of candidate tsRNAs. ResultsThe learning and memory deficits of Aβ1–42-induced AD rats, assessed by MWM tests, were clearly ameliorated by BSTSF treatment. A total of 387 tsRNAs were detected in the rat hippocampus. Among them, 13 were significantly dysregulated in AD rats compared with sham control rats, while 57 were markedly altered by BSTSF treatment, relative to untreated AD rats (fold change ≥ 2 and P < 0.05). Moreover, six BSTSF treatment-related tsRNAs were identified and validated by qRT-PCR. Bioinformatic analyses indicated that the six treatment-related tsRNAs had potential therapeutic roles, via multiple signaling pathways and Gene Ontology biological functions, including cyclic adenosine monophosphate and retrograde endocannabinoid signaling. ConclusionThis study identified a previously uncharacterized mechanism underlying the effects of BSTSF in alleviating the learning and memory deficits in Aβ1–42-induced AD rats, demonstrating that tsRNAs are potential therapeutic targets of BSTSF in the treatment of AD.

Differential expression of transfer RNA-derived small RNAs in IgA nephropathy.

Background:IgA nephropathy (IgAN) is one of the most common forms of primary glomerulonephritis. Recent studies have indicated that small noncoding RNAs, such as tRNA-derived small RNAs (tsRNAs), might be novel biomarkers for glomerulonephritis. We therefore investigated the potential roles and possible functions of the tsRNAs in IgAN.Method:Peripheral blood mononuclear cells (PBMCs) were extracted from blood samples of the patients with IgAN and healthy control groups. The expression profiles of tsRNAs were assessed by small RNA sequencing (RNA-Seq) in PBMCs of the IgAN and control groups. Dysregulated tsRNAs were selected for validation by quantitative real-time polymerase chain reaction (qRT-PCR). Target gene prediction and enrichment were performed by bioinformatics analysis.Results:The results revealed that 143 significantly upregulated and 202 significantly downregulated tsRNAs were differentially altered in the IgAN group compared with the control group. Five upregulated tsRNAs (tRF-Val-AAC-007, tRF-Ala-AGC-063, tRF-Gln-CTG-010, tRF-Tyr-GTA-011 and tRF-Thr-AGT-007) and 3 downregulated tsRNAs (tiRNA-Val-TAC-004, tRF-Gly-CCC-005 and tRF-His-GTG-006) were selected for validation by qRT-PCR; the results were consistent with the sequencing data. Gene Ontology (GO) analysis revealed that the target genes predicted by upregulated tsRNAs were mostly enriched in “nucleic acid metabolic process," “intracellular part," and “ion binding," whereas the target genes predicted by downregulated tsRNAs were mostly enriched in “regulation of cellular component organization," “membrane-bound organelle," and “ion binding." Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the target genes predicted by upregulated tsRNAs were mostly enriched in “herpes simplex virus 1 infection," whereas the target genes predicted by downregulated tsRNAs were mostly enriched in “circadian rhythmConclusions:The present study confirmed the differential expression of tsRNAs in patients with IgAN, and these dysregulated tsRNAs might be novel potential targets for the diagnosis and treatment of IgAN.

Systematic Analysis of tRNA-Derived Small RNAs Discloses New Therapeutic Targets of Caloric Restriction in Myocardial Ischemic Rats.

