Similar Datasets
Project description:During stress conditions, particular tRNAs are cleaved by stress-induced endonucleases resulting in distinct tRNA-derived small RNAs (tsRNAs). These small RNAs have been implicated in a wide array of mostly stress-related biological processes, however how exactly they exert their functions mechanistically is still largely unknown. Since parental tRNAs carry post-transcriptional modifications, stress-induced tsRNAs are likely modified, too. In order to use endogenously modified tsRNAs, we developed a biochemical pipeline for the production and purification of specific tsRNAs using a human cell culture system. Ectopic expression of Angiogenin combined with chromatography of small RNAs resulted in the production of endogenously modified 5’ tsRNAs on a preparative scale. Small RNA sequencing on purified tsRNAs was used to determine the identity and purity of the 5’ tsRNA preparations.
2020-03-01 | GSE139124 | GEO
Project description:Liquid biopsy is noninvasive and convenient to detect cancer-derived materials in blood or other body fluids. The aim of this study was to identify tRNA-derived small RNAs (tsRNAs) in plasma that could distinguish patients with breast cancer (BC) from healthy controls. Basing on high-throughput sequencing, 15 significantly upregulated tsRNAs were selected and assessed in cell supernatants and cell lines. 6 tsRNAs were identified and verified in a large cohort of 120 patients with BC and 112 healthy controls. tRF-Arg-CCT-017, tRF-Gly-CCC-001 and tiRNA-Phe-GAA-003 could serve as novel diagnostic biomarkers. Meanwhile, tRF-Arg-CCT-017 and tiRNA-Phe-GAA-003 could also act as prognostic biomarkers. Target genes of these tsRNAs were related to the development of cancer. These results suggest that specific tsRNAs in plasma might serve as diagnostic and prognostic biomarkers of BC.
2020-10-08 | GSE158945 | GEO
Project description:Our previous work has focused on the relationship between non-coding RNAs and sepsis, so we chose to use microarray analysis to investigate the relationship between septic cardiomyopathy and a novel class of small non-coding RNA - tRNA-derived small RNAs(tsRNAs). Meanwhile, tRNA-derived small RNA has been studied in many cardiovascular diseases, but the relationship between tsRNAs and septic cardiomyopathy has not been investigated. We sought to analyze changes of tsRNAs expression profile in septic cardiomyopathy and reveal an important role for tsRNAs.
2022-09-29 | GSE214251 | GEO
Project description:Purpose: Next-generation sequencing (NGS) is the main way to mine ncRNA. The purpose of this study is to screen out tRNA-derived small RNAs (tsRNAs) that are differentially expressed in proliferative and quiescent HASMCs Methods: tsRNAs profiles of proliferative and quiescent HASMCs were generated by deep sequencing, in triplicate, using Illumina NextSeq 500. The sequence reads that passed Illumina chastity filter were used for the following analysis. Trimmed reads (with 5ʹ, 3ʹ-adaptor bases removed) were aligned to mature-tRNA and pre-tRNA reference sequences. The alignment statistical analysis was applied to retain the valid sequences for subsequent tsRNAs expression profiles and differential expression analysis. Results: Using an optimized data analysis workflow, we mapped about 8 million sequence reads per sample to mature-tRNA and pre-tRNA sequences from GtRNAdb and identified 3,891 tsRNAs in the proliferative and quiescent HASMCs. According to the standardized TPM, 887 up-regulated and 951 down-regulated tsRNAs were found in the proliferative HASMCs (fold change > 2, P < 0.05).
