tRFs结构及其生物学功能

tRFs（tRNA-derived RNA fragments）是来源于tRNA的小分子非编码RNA,由前体tRNA或成熟tRNA经加工和修饰而成,在生物界中广泛存在。tRFs深度测序结果表明,tRFs可能并不是由tRNA随机裂解产生的,而是通过某个特定机制生成。根据来源不同,tRFs可被分为tRF-1、tRF-2、tRF-3、tRF-5和tiR。tRFs具有类似于miRNA的调控功能,并能参与调控基因转录和翻译,细胞增殖以及细胞应激反应。新近研究表明,乳腺癌细胞中某些特异性的tRFs（如tRF^GlyTCC和tRF^AspGTC）,可通过与Y-box结合蛋白1（Y box binding protein 1, YB-1）结合进而抑制癌细胞的生长和转移。另有研究表明,tRFs还可通过细胞色素c介导的信号转导途径来发挥其抑制癌细胞凋亡的功能。由此可见,tRFs在调控癌症发生发展过程中也具有重要调控作用,然而其机制仍不清楚。本文综述了tRFs结构和分布、生物学功能及其作用机制的研究现状,旨在为tRFs相关研究提供参考。     

The MELAS mutation m.3243A>G alters the expression of mitochondrial tRNA fragments

Recent evidences highlight the importance of mitochondria-nucleus communication for the clinical phenotype of oxidative phosphorylation (OXPHOS) diseases. However, the participation of small non-coding RNAs (sncRNAs) in this communication has been poorly explored. We asked whether OXPHOS dysfunction alters the production of a new class of sncRNAs, mitochondrial tRNA fragments (mt tRFs), and, if so, whether mt tRFs play a physiological role and their accumulation is controlled by the action of mt tRNA modification enzymes. To address these questions, we used a cybrid model of MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes), an OXPHOS disease mostly caused by mutation m.3243A>G in the mitochondrial tRNA^Leu(UUR) gene. High-throughput analysis of small-RNA-Seq data indicated that m.3243A>G significantly changed the expression pattern of mt tRFs. A functional analysis of potential mt tRFs targets (performed under the assumption that these tRFs act as miRNAs) indicated an association with processes that involve the most common affected tissues in MELAS. We present evidences that mt tRFs may be biologically relevant, as one of them (mt i-tRF GluUUC), likely produced by the action of the nuclease Dicer and whose levels are Ago2 dependent, down-regulates the expression of mitochondrial pyruvate carrier 1 (MPC1), promoting the build-up of extracellular lactate. Therefore, our study underpins the idea that retrograde signaling from mitochondria is also mediated by mt tRFs. Finally, we show that accumulation of mt i-tRF GluUUC depends on the modification status of mt tRNAs, which is regulated by the action of stress-responsive miRNAs on mt tRNA modification enzymes.     

Comparative expression analysis of tRF-3001a and tRF-1003 with corresponding miRNAs (miR-1260a and miR-4521) and their network analysis with breast cancer biomarkers

Molecular Biology Reports - MicroRNAs and tRFs (tRNA-derived fragments) are small non-coding RNAs that are promising breast cancer (BC) biomarkers. miRNA sequences are found within tRFs. For...     

Biochemical properties and progress in cancers of tRNA-derived fragments

tRNA-derived small RNAs (tRFs), a kind of noncoding RNAs, are generated from transfer RNAs. tRFs have some types according to their source and sizes. They play important roles in cell life and carcinogenesis. In this paper, we review the biogenesis and biological properties. We also focus on current progress of tRFs and some tsRNAs such as tRF-Leu-CAG, which have been studied or will be further investigated in tumorgenesis and diagnostic biomarkers in the clinic.     

tRNA来源的小片段RNA——新的基因表达调控因子

转移核糖核酸(tRNA)是蛋白质合成的关键接头分子,特异性识别信使RNA(mRNA)的密码子信息,将其接载的氨基酸基团掺入到新生多肽链中。最新研究表明,在很多物种中,在某些特定情况下,tRNA或其前体被特异性剪切产生tRNA来源的小片段RNA(tRNA-derived fragment,tRF)。这类tRF是一类新的基因表达调控因子,其发挥作用的机制多样,如某些tRF以microRNA方式抑制mRNA翻译;某些tRF作为逆转录病毒RNA基因组的逆转录引物;而某些tRF参与了前体rRNA剪切复合物的组装。此外,细胞受胁迫产生的带有多聚鸟苷酸模块的tRF则会竞争性抑制延伸因子elF4G与mRNA的结合,从而抑制蛋白质翻译。随着研究的继续深入,对tRF的发生发展、作用机制以及在疾病中的潜在作用将会进一步丰富。拟从tRF作为新的基因表达调控分子的角度,简要介绍tRF发挥作用的分子机制。     

Transfer RNA-derived fragments target and regulate ribosome-associated aminoacyl-transfer RNA synthetases

Ribosome-associated noncoding (ranc) RNAs are a novel class of short regulatory RNAs with functions and origins that have not been well studied. In this present study, we functionally characterized the molecular activity of Saccharomyces cerevisiae transfer RNA (tRNA)-derived fragments (tRFs) during protein biosynthesis. Our results indicate ribosome-associated tRFs derived from both 5′ (ranc-5′-tRFs) and 3′-part of tRNAs (ranc-3′-tRFs) have regulatory roles during translation. We demonstrated five 3′-tRFs and one 5′-tRF associate with a small ribosomal subunit and aminoacyl-tRNA synthetases (aa-RSs) in yeast. Furthermore, we discovered that four yeast aa-RSs interact directly with yeast ribosomes. tRFs interactions with ribosome-associated aa-RSs correlate with impaired efficiency of tRNA aminoacylation.     

