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TRNA-Derived Fragments Expression Profile and Their Potential Roles in Lung Adenocarcinoma Tissues

ABSTRACT: tRNA-Derived Fragments Expression Profile and Their Potential Roles in Lung Adenocarcinoma Tissues

PROVIDER: PRJNA698574 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13602452.fastq.gz	Fastqsanger.gz
	SRR13602453.fastq.gz	Fastqsanger.gz
	SRR13602454.fastq.gz	Fastqsanger.gz
	SRR13602455.fastq.gz	Fastqsanger.gz
	SRR13602456.fastq.gz	Fastqsanger.gz

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tRNA-Derived Fragments Expression Profile and Their Potential Roles in Lung Adenocarcinoma Tissues

Project description:Transfer RNA-derived fragments (tRFs) and transfer RNA halves (tiRNAs) have been shown to play crucial roles in gene regulation. This study targets to reveal the expression profile of tRFs and tiRNAs and their possible biological roles in lung adenocarcinoma (LUAD). Five paired clinical lung adenocarcinoma tissues (LAT) and adjacent normal lung tissues (ANLT) were selected to conduct the expression of tRFs and tiRNAs. The sequencing results showed that 109 tRFs and tiRNAs were differentially expressed between LAT and ANLT, out of which 60 were upregulated and 49 were downregulated. Compared with ANLT, lower expression levels of three tRF-1s (tRF-Ser-TGA-010, tRF-Arg-CCT-018 and tRF-Val-CAC-017) in LAT were verified by quantitative real-time polymerase chain reaction. Subsequently, the putative target genes of tRF-1s were analyzed by computational prediction and the top ten significant results of GO and KEGG pathway enrichment analysis were presented. These signaling pathways are involved in the carcinogenesis of LUAD. This study has showed a landscape of tRFs and tiRNAs expression proﬁles in LUAD. Three newly found diﬀerentially expressed down-regulated tRF-1s may be involved in the pathogenesis of LUAD and might serve as potential diagnostic biomarkers.

2022-01-19 | GSE165918 | GEO

Unravelling tRNA Fragments in DENV Pathogenesis: Insights from RNA Sequencing

Project description:tRNA-derived small RNA including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs) plays significant roles in the various molecular mechanisms that underlie certain human diseases. of the generation of tRFs/tiRNAs and their potential roles during Dengue virus (DENV) infection is not yet known. Here, we have performed small RNA sequencing to identify the generation and alterations in tRF expression profiles of DENV infected Huh7 cells. Our results suggest that 733 tiRNAs/tRFs were found to be differentially expressed during DENV infection. Interestingly, 3’tRF population were found to be upregulated and i-tRF population were found to be downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed to analyze the impact of differentially expressed tRFs on DENV pathogenesis. Our results suggest the significant involvement in transcriptional regulation via RNA polymerase II promoter and metabolic pathways. Overall, our study contributes significantly to our understanding of the roles played by tRFs in the complex dynamics of DENV infection.

2024-08-10 | GSE245081 | GEO

tRNAArg-derived fragments mediate protein arginylation [tRNA]

Project description:tRNAArg-derived fragments mediate protein arginylation [tRNA]

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Expression profiles of tRNA-derived small RNAs and their potential roles in primary nasopharyngeal carcinoma

Project description:Transfer-RNA-Derived Small RNA (tsRNA) is a novel class of short non-coding RNA including stress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF). Using RNA sequencing, we evaluated the tsRNA expression profiles in the fresh nasopharyngeal carcinoma tissue specimens (n = 4) and mucosal tissue specimens (n = 4) in patients’ primary nasopharyngeal carcinoma (P-NPC) and nasopharyngitis. Bioinformatics analyses indicated that tsRNAs were the important regulators and potential new biomarkers of P-NPC.

2022-01-11 | GSE159746 | GEO

Human ANGIOGENIN is sufficient but not required for tRNA cleavage to generate tRNA fragments

Project description:To identify tRNA fragments regulated by angiogenin (ANG, Rnase 5), we sequenced 15-50nt small RNAs upon ANG overexpression and ANG knockout.

