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Small RNA sequencing from leaf of Arabidopsis to identify tsRNA

ABSTRACT: tsRNA is newly found small non-coding RNA with important biological function. However, the knowlede of diversity, biogeneis and function of tsRNA in plant is still lacking. Here, we selected 10-60 nt small RNA for high-throughput sequencing and uncovered the diversity,biogenesis and potentical function of tsRNA in Arabidopsis.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE250167 | GEO | 2024/12/31

REPOSITORIES: GEO

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small RNA sequencing from leaf of Arabidopsis to identify tsRNA

Project description:tsRNA is newly found small non-coding RNA with important biological function. However, the knowlede of diversity, biogeneis and function of tsRNA in plant is still lacking. Here, we selected 10-60 nt small RNA for high-throughput sequencing and uncovered the diversity,biogenesis and potentical function of tsRNA in Arabidopsis.

2021-03-07 | GSE95768 | GEO

small RNA sequencing from leaf of Arabidopsis to identify tsRNA

Project description:small RNA sequencing from leaf of Arabidopsis to identify tsRNA

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A novel tsRNA, m7G-3' tiRNA LysTTT, promotes bladder cancer malignancy via regulating ANXA2 phosphorylation

Project description:Emerging evidence indicates that tRNA-derived small RNAs (tsRNAs) with the most abundant RNA modifications play an important role in many complex physiological and pathological processes. However, the biological function and regulation mechanism of modified tsRNA in cancer are still poorly understood. Here, we screened and confirmed a novel m7G modified tsRNA, m7G-3'tiRNA LysTTT (mtiRL) in a variety of chemical carcinogenic models by combined small RNA sequencing with m7G small RNA modified Chip. Moreover, we found that mtiRL catalyzed by tRNA m7G modifying enzyme mettl1 promoted bladder cancer malignancy in vitro and in vivo. Mechanistically, mtiRL specifically bound to oncoprotein Annexin A2 (ANXA2) to promote Tyr24 phosphorylation of ANXA2 by enhancing interactions between ANXA2 and YES1, leading to ANXA2 activation and increased ANXA2 nuclear distribution in bladder cancer cells. Together, these findings define a critical role for mtiRL, targeting this novel m7G modified tsRNA would be an efficient way for the treatment of BC.

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Modulation of tsRNA and mRNA expression by mesenchymal stem cells in COPD model mice

Project description:Chronic obstructive pulmonary disease (COPD) is characterized by lung parenchymal destruction and small airway remodeling, involving processes like inflammation, cell apoptosis, epithelial-mesenchymal transition (EMT), and collagen deposition. There are currently no targeted drugs for airway remodeling. Bone marrow mesenchymal stem cells (BMSCs) show promise in COPD treatment, yet their impact on airway remodeling and underlying mechanisms remain elusive. Transfer RNA-derived small RNAs (tsRNAs) are non-coding RNAs implicated in disease regulation, but their role in COPD and their modulation by BMSCs remain unexplored. Our study assessed BMSC effects on airway remodeling in a COPD mouse model and constructed tsRNA and mRNA expression profiles. Based on the differentially expressed tsRNA-mRNA target pairs identified by tsRNA and mRNA sequencing, we constructed a tsRNA regulatory network linked to COPD airway remoding. The modulation of tsRNA by MSCs may represent one of the pathways through which they ameliorate COPD airway remodeling. Our research will enrich the understanding of BMSC therapy for COPD and provide greater insight into the molecular mechanisms underlying the progression and treatment of airway remodeling.

2024-12-05 | GSE262564 | GEO

Transcriptome and Translatome in Drosophila S2 cells treated by tsRNA transfection, serum deprivation, ago2 knockdown and rapamycin

Project description:Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of small RNAs, yet their regulatory roles have not been well understood. Here we studied the molecular mechanisms and consequences of tsRNA-mediated regulation in Drosophila. By carrying out mRNA sequencing and ribosome profiling of S2 cells transfected with single-stranded tsRNA mimics and mocks, we show that tsRNAs recognize target mRNAs through conserved complementary sequence matching and suppress target genes by translational inhibition. Serum starvation experiments confirm tsRNAs participate in cellular starvation responses by preferential targeting the ribosomal proteins and translational initiation or elongation factors. Knock-down of AGO2 in S2 cells under normal and starved conditions reveals a dependence of the tsRNA-mediated regulation on AGO2. Our study suggests the tsRNA-mediated regulation might be crucial for the energy homeostasis and the metabolic adaptation in the cellular systems.