Caloric restriction (CR) is a novel dietary therapy that has a protective effect on myocardial ischemia. However, the mechanisms underlying the therapeutic effect of CR remain unclear. Transfer RNA–derived small RNAs (tsRNAs) are a novel type of short non-coding RNAs that have potential regulatory functions in various physiological and pathological processes. In this study, we explored new therapeutic targets of CR through tsRNA sequencing. Rats were randomly divided into three groups: a normal control group (norm group), isoproterenol (ISO)–induced myocardial ischemic group (MI group), and CR pretreatment plus ISO-induced myocardial ischemic group (CR + MI group). Triphenyl tetrazolium chloride staining, terminal deoxynucleotidyl transferase dUTP nick-end labeling staining, serum creatine kinase (CK) and lactic acid dehydrogenase activity detection kits, and creatine kinase isoenzyme 1 levels were used to measure the degree of myocardial ischemic injury. These indicators of myocardial ischemia were significantly improved in the CR + MI group compared with those in the MI group. In the ischemic myocardial tissue of the MI group, a total of 708 precisely matched tsRNAs were identified, and 302 tsRNAs (fold change >1.5, P < 0.05) were significantly changed when compared with those in the norm group. Furthermore, 55 tsRNAs were significantly regulated by CR pretreatment, among which five tsRNAs (tiRNA-His-GTG-004, tRF-Gly-TCC-018, tRF-Cys-GCA-022, tRF-Lys-CTT-026, tRF-Met-CAT-008) were randomly selected and verified by quantitative real-time polymerase chain reaction. In addition, predictions of target genes and bioinformatics analysis indicated that these tsRNAs may play a therapeutic role through the regulation of macromolecular metabolism. In conclusion, our findings reveal that tsRNAs are potential therapeutic targets for CR pre-pretreatment to improve myocardial ischemic injury. This study provides new ideas for future research on elucidating the mechanisms of CR pretreatment in ameliorating myocardial ischemic injury.

Small RNA sequencing reveals a novel tsRNA-06018 playing an important role during adipogenic differentiation of hMSCs.

Transfer RNA‐derived small RNAs (tsRNAs), a novel type of non‐coding RNA derivative, are able to regulate a wide range of biological processes. What role these tsRNAs play in the regulation of human bone marrow mesenchymal stem cell (hMSCs) adipogenic differentiation remains uncertain. We induced the adipogenic differentiation of human bone marrow mesenchymal cells (hMSCs) and then performed small RNA transcriptomic sequencing, leading us to identify tsRNA‐06018 as a target of interest based upon resultant the tsRNA expression profiles. When tsRNA‐06018 was knocked down, this led to the inhibition of adipogenesis and a decrease in adipogenic marker expression. When STC2 was overexpressed, this impaired the adipogenic differentiation of these cells. We further used luciferase reporter assays to confirm that tsRNA‐06018 directly binds the 3′‐untranslated region (3′‐UTR) of STC2. In addition, we determined that both knocking down tsRNA‐06018 and overexpressing STC2 increased extracellular signal‐regulated kinase 1/2 (ERK1/2) phosphorylation within cells. We also assessed that the adipogenic differentiation of hMSCs in which tsRNA‐06018 was knocked down was further enhanced upon the addition of the ERK1/2 inhibitor U0126 as compared tsRNA‐06018 knockdown alone. Taken together, using small RNA sequencing we profiled tsRNAs in hMSCs during the process of adipogenesis, leading us to identify tsRNA‐06018 as a novel regulator of this differentiation process. This tsRNA was able to regulate adipogenic differentiation by targeting STC2 via the ERK1/2 signalling pathway.

Transfer RNA-derived small RNAs: potential applications as novel biomarkers for disease diagnosis and prognosis.

Transfer RNA-derived small RNA (tsRNA)s are novel non-coding RNAs, expressed in a variety of tissues and organs. Two subtypes of tsRNAs have been reported: tRNA-derived stress-induced RNA (tiRNA)s and tRNA-derived fragment (tRF)s. tsRNAs have been reported to play essential roles and possess different biological functions in a variety of physiological activities. Recently, tsRNAs have been implicated in a large number of diseases, such as cancers (including breast cancer, ovarian cancer, lung cancer, prostate cancer, colorectal cancer, etc.), neurological disorders, viral infections, metabolic diseases and angiogenesis-related diseases. Although the biological functions of tsRNAs are still poorly understood, correlations between dysregulated tsRNA expression and disease development have been recently reported. Additionally, their capabilities as potential biomarkers for disease diagnosis and prognosis have been revealed in clinical studies. In this review, we summarize the current knowledge of tsRNAs, and discuss their potential clinical applications as biomarkers in different diseases. Although the regulation of tsRNAs is similar to miRNAs in regards to the related physiological and pathological processes, the higher stability and expression levels of tsRNAs place them as ideal biomarkers for the diagnosis and prognosis in cancer and other diseases. Therefore, it is worth to verify the possibility and reliability of these reported tsRNAs as potential biomarkers for clinical applications in disease diagnosis and prognosis.