水稻雄配子体发育过程中tRNA片段的生物信息学分析

tRNA片段(tRF)是tRNA通过非随机剪切产生的RNA片段, 其产生和功能机制尚不明确; 而在水稻(Oryza sativa)雄配子体发育过程中, 人们对tRNA更是知之甚少。通过高通量测序, 在水稻雄配子体发育过程中发现了长度范围较大的tRFs; 进一步采用logo对tRFs两端的序列进行分析, 发现了4个有序列特征(其中3个未见报道)和1个无序列特征的酶切位点; 通过NCBI Blast预测了tRF靶基因, 发现其大多靶向转座因子。研究结果对揭示tRF产生机制以及水稻雄配子体发育研究有一定的参考价值。     

Effects of G-quadruplex topology on translational inhibition by tRNA fragments in mammalian and plant systems in vitro

The folding of tRNA fragments (tRFs) into G-quadruplex structures and the implications of G-quadruplexes in translational inhibition have been studied mainly in mammalian systems. To increase our knowledge of these phenomena, we determined the influence of human and plant tRFs and model G-quadruplexes on translation in rabbit reticulocyte lysate and wheat germ extract. The efficiency of translational inhibition in the mammalian system was strongly associated with the type of G-quadruplex topology. In the plant system, the ability of a small RNA to adopt the G-quadruplex conformation was not sufficient to repress translation, indicating the importance of other structural determinants.     

A novel 3’tRNA-derived fragment tRF-Val promotes proliferation and inhibits apoptosis by targeting EEF1A1 in gastric cancer

At present, it is commonly believed that tRFs and tiRNAs are formed by the specific and selective shear of tRNAs under certain pressure stimulation, rather than by random degradation of tRNA. tRFs and tiRNAs have been reported to contribute to the biological process of a variety of human cancers. However, the evidence for the mechanisms of tRFs and tiRNAs in the occurrence and development of gastric cancer (GC) is still insufficient. Here, we aimed to explore the carcinogenic roles of tRFs and tiRNAs in GC with RNA-sequencing technique, and found a novel 3’tRNA-derived fragment tRF-Val was significantly upregulated in GC tissues and cell lines. tRF-Val expression was positively correlated with tumor size and the depth of tumor invasion in GC tissues. Functionally, tRF-Val promoted proliferation and invasion, and inhibited apoptosis in GC cells. Mechanistically, tRF-Val directly bound to the chaperone molecule EEF1A1, mediated its transport into the nucleus and promoted its interaction with MDM2 (a specific p53 E3 ubiquitin ligase), thus inhibiting the downstream molecular pathway of p53 and promoting GC progression. These findings provided a new potential therapeutic target for GC and a new explanation for the occurrence of GC.Subject terms: Cancer genomics, Small RNAs     

An emerging role of the 5′ termini of mature tRNAs in human diseases: Current situation and prospects

The fundamental biological roles of a class of small noncoding RNAs (sncRNAs), derived from mature tRNAs or pre-tRNAs, in human diseases have received increasing attention in recent years. These ncRNAs are called tRNA-derived fragments (tRFs) or tRNA-derived small RNAs (tsRNAs). tRFs mainly include tRF-1, tRF-5, tRF-3 and tRNA halves (tiRNAs or tRHs), which are produced by enzyme-specific cleavage of tRNAs. Here, we classify tRF-5 and 5′ tiRNAs into the same category: 5′-tRFs and review the biological functions and regulatory mechanisms of 5′-tRFs in cancer and other diseases (metabolic diseases, neurodegenerative diseases, pathological stress injury and virus infection) to provide a new theoretical basis for the diagnosis and treatment of diseases.     

Characterization of Sus scrofa Small Non-Coding RNAs Present in Both Female and Male Gonads

Small non-coding RNAs (sncRNAs) are indispensable for proper germ cell development, emphasizing the need for greater elucidation of the mechanisms of germline development and regulation of this process by sncRNAs. We used deep sequencing to characterize three families of small non-coding RNAs (piRNAs, miRNAs, and tRFs) present in Sus scrofa gonads and focused on the small RNA fraction present in both male and female gonads. Although similar numbers of reads were obtained from both types of gonads, the number of unique RNA sequences in the ovaries was several times lower. Of the sequences detected in the testes, 2.6% of piRNAs, 9% of miRNAs, and 10% of tRFs were also present in the ovaries. Notably, the majority of the shared piRNAs mapped to ribosomal RNAs and were derived from clustered loci. In addition, the most abundant miRNAs present in the ovaries and testes are conserved and are involved in many biological processes such as the regulation of homeobox genes, the control of cell proliferation, and carcinogenesis. Unexpectedly, we detected a novel sncRNA type, the tRFs, which are 30–36-nt RNA fragments derived from tRNA molecules, in gonads. Analysis of S. scrofa piRNAs show that testes specific piRNAs are biased for 5′ uracil but both testes and ovaries specific piRNAs are not biased for adenine at the 10^th nucleotide position. These observations indicate that adult porcine piRNAs are predominantly produced by a primary processing pathway or other mechanisms and secondary piRNAs generated by ping-pong mechanism are absent.