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TRNAArg-derived fragments mediate protein arginylation [tRF]

ABSTRACT: tRNAArg-derived fragments mediate protein arginylation [tRF]

PROVIDER: PRJNA610190 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11235161.fastq.gz	Fastqsanger.gz
	SRR11235162.fastq.gz	Fastqsanger.gz
	SRR11235163.fastq.gz	Fastqsanger.gz
	SRR11235164.fastq.gz	Fastqsanger.gz
	SRR11235165.fastq.gz	Fastqsanger.gz

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tRNAArg-derived fragments mediate protein arginylation

Project description:tRNAArg-derived fragments mediate protein arginylation

| PRJNA610185 | ENA

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

tRNAArg-derived fragments mediate protein arginylation [tRNA]

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

| PRJNA610189 | ENA

tRNAArg-derived fragments mediate protein arginylation [tRNA]

2020-08-12 | GSE146343 | 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

| PRJNA604603 | ENA

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.

2021-06-05 | GSE144698 | GEO

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

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

Genetic Control of tRNA-Derived Fragments Contributes to Cancer Risk

Project description:Transfer RNA-derived fragments (tRFs) are a class of small non-coding RNAs that have exhibited several functions in cancer. Recent studies have shown that mutations in tRNA genes can lead to global changes in tRF expression levels and may affect tRF function, highlighting the need to further elucidate the regulation and functions of tRFs in cancer. Here, we conducted a pan-cancer analysis of tRF quantitative trait loci (tRFQTLs), encompassing 16,703 genetic variants associated with tRF expression across 31 cancer types. A joint analysis of GWAS data revealed that tRFQTLs were preferentially enriched in cancer risk loci and colocalized with 106 GWAS variants, explaining a substantial portion of cancer heritability. Moreover, tRFs regulated by tRFQTLs were enriched in cancer-related pathways and correlated with drug response and immune infiltration. Notably, polygenic risk score models incorporating tRFQTLs improved high-risk population identification. Investigation of large-scale population cohorts revealed a tRFQTL, rs9461276, associated with colorectal cancer (CRC) risk. In biological assays, the rs9461276-C allele increased tRF-18-HSQS52D2 expression, which suppressed CRC malignant phenotypes. Mechanistically, tRF-18-HSQS52D2 bound to the 3'UTR of POU2F1, destabilizing the oncogenic transcript. Integrated RNA sequencing and ChIP-seq assays indicated that POU2F1 enhanced CRC cell proliferation by activating various pathological pathways associated with oxidative and glycolytic metabolism, mitotic stability, and cell cycle regulation. Finally, a database (Cancer-tRFQTL) was generated as a resource to support investigation into tRF-mediated mechanisms and genetic basis of tRF expression in human cancers. Overall, this study helps advance the understanding of tRFs in cancer pathogenesis.

2025-08-05 | GSE304444 | GEO

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