The role of Transfer RNA-Derived Small RNAs (tsRNAs) in Digestive System Tumors.

Transfer RNA-derived small RNA(tsRNA) is a type of non-coding tRNA undergoing cleavage by specific nucleases such as Dicer. TsRNAs comprise of tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs). Based on the splicing site within the tRNA, tRFs can be classified into tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF. TiRNAs can be classified into 5′-tiRNA and 3′-tiRNA. Both tRFs and tiRNAs have important roles in carcinogenesis, especially cancer of digestive system. TRFs and tiRNAs can promote cell proliferation and cell cycle progression by regulating the expression of oncogenes, combining with RNA binding proteins such as Y-box binding protein 1 (YBX1) to prevent transcription. Despite many reviews on the basic biological function of tRFs and tiRNAs, few have described their correlation with tumors especially gastrointestinal tumor. This review focused on the relationship of tRFs and tiRNAs with the biological behavior, clinicopathological characteristics, diagnosis, treatment and prognosis of digestive system tumors, and would provide novel insights for the early detection and treatment of digestive system tumors.

Transfer RNA-Derived Small Non-Coding RNA: Dual Regulator of Protein Synthesis.

Transfer RNA-derived small RNAs (tsRNAs) play a role in various cellular processes. Accumulating evidence has revealed that tsRNAs are deeply implicated in human diseases, such as various cancers and neurological disorders, suggesting that tsRNAs should be investigated to develop novel therapeutic intervention. tsRNAs provide more complexity to the physiological role of transfer RNAs by repressing or activating protein synthesis with distinct mechanisms. Here, we highlight the detailed mechanism of tsRNA-mediated dual regulation in protein synthesis and discuss the necessity of novel sequencing technology to learn more about tsRNAs.

Differential Expressions of microRNAs and Transfer RNA-derived Small RNAs: Potential Targets of Choroidal Neovascularization

ABSTRACTPurpose: Choroidal neovascularization (CNV) is one of the major clinical characteristics of neovascular age-related macular degeneration (AMD). Small non-coding RNAs, such as microRNAs (miRNAs) and transfer RNA-derived small RNAs (tsRNAs) play key roles in diverse biological functions. The purpose of the study was to investigate the roles and possible functions of the miRNAs and tsRNAs in CNV.Methods: The mouse model of laser-induced CNV was conducted by laser photocoagulation. The expression profiles of miRNAs and tsRNAs were accessed by small RNA sequencing (RNA-Seq) in RPE-choroid-sclera complexes of mice in CNV group and control group. Selected altered miRNAs and tsRNAs were validated by qRT-PCR. Target genes were predicted by informatics analysis and intersected with the previous microarray study of altered mRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted to reveal the biological functions and signaling pathways with which these target genes are most enriched.Results: The results revealed that 79 miRNAs and 72 tsRNAs in total were significantly altered in the RPE-choroid-sclera complexes of CNV mice. GO analysis revealed that the altered target genes of the selected miRNAs most enriched in immune response, integral component of membrane and peptide binding, while the altered target genes of tsRNAs most enriched in regulation of immune system process, extracellular region, and core promoter binding. Moreover, KEGG pathway analysis demonstrated that altered target genes of miRNAs and tsRNAs most enriched in hematopoietic cell lineage and nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway, respectively.Conclusions: Our study identified differential expressions of miRNAs and tsRNAs in CNV model, and these altered miRNAs and tsRNAs might be novel potential targets in treating CNVs in patients with neovascular AMD.