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tsRNA microarray of parental normal-like and breast cancer cell lines and with inhibited or induced RUNX1 expression

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2020-01-01 | GSE142382 | GEO

Global gene expression profiling from LeuCAG3'tsRNA depleted- HeLa and HCT-116 cell lines through 50 base pair paired-end RNA-seq

Project description:We sequenced mRNA expression from 3 HeLa and 3 HCT-116 cell lines transfected with LNA (Locked nucleic acid) GL2, LNA CAGMM, or LNA CAGPM respectively. In order to dissect the biological role of 3?tsRNAs (type I tsRNAs) in mammals, we reduced the bioavailable abundance of specific tsRNA species using complementary locked nucleic acid/DNA-mixed antisense oligonucleotides (LNA). The LNA forms a highly stable complex with the target RNA in a sequence specific manner, essentially inhibiting its ability to interact with their biological targets. In our tsRNA-knockdown experiments of HeLa and HCT-116 cell lines, we used three different LNA probes. GL2, is the LNA probe complementary to firefly luciferase gene from pGL2 vector (Promega, WI, USA), which serve as negative control. CAGPM, is the LNA probe perfect complementary to LeuCAG3?tsRNA. CAGMM, is the LNA probe complementary to LeuCAG3?tsRNA with 2 nt mismatches. The sequences for LNA probes are as follows. LNA bases are upper-case letter and DNA bases are lower ?case letter. GL2: GtaCgCgGaaTaCTtC CAGPM: tGTcAGgAgTggGaT CAGMM: tCTcACgAgTggGaT

2017-09-27 | GSE54878 | GEO

tsRNA sequencing of 3 primary tumor tissues and 3 metastastic tumor tissues of pancreatic cancer

Project description:To identify and characterize differentially expressed tsRNA, we collected 3 primary tissues and 3 liver metastasis tissues in pancreatic cancer, and compared the tsRNA expression profiles between primary tissues and liver metastasis tissues in pancreatic cancer using tsRNA sequencing.

2024-01-01 | GSE251943 | GEO

tsRNA epitranscriptomics

Project description:Quantification of substoichiometric tRNA and tsRNA modification sites in human neuronal cell lines upon angiogenin exposure

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Curcumin improves atrial fibrillation susceptibility by regulating tsRNA expression in aging mouse atrium

Project description:Age is an independent risk factor for atrial fibrillation (AF), and curcumin can delay aging related disease through reducing oxidative stress and inflammation. However, its target in aging-related AF remains unclear. Transfer RNA-derived small RNA (tsRNA) is a novel short non-coding RNA (sncRNA), and exerts a potential regulatory function in aging. This study was to explore the therapeutic targets of curcumin in atrium of aged mice by PANDORA-seq. Aged mice (18 month) were treated with curcumin (100mg/kg). Rapid transjugular atrial pacing was performed to observe AF inducibility. SA-β-gal staining, ROS detection and qRT-PCR were used to assess the degree of aging and oxidative stress/inflammation levels. PANDORA-seq was performed to reveal the differentially expressed sncRNAs in the atrium of mice. The results showed that curcumin reduced the susceptibility AF of aged mice by improving aging-related atrial fibrosis. Compared to young mice (5 month) group, aged mice yielded 473 significantly altered tsRNA sequences, while 947 tsRNA sequences were significantly altered after treated with curcumin. Enrichment analysis revealed that the target genes were mainly related to DNA damage and protein modification. Compared with the 5mo group, the expression levels of mature-mt_tRNA-Val-TAC_CCA_end, mature-mt_tRNA-Glu-TTC_CCA_end, and mature-tRNA-Asp-GTC_CCA_end were up-regulated in the 18mo group, while the expression of mature-mt_tRNA-Thr-TGT_5_end was down-regulated. This trend was reversed in the 18mo+curcumin group. Increased cellular ROS levels, inflammation expression and senescence in aged mice atrium were improved by the down-regulation of mature-mt_tRNA-Val-TAC_CCA_end. In conclusion, our findings identified mature-mt_tRNA-Val-TAC_CCA_end participated in the mechanism of aging-related atrial fibrosis, providing new intervention target of aging-related AF.

2024-05-30 | GSE217761 | GEO

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