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Role of tRNA-derived fragments in the cross-talk between immune cells and beta cells during type 1 diabetes pathogenesis (tRF overexpression)

ABSTRACT: Role of tRNA-derived fragments in the cross-talk between immune cells and beta cells during type 1 diabetes pathogenesis (tRF overexpression)

PROVIDER: PRJNA1013944 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25940933.fastq.gz	Fastqsanger.gz
	SRR25940934.fastq.gz	Fastqsanger.gz
	SRR25940935.fastq.gz	Fastqsanger.gz
	SRR25940936.fastq.gz	Fastqsanger.gz
	SRR25940937.fastq.gz	Fastqsanger.gz

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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

Altered Expression Profiles of tRNA-derived fragments in relapsed/refractory multiple myeloma

Project description:tRNA related fragments(tRF) and tRNA halves(tiRNA) are novel class of short non-coding RNA derived from tRNAs. Using RNA sequencing, we evaluated the tRFs/tiRNAs expression profiles in relapsed/refractory multiple myeloma and multiple myeloma patients. Bioinformatics analyses indicated that tRFs/tiRNAs may be involved in the progression and drug-resistance of multiple myeloma.

2021-05-19 | GSE171003 | GEO

tRF-seq landscapes the variation of tRNA derived fragments after mouse liver injury

Project description:tRF-seq landscapes the variation of tRNA derived fragments after mouse liver injury

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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

Role of tRNA-derived fragments in the cross-talk between immune cells and beta cells during type 1 diabetes pathogenesis (tRF overexpression)

Project description:Transfer RNAs (tRNAs) play a central and well recognized role in protein synthesis. Recent studies revealed that these molecules can be cleaved to generate tRNA fragments (tRFs) with regulatory functions. Here, we studied the contribution of tRFs to pancreatic β-cell loss during the initial phases of type 1 diabetes (T1D), an autoimmune disorder characterized by the invation of immune cells in the pancreas and progressive loss of insulin-secreting cells. Small RNA-profiling showed that the pool of tRFs present in pancreatic β-cells is altered in non-obese diabetic (NOD) mice, a mouse model used to study T1D. We found that part of these changes is triggered by the exposure of β-cells to proinflammatory cytokines released during the autoimmune reaction while others result from the direct transfer of tRFs from autoreactive T lymphocytes to insulin-secreting cells via extracellular vesicles. Indeed, using an RNA-tagging approach, we could demonstrate that a group of tRFs are transferred in vivo in from CD4+CD25- T lymphocytes to pancreatic β-cells, upon T cell adoptive transfer in NOD scid mice. Morevoer, the up-regulation of selected tRFs associated with the autoimmune reaction triggers β-cell apoptosis and gene expression changes that affect the immune regulatory capacity of β-cells. Our data point to tRFs as novel players in type 1 diabetes and potentially in other autoimmune disorders.

2024-05-24 | GSE242561 | GEO

Global gene repression by Dicer-independent tRNA fragments

Project description:We have performed RNA sequencing after tRNA/tRF overexpression

2018-06-11 | GSE99769 | GEO

tRNAArg-derived fragments mediate protein arginylation [tRF]

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

| PRJNA610190 | ENA

Human tRF & tiRNA sequencing in serum of sarcoidosis

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 serum of sarcoidosis (n = 3) compared with healthy control group (n = 3). Bioinformatics analyses indicated that tsRNAs were the important regulators and potential new biomarkers of sarcoidosis.

2022-03-15 | GSE198490 | GEO

Differences in the tRF & tiRNA Profiles of Sperm after Neonatal Sevoflurane Exposure

Project description:The ncRNAs derived from transfer RNAs (tRNAs), such as tRFs (tRNA-derived fragments) and tiRNAs (tRNA halves), play crucial roles in sperm development, maturation, and function, ultimately affecting the health of offspring. To further elucidate the changes in sperm tRF & tiRNA profiles induced by neonatal sevoflurane exposure, we collected sperm from the caudal epididymis of rats and isolated total RNA for tRF & tiRNA sequencing.

2024-07-05 | GSE271145 | GEO

tRNAArg-derived fragments mediate protein arginylation [tRF]

Project description:Arginyltransferase ATE1 mediates posttranslational arginylation that plays key roles in mammalian embryogenesis, cell migration, and normal brain function. The molecular mechanisms of arginylation remain elusive. ATE1 utilizes arginyl-tRNAArg as the donor of Arg, putting this reaction into a direct competition with the protein synthesis machinery. Here, we addressed these questions of ATE1- arginyl-tRNAArg specificity as a potential mechanism enabling this competition in vivo. Using in vitro arginylation assays and ATE1 knockout models, we find that while arginylation is specific to tRNAArg, it is able to utilize short tRNAArg derivatives that bear structural resemblance to tRNA-derived fragments (tRF), a new class of small regulatory non-coding RNAs with poorly characterized but critical functions in vivo. Arginyl-tRFArg can be generated in vitro directly from pre-charged -tRNAArg, and ATE1 is able to utilize these arginyl-tRFArg fragments with similar efficiency as arginyl-tRNAArg. Lack of arginylation in ATE1 knockout cells leads to a decrease in tRFArg generation and a significant increase in the ratio of tRNAArg to tRFArg compared to wild type, suggesting a functional link between tRFArg and arginylation in vivo. We propose that generation of physiologically important tRFs can play a critical role as a switch between protein translation and arginylation in vivo.

2020-08-12 | GSE146342 | GEO

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