Alterations in sperm-inherited noncoding RNAs associate with late-term fetal growth restriction induced by preconception paternal alcohol use

Using a mouse model, our group recently described an association between chronic paternal alcohol use prior to conception and deficits in offspring growth. Here, we sought to determine the impact of alcohol exposure on male reproductive physiology and the association of sperm-inherited noncoding RNAs with the transmission of the observed growth defects. Alcohol exposure did not appreciably alter male reproductive physiology or fertility. However, chronic alcohol use reproducibly induced late-term fetal growth restriction in the offspring, which correlated with a shift in the proportional ratio of transfer RNA-derived small RNAs to Piwi-interacting RNAs, as well as altered enrichment of microRNAs miR21, miR30, and miR142 in alcohol-exposed sperm. Although our dataset share similarities to prior works examining the impact of paternal stress on offspring phenotype, we were unable to identify any changes in plasma corticosterone, indicating alcohol may alter sperm-inherited noncoding RNAs through distinct mechanisms.

Metazoan tsRNAs: Biogenesis, Evolution and Regulatory Functions.

Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of regulatory non-coding RNAs that play important roles in post-transcriptional regulation across a variety of biological processes. Here, we review the recent advances in tsRNA biogenesis and regulatory functions from the perspectives of functional and evolutionary genomics, with a focus on the tsRNA biology of Drosophila. We first summarize our current understanding of the biogenesis mechanisms of different categories of tsRNAs that are generated under physiological or stressed conditions. Next, we review the conservation patterns of tsRNAs in all domains of life, with an emphasis on the conservation of tsRNAs between two Drosophila species. Then, we elaborate the currently known regulatory functions of tsRNAs in mRNA translation that are independent of, or dependent on, Argonaute (AGO) proteins. We also highlight some issues related to the fundamental biology of tsRNAs that deserve further study.

Genome-wide identification and characterization of transfer RNA-derived small RNAs in Plasmodium falciparum

BackgroundTransfer RNA (tRNA)-derived fragments (tRFs) have been widely identified in nature, functioning in diverse biological and pathological situations. Yet, the presence of these small RNAs in Plasmodium spp. remains unknown. Systematic identification and characterization of tRFs is therefore highly needed to understand further their roles in Plasmodium parasites, particularly in the virulent Plasmodium falciparum parasite.ResultsGenome-wide small RNAs with sizes ranging from 18–30 nucleotides from P. falciparum were deep-sequenced via Illumina HiSeq 2000 technology. In-depth analysis revealed the presence of a vast number of small RNAs originating from tRNA-coding genes, responsible for 22.4% of the total reads as the second predominant group. Three P. falciparum-derived tRF types (ptRFs) were identified as 5'ptRFs, mid-ptRFs and 3'ptRFs. The majority (90%) of ptRFs were derived from tRNAs that coded eight amino acids: Pro, Phe, Asn, Gly, Cys, Gln, His and Ala. Stem-loop reverse transcription polymerase chain reaction further confirmed the presence of tRFs in the blood stages of P. falciparum. Four new motifs with an enriched G/C feature were determined at cleavage sites that might guide the generation of ptRFs.ConclusionsTo our knowledge, this is the first report of a genome-wide investigation of ptRFs from Plasmodium species. The identification of ptRFs reveals a complex small RNA system manipulated by the malaria parasite, and might promote research on the function of tRFs in the pathogenesis of Plasmodium infections.