2019-10-01 | GSE130764 | GEO

Endogenous tRNA fragments suppress hypoxia-driven bone cancer progression

Project description:We report a modulated expression of tRNA fragments and microRNAs linked to chondrosarcoma progression and demonstrate a method for re-modulating this pathway

2022-05-20 | GSE86576 | GEO

Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals

Project description:Parental dietary conditions can influence the metabolic traits of offspring. In mice, paternal consumption of low protein diet alters cholesterol and lipid metabolism of progeny. Here, we examine RNA species expressed in male reproductive tissues of mice. Protein restriction leads to altered levels of multiple small RNAs in mature sperm, as well as throughout the male reproductive tract, with decreased levels of let-7 family members and increased levels of 5â?? fragments of tRNA-Gly isoacceptors. Intriguingly, tRNA fragments are scarce in the testis, but their levels increase in sperm during posttesticular maturation in the epididymis. We find that epididymosomes â?? extracellular vesicles which fuse with sperm during epididymal transit â?? exhibit RNA payloads closely matching those of mature sperm, and can deliver tRNA fragments to immature sperm in vitro both in mouse and in bull. Finally, we show that tRNA-Gly-GCC fragments play a role in repressing genes associated with the endogenous retroelement MERVL, both in ES cells and in preimplantation embryos. Our results shed light on small RNA biogenesis during post-testicular sperm maturation, and link tRNA fragments to regulation of endogenous retroelements active in the early embryo. E14 mESCs were transfected with LNA-containing oligos antisense to tRF-GG or GFP-esiRNA as control, then either total RNA was isolated or 80S ribosomes were isolated from Rnase-digested whole cell lysate, and footprints between 26-32nt were collected for ribosome profiling library construction using a kit-free protocol based on Heyer et al. 2015 NAR.

2016-01-04 | E-GEOD-74537 | biostudies-arrayexpress

Expression profiles of tRNA-derived fragments and their potential roles in lung adenocarcinoma.

Project description:BackgroundTransfer RNA-derived fragments (tRFs) and transfer RNA halves (tiRNAs) have been shown to play crucial roles in gene regulation. This study aims to reveal the expression profiles of tRFs and tiRNAs and their possible biological roles in lung adenocarcinoma (LUAD).MethodsFive paired clinical lung adenocarcinoma tissues (LAT) and adjacent normal lung tissues (ANLT) were selected to analyze the expression of tRFs and tiRNAs. Six significantly expressed tRFs and tiRNAs were selected and validated by Quantitative Real-time PCR (qPCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed.ResultsThe sequencing results showed that 109 tRFs and tiRNAs were differentially expressed between LAT and ANLT, out of which 60 were upregulated and 49 were downregulated. Compared with ANLT, lower expression levels of 3 tRF-1s (tRF-Ser-TGA-010, tRF-Arg-CCT-018, and tRF-Val-CAC-017) in LAT were verified by qPCR. Subsequently, the putative target genes of tRF-1s were analyzed by computational prediction and the top 10 significant results of GO and KEGG pathway enrichment analysis were presented.ConclusionsThis study has revealed the landscape of tRF and tiRNA expression proﬁles in LUAD. Three newly found differentially expressed downregulated tRF-1s may be involved in the pathogenesis of LUAD and may serve as potential diagnostic biomarkers, or otherwise reconcile target genes for drug development.

| S-EPMC8908152 | biostudies-literature

Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals (smallRNA-seq)

Project description:Parental dietary conditions can influence the metabolic traits of offspring. In mice, paternal consumption of low protein diet alters cholesterol and lipid metabolism of progeny. Here, we examine RNA species expressed in male reproductive tissues of mice. Protein restriction leads to altered levels of multiple small RNAs in mature sperm, as well as throughout the male reproductive tract, with decreased levels of let-7 family members and increased levels of 5â fragments of tRNA-Gly isoacceptors. Intriguingly, tRNA fragments are scarce in the testis, but their levels increase in sperm during post-testicular maturation in the epididymis. We find that epididymosomes â extracellular vesicles which fuse with sperm during epididymal transit â exhibit RNA payloads closely matching those of mature sperm, and can deliver tRNA fragments to immature sperm in vitro both in mouse and in bull. Finally, we show that tRNA-Gly-GCC fragments play a role in repressing genes associated with the endogenous retroelement MERVL, both in ES cells and in preimplantation embryos. Our results shed light on small RNA biogenesis during post-testicular sperm maturation, and link tRNA fragments to regulation of endogenous retroelements active in the early embryo. Small RNA (<40nt) profile of various tissues and cells was examined by deep sequencing

2015-12-31 | E-GEOD-75613 | biostudies-arrayexpress

tRNA-derived fragments regulate the functional maturation of neonatal β-cells [ncRNA-Seq]

Project description:Annotation of tRNA fragments relies on the alignment of signals obtained from small RNA-seq on mature tRNA positions and requires the pretreatment of the RNA to remove tRNA modifications that may interfere with sequencing.

2022-06-10 | GSE163582 | GEO

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