Silencing of mt-tRF-LeuTAA fragment in pancreatic rat islets and investigation by RNA-sequencing of the downstream mechanisms activated by this fragment
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ABSTRACT:
PROVIDER: PRJNA1003495 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25573200.fastq.gz | Fastqsanger.gz | |||
| SRR25573201.fastq.gz | Fastqsanger.gz | |||
| SRR25573202.fastq.gz | Fastqsanger.gz | |||
| SRR25573203.fastq.gz | Fastqsanger.gz | |||
| SRR25573204.fastq.gz | Fastqsanger.gz |
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Project description:In this study, we discovered cytosolic and mitochondrial fragments resulting from tRNA and mt-tRNA cleavage, which may act as new regulators of cellular and metabolic functions. We selected the mt-tRF-LeuTAA fragment for further investigation, as its level is altered in the islets diabetes-susceptible animal models, while being abundant in ß-cells. mt-tRF-LeuTAA fragment is derived from the cleavage of tRNA-LeuTAA encoded by the mitochondrial genome. We demonstrated that mt-tRF-LeuTAA acts as a key regulator of mitochondrial OXPHOS functions, mitochondrial membrane potential, the insulin secretory capacity of ß-cells, and the insulin sensitivity of myotube muscle cells. To gain a comprehensive understanding, we conducted transcriptomic and proteomic analyses on rat islets with silenced mt-tRF-LeuTAA for 72 hours. We transfected rat islet cells with an antisense oligonucleotides (antisense oligonucleotides to reduce mt-tRF-LeuTAA levels versus control oligos). These oligos specifically decreased the levels of the fragment (anti-tRF-LeuTAA) by more than 95% without affecting the host full-length tRNA mt-tRNA-LeuTAA. Inhibiting mt-tRF-LeuTAA led to significant differential expression of 4843 mRNA transcripts, cut-off adjusted P ≤ 0.05. To further investigate the cellular rearrangement associated with the inhibition of mt-tRF-LeuTAA, we conducted enrichment analysis using Gene Ontology Molecular Function terms on RNA-sequencing. At the transcriptomic level, we observed enrichment of pathways related to ion transport and various enzymatic activities, including mitochondrial oxidoreductase activity, when the mitochondrial fragment was repressed in rat islets.
2024-05-14 | GSE240395 | GEO
Project description:In this study, we discovered cytosolic and mitochondrial fragments resulting from tRNA and mt-tRNA cleavage, which may act as new regulators of cellular and metabolic functions. We selected the mt-tRF-LeuTAA fragment derived from a tRNA encoded by the mitochondrial genome for further investigation, as its level is reduced in the islets of diabetes-susceptible animal models, while being abundant in ß-cells. mt-tRF-LeuTAA fragment is derived from the cleavage of tRNA-LeuTAA encoded by the mitochondrial genome. We demonstrated that mt-tRF-LeuTAA acts as a key regulator of mitochondrial OXPHOS functions, mitochondrial membrane potential, the insulin secretory capacity of ß-cells, and the insulin sensitivity of myotube muscle cells. We sought to investigate the downstream mechanisms activated by this fragment. To gain a comprehensive understanding, we conducted proteomic analyses on rat islets with silenced mt-tRF-LeuTAA for 72 hours. Inhibiting mt-tRF-LeuTAA led to significant differential expression of 642 proteins, cut-off adjusted p ≤ 0.05. To further investigate the cellular rearrangement associated with the inhibition of mt-tRF-LeuTAA, we conducted enrichment analysis using Gene Ontology Molecular Function terms on mass spectrometry data. At the protein level, there was a significant enrichment of mitochondrial pathways, such as oxidoreductase activity, ATPase activity, hydrogen transport, NADH dehydrogenase activity, cytochrome-c oxidase activity, and oxygen transport. To elucidate the mechanisms by which mt-tRF-LeuTAA operates, we also conducted pull-down experiments in insulin-secreting INS832/13 cells, followed by mass spectrometry using 3'-biotinylated mimic sequence oligonucleotides of mt-tRF-LeuTAA. Our analysis unveiled interactions between mt-tRF-LeuTAA and 24 proteins, meeting the criteria of a fold change ≥ 6 and an adjusted p-value ≤ 0.05. Notably, among these proteins, 13 are localized within the mitochondria and play significant roles in mitochondrial oxidative functions. Some of these key proteins include Suclg2, Nme3, Sdha, Lrpprc, and Ndufa12. Pathway enrichment analysis of the binding partners associated with the mitochondrial fragment mt-tRF-LeuTAA indicates an over-representation of signaling pathways crucial to maintaining mitochondrial metabolism. These pathways include oxidative phosphorylation (OXPHOS), ROS-induced stress responses, the tricarboxylic acid (TCA) cycle, calcium homeostasis regulation, lipid metabolism, RNA splicing, and mitochondrial import, which all contribute fundamentally to the maintenance of mitochondrial metabolism. These findings collectively provide insights into the essential mechanisms underlining the functionality of mitochondrially-encoded tRNA-derived fragments with the view to sustaining mitochondrial metabolism.