Prognostic and Biologic Significance of Transfer RNA-Derived Small RNAs (tsRNAs) Expression in Younger Adult Patients (Pts) with Cytogenetically Normal Acute Myeloid Leukemia (CN-AML)

Introduction: tsRNAs constitute a novel class of small non-coding RNAs (~18-40 nucleotides), which are generated during stress-induced cleavage or the maturation processes of transfer RNAs (tRNAs). This class of RNA has been recently shown (Balatti et al. PNAS 2017;114:8071; Kim et al. Nature 2017;552:57) to be dysregulated in some forms of cancer (i.e., chronic lymphocytic leukemia, lung, colon, breast and ovarian cancer). However, to our knowledge, the prognostic value and biologic implications of tsRNA expression in AML pts have not been previously studied.Aims: The aims of our study were to determine whether tsRNA expression associates with pretreatment characteristics and clinical outcome of younger [aged <60 years (y)] adults with de novo CN-AML, and to gain biological insights into the functional role of tsRNA expression in AML.Methods: We conducted small RNAseq in a training set (n=208; median age, 48 y; range, 18-59 y) and a validation set (n=90; median age, 45 y; range 17-59 y) of younger adults with de novo CN-AML. None of the clinical or molecular parameters analyzed in this study were significantly different between the two sets. All pts were treated on frontline Cancer and Leukemia Group B/Alliance protocols. To obtain the expression of tsRNAs, we applied a bioinformatics workflow to small RNAseq data of a cohort of 20 CN-AML pts, in association with data, which were collected via custom array assay (Pekarsky et al. PNAS 2016;113:5071).Results: We obtained the expression data of 136 tsRNAs in both sets. Next, we derived a signature (3-tsRNA) composed of 3 tsRNAs (tsRNA20, tsRNA64, and tsRNA66), which were associated with event-free survival at the significance level of P<.001. We used the 3rd quartile as a cutoff in each set to discriminate between pts with a 3-tsRNAlow (1st to 3rd quartile) and those with 3-tsRNAhigh (4th quartile) score. With respect to clinical outcome, pts with 3-tsRNAhigh score had a worse disease-free survival (DFS; 5-y rates, 23% v 43%; P=.01) and overall survival (OS; 5-y rates, 25% v 45%; P=.003) in the training set (Figure 1). These results were confirmed in the validation set (5-y DFS rates, 12% v 50%; P=.003; 5-y OS rates, 18% v 58%; P=.002). In multivariable analyses, 3-tsRNAhigh score independently associated with shorter DFS (P=.02; HR: 2.34) and OS (P=.03; HR: 1.98) after adjusting for other co-variates [i.e., internal tandem duplication of the FLT3 gene (FLT3-ITD) and MN1 expression].Regarding pretreatment clinical and molecular features in the training set, pts with a 3-tsRNAhigh score had a higher percent of bone marrow blasts (P=.03) and tended to have a higher percent of blood blasts (P=.06). 3-tsRNAhigh scorers had a higher frequency of FLT3-ITD (P=.01) and DNMT3A non-R882 mutations (P=.03), and were marginally more likely to have an ASXL1 (P=.06) or RUNX1 mutation (P=.06). Pts with 3-tsRNAhigh score were less likely to harbor NPM1 mutations (P=.03).To gain initial insights into the biological significance of tsRNA expression in AML, we performed loss of function experiments and knocked-down (KD) all 3 tsRNAs using customized single strand RNA-inhibitors. Of the tsRNAs tested, only KD of tsRNA20 and tsRNA66 decreased the proliferative capacity of THP-1 and OCI-AML3 cells, as measured by MTS reagent degradation (tsRNA20: P=.002 and P=.04, respectively; tsRNA66: P=.009 and P=.07, respectively). Additionally, these cell lines showed higher frequency of apoptotic cells 48 hours after KD (tsRNA20: P=.007 and P=.008, respectively; tsRNA66: P<.001 and P=.009, respectively).Conclusion: We conclude that tsRNAs represent a novel prognostic and biologically important class of non-coding RNAs in CN-AML. DisclosuresPowell:Rafael Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees. Uy:Curis: Consultancy; GlycoMimetics: Consultancy. Kolitz:Magellan Health: Consultancy, Honoraria. Wang:Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees; Jazz: Speakers Bureau; Novartis: Speakers Bureau; Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy; Jazz: Speakers Bureau; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees; Novartis: Speakers Bureau.

