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

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

PROVIDER: PRJNA604603 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11007000.fastq.gz	Fastqsanger.gz
	SRR11007001.fastq.gz	Fastqsanger.gz
	SRR11006990.fastq.gz	Fastqsanger.gz
	SRR11006991.fastq.gz	Fastqsanger.gz
	SRR11006992.fastq.gz	Fastqsanger.gz

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

Project description:In order to intensively elucidate the metabolic characteristics of tRFs after liver injury, we performed tRF-seq by high throughput sequencing. We found that after liver injury, large abundance of tRFs were produced. Especially, the tRF-1s largely vary during the liver injury process and may play important role in the liver disease.

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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.

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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.

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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.

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Global gene repression by Dicer-independent tRNA fragments

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

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tRNAArg-derived fragments mediate protein arginylation [tRF]

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

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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.

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Effect of tRF-1-Ser on the gene expression of breast cancer cell MDA-MB-453

Project description:tRNA-derived small RNAs (tsRNA) are a new type of noncoding RNAs that can be mainly classified into two groups: tRFs (tRNA-derived fragments) and tiRNAs (tRNA halves). The abnormal expression of tsRNAs is known to play an important role in the biological progression of breast cancer. However, it's still unclear about the mechanism of tsRNAs in cancer. tRF-1-Ser is a tRF that is high expression in breast cancer and negatively regulated by 25(OH)D. Our study aims to find out the effect of tRF-1-Ser on breast cancer and explore the change of RNA in tRF-1-Ser knock-down breast cancer cells.

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