2021-01-12 | GSE164540 | GEO
Project description:Sequencing profiling data of tRNA-derived small RNAs (tsRNAs) in human colorectal cancer.
| PRJNA589298 | ENA
Project description:Small RNA sequencing on affinity capture-purified tRNA-derived small RNAs (tsRNAs)
| PRJNA578532 | ENA
Project description:Rheumatic heart disease (RHD) remains a serious public health problem in developing countries. Atrial fibrillation (AF) is a medical complication of RHD. Although the understanding of disease pathogenesis has advanced in recent years, the key questions need to be addressed. 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. The present study used tsRNAs sequencing to investigate the relationship between RHD and atrial fibrillation (AF). Three paired myocardial papilla were taken from six rheumatic RHD patients with AF (3 cases) or without AF (3 cases) from January 2016 to January 2017 in Xiangya Hospital, Central South University. A total of 219 precisely matched tsRNAs were identified, and 77 tsRNAs (fold change > 2.0 and P < 0.05) were differently changed. Three tsRNAs (AS-tDR-001269, AS-tDR-001363, AS-tDR-006049) were randomly selected and verified by qRT-PCR. The results of qRT-PCR were consistent with tsRNAs sequencing, suggesting the tsRNAs sequencing was reliable. Then bioinformatics analysis indicated that the target genes were abundant in regulation of transcription, DNA binding, intracellular. Most of the genes were predicted to interplay with cytokine-cytokine receptor by KEGG analysis. Our findings uncover the pathological process of AF in RHD through tsRNAs sequencing. This study provides new ideas for future research on elucidating the mechanism of AF in RHD and offers potential new candidates for the treatment and diagnosis of RHD.
2021-12-23 | GSE185581 | GEO
Project description:Liquid biopsy is noninvasive and convenient to detect cancer-derived materials in blood or other body fluids. The aim of this study was to identify tRNA-derived small RNAs (tsRNAs) in plasma that could distinguish patients with breast cancer (BC) from healthy controls. Basing on high-throughput sequencing, 15 significantly upregulated tsRNAs were selected and assessed in cell supernatants and cell lines. 6 tsRNAs were identified and verified in a large cohort of 120 patients with BC and 112 healthy controls. tRF-Arg-CCT-017, tRF-Gly-CCC-001, and tiRNA-Phe-GAA-003 could serve as novel diagnostic biomarkers. Meanwhile, tRF-Arg-CCT-017 and tiRNA-Phe-GAA-003 could also act as prognostic biomarkers. Target genes of these tsRNAs were related to the development of cancers. These results suggested that specific tsRNAs in plasma might serve as diagnostic and prognostic biomarkers of BC.
| S-EPMC7785726 | biostudies-literature
Project description:Malignant tumours area leading cause of death globally, accounting for approximately 13% of all deaths. A detailed understanding of the mechanism(s) of the occurrence and development of malignant tumours and identification of relevant therapeutic targets are therefore key to tumour treatment. tsRNAs(tRNA-derived small RNAs)-also known as TRFs (tRNA-derived fragments), tiRNAs (tRNA-derived stress-induced RNAs), tRNA halves, etc.-are a recently identified class of small noncoding RNAs that are generated from mature tRNA or tRNA precursors through cleavage by enzymes such as angiogenin, Dicer, RNase Z, and RNase P. Several studies have confirmed that dysregulation of tsRNAs is closely related to the tumorigenesis of breast cancer, nasopharyngeal cancer, lung cancer, and so on. Furthermore, research indicates that tsRNAs can be used as clinical diagnostic markers and therapeutic targets for cancer. In our review, we summarized the recent research progress on the role and clinical application of tsRNAs in tumorigenesis and progression. Video Abstract.
| S-EPMC10362710 | biostudies-literature
Project description:Microarray detected 816 statistically differentially expressed tsRNAs, of which 243 tsRNAs were upregulated and 573 were downregulated. Eight validated tsRNAs in the results of Real Time-PCR were consistent with the small RNA microarray: four upregulations (tRF3a-AspGTC-9, 5'tiRNA-31-GluCTC-16, i-tRF-31:54-Val-CAC-1 and tRF3b-TyrGTA-4) and four downregulation (5'tiRNA-33-LysTTT-4, i-tRF-8:32-Val-AAC-2, i-tRF-2:30-His-GTG-1, and i-tRF-15:31-Lys-CTT-1).
2023-06-30 | GSE228750 | GEO