Abstract LB-390: A transfer RNA derived small RNA affects translation in rapidly dividing cells and a target for hepatocellular carcinoma

Abstract There are tens of thousands of different transfer RNA-derived small RNAs (tsRNAs) of 18-40 nucleotides in length in mammalian cells. In recent years there is accumulating evidence suggesting that these RNAs can play different yet important roles in gene regulations. Nevertheless, in most cases, the biological roles of these RNAs have yet to be defined. Using a variety of locked nucleic acid/antisense oligonucleotide (LNA/ASO)-mediated strategies, we found that inhibition of one specific 3'tsRNA, induces apoptosis in rapidly dividing cells. Inhibition of the tsRNA but not the mature tRNA reduced the translation of ribosomal protein S28 (RPS28) and S15 (RPS15) mRNAs and led to a block in pre-18S ribosomal RNA processing, and ultimately a decrease in the number of 40S ribosomal subunits. Using a modified ChIRP method, we found that the tsRNA binds to ribosomal protein S28 mRNA and by genetic complementation analyses established the binding sites contained within the mRNAs. Furthermore, we established that tsRNA binds to duplexed target sites in RPS28 and RPS15 mRNAs and enhances their translation by perhaps helping to unfold their secondary structures. The systemic delivery of a specific anti-tsRNA oligonucleotides into mice (the tsRNA sequence is the same in mouse and humans) did not cause liver injury in normal mice but induced apoptosis and a significant growth retardation of patient-derived orthotopic hepatocellular carcinomas surgically implanted into mouse livers. Our result establishes a newly defined post-transcriptional mechanism of gene regulation and provides a novel target for cancer therapeutics. Citation Format: Hak Kyun Kim, Gabriele Fuchs, Shengchun Wang, Wei Wei, Yue Zhang, Hyesuk Park, Biswajoy Roy-Chaudhuri, Pan Li, Jianpeng Xu, Kirk Chu, Feijie Zhang, Mei-sze Chua, Samuel So, Cliff Zhang, Peter Sarnow, Mark A. Kay. A transfer RNA derived small RNA affects translation in rapidly dividing cells and a target for hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-390.

Drosophila tsRNAs preferentially suppress general translation machinery via antisense pairing and participate in cellular starvation response.

Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of small RNAs, yet their regulatory roles have not been well understood. Here we studied the molecular mechanisms and consequences of tsRNA-mediated regulation in Drosophila. By analyzing 495 public small RNA libraries, we demonstrate that most tsRNAs are conserved, prevalent and abundant in Drosophila. By carrying out mRNA sequencing and ribosome profiling of S2 cells transfected with single-stranded tsRNA mimics and mocks, we show that tsRNAs recognize target mRNAs through conserved complementary sequence matching and suppress target genes by translational inhibition. The target prediction suggests that tsRNAs preferentially suppress translation of the key components of the general translation machinery, which explains how tsRNAs inhibit the global mRNA translation. Serum starvation experiments confirm tsRNAs participate in cellular starvation responses by preferential targeting the ribosomal proteins and translational initiation or elongation factors. Knock-down of AGO2 in S2 cells under normal and starved conditions reveals a dependence of the tsRNA-mediated regulation on AGO2. We also validated the repressive effects of representative tsRNAs on cellular global translation and specific targets with luciferase reporter assays. Our study suggests the tsRNA-mediated regulation might be crucial for the energy homeostasis and the metabolic adaptation in the cellular systems.

Transfer RNA-derived small RNAs in plants.

Rather than random degradation products, the 18 to 40 nucleotides (nt) transfer RNA-derived small RNAs (tsRNAs) are RNA species generated specifically from pre-RNAs or mature tRNAs in archaea, bacteria and eukaryotes. Recent studies from animal systems have shown that tsRNAs are important non-coding RNAs that regulate gene expression at the transcriptional and/or post-transcriptional levels. They are involved in various biological processes, such as cell proliferation, tumor genesis, stress response and intergenerational epigenetic inheritance. In this review, we will summarize the discovery, biogenesis, and function of tsRNAs in higher plants. In addition, analysis on tsRNAs from lower plants is shown.

Transfer RNA-derived small RNAs in the cancer transcriptome.

The cellular lifetime includes stages such as differentiation, proliferation, division, senescence and apoptosis. These stages are driven by a strictly ordered process of transcription dynamics. Molecular disruption to RNA polymerase assembly, chromatin remodelling and transcription factor binding through to RNA editing, splicing, post-transcriptional regulation and ribosome scanning can result in significant costs arising from genome instability. Cancer development is one example of when such disruption takes place. RNA silencing is a term used to describe the effects of post-transcriptional gene silencing mediated by a diverse set of small RNA molecules. Small RNAs are crucial for regulating gene expression and microguarding genome integrity. RNA silencing studies predominantly focus on small RNAs such as microRNAs, short-interfering RNAs and piwi-interacting RNAs. We describe an emerging renewal of interest in a ‘larger’ small RNA, the transfer RNA (tRNA). Precisely generated tRNA-derived small RNAs, named tRNA halves (tiRNAs) and tRNA fragments (tRFs), have been reported to be abundant with dysregulation associated with cancer. Transfection of tiRNAs inhibits protein translation by displacing eukaryotic initiation factors from messenger RNA (mRNA) and inaugurating stress granule formation. Knockdown of an overexpressed tRF inhibits cancer cell proliferation. Recovery of lacking tRFs prevents cancer metastasis. The dual oncogenic and tumour-suppressive role is typical of functional small RNAs. We review recent reports on tiRNA and tRF discovery and biogenesis, identification and analysis from next-generation sequencing data and a mechanistic animal study to demonstrate their physiological role in cancer biology. We propose tRNA-derived small RNA-mediated RNA silencing is an innate defence mechanism to prevent oncogenic translation. We expect that cancer cells are percipient to their ablated control of transcription and attempt to prevent loss of genome control through RNA silencing.

Role of Small RNAs in Trypanosomatid Infections.

Trypanosomatid parasites survive and replicate in the host by using mechanisms that aim to establish a successful infection and ensure parasite survival. Evidence points to microRNAs as new players in the host-parasite interplay. MicroRNAs are small non-coding RNAs that control proteins levels via post-transcriptional gene down-regulation, either within the cells where they were produced or in other cells via intercellular transfer. These microRNAs can be modulated in host cells during infection and are among the growing group of small regulatory RNAs, for which many classes have been described, including the transfer RNA-derived small RNAs. Parasites can either manipulate microRNAs to evade host-driven damage and/or transfer small RNAs to host cells. In this mini-review, we present evidence for the involvement of small RNAs, such as microRNAs, in trypanosomatid infections which lack RNA interference. We highlight both microRNA profile alterations in host cells during those infections and the horizontal transfer of small RNAs and proteins from parasites to the host by membrane-derived extracellular vesicles in a cell communication mechanism.

Transfer RNA-derived Small RNAs: Degradation Fragments or Novel Regulatory Molecules?*

Transfer RNAs (tRNAs) with classic clover structure, have been researched as a key component of cellular protein synthesis machine for decades. However, the pace of progress in the understanding of tRNA function is still staggering, especially in the role of tRNA as the precursor of potential molecules to regulate gene expression globally. Several recent studies suggest that some tRNA-derived small RNAs have been detected in many cell lines by deep sequencing. These cleavage products of tRNAs are indicated to interact with some important protein factors like Dicer and Ago family in microRNA processing system. In additional, luciferase reporter assay results implied that the small RNAs derived from tRNA might play some roles in response to the stress as regulatory molecules with microRNA-like features. If their regulatory functions were to be confirmed by more evidence, these newly revealed RNAs would provide expanding insight into the repertoire of small noncoding RNAs.