2024-06-16 | PXD046117 | Pride
Project description:In this study, we discovered cytosolic and mitochondrial fragments resulting from tRNA and mt-tRNA cleavage, which may act as new regulators of cellular and metabolic functions. The so-called LP rat model consists of 22-day-old rats whose mothers have been subjected to a low protein diet during gestation and lactation. These offspring have impaired pancreatic development with reduced ß-cell mass, glucose-stimulated insulin secretion defect and are more prone to develop diabetes in adulthood. We identified hundreds of these fragments as being changed in the pancreatic islets of LP rats and compared them to chow diet (CD) exposed rats. In our analysis, we identified 6164 tRFs in the islets of LP rats, among which 256 exhibited significant changes (≥ 2 fold; adjusted p value ≤ 0.05) compared to controls. Of these, 113 tRFs showed increased levels, while 143 tRFs showed decreased levels in the LP rats. We focused our investigations on mitochondrial tRFs (mt-tRFs) that show significant alterations in both, adult pre-diabetic mice (db/db) and LP rats. We selected the mt-tRF-LeuTAA fragment for further investigation, as its level is reduced in the islets of db/db mice and LP rats, while being abundant in ß-cells. mt-tRF-LeuTAA fragment is derived from the cleavage of tRNA-LeuTAA encoded by the mitochondrial genome. We demonstrated that mt-tRF-LeuTAA acts as a key regulator of mitochondrial OXPHOS functions, mitochondrial membrane potential, the insulin secretory capacity of ß-cells, and the insulin sensitivity of myotube muscle cells.
2024-05-14 | GSE239981 | GEO
Project description:In this study, we discovered cytosolic and mitochondrial fragments resulting from tRNA and mt-tRNA cleavage, which may act as new regulators of cellular and metabolic functions. We analyzed hundreds of these fragments in the pancreatic islets of db/db mice and compared them to heterozygous control db/+ mice. At 16 weeks of age, db/db mice exhibit obesity, insulin resistance, and glucose intolerance. In our analysis, we identified 3858 tRFs in the islets of db/db mice, among which 342 exhibited significant changes (≥ 2 fold; adjusted p value ≤ 0.05) compared to controls. Of these, 199 tRFs showed increased levels, while 170 tRFs showed decreased levels in the pre-diabetic mice. Notably, a striking majority (147 out of 170) of the tRFs with reduced abundance in the islets of db/db mice were derived from the cleavage of tRNAs encoded by the mitochondrial genome. Our findings reveal a significant reshaping of mitochondrial tRFs in pre-diabetic conditions, coinciding with a well-established mitochondrial metabolic defect under these conditions. Specifically, we demonstrated that a fragment (named mt-tRF-LeuTAA) resulting from the cleavage of mt-tRNA-LeuTAA, encoded by the mitochondrial genome and found to be reduced in the islets of db/db mice, acts as a key regulator of mitochondrial OXPHOS functions, mitochondrial membrane potential, the insulin secretory capacity of ß-cells, and the insulin sensitivity of myotube muscle cells.
2024-05-14 | GSE239786 | GEO
Project description:Small RNAs derived from mature tRNAs, referred to as tRNA fragments or “tRFs”, are an emerging class of regulatory RNAs with poorly understood functions in cellular regulation. We recently identified a role for one specific tRF – 5’ tRF-Gly-GCC, or tRF-GG – in repression of genes associated with the endogenous retroelement MERVL, but the mechanistic basis for this regulation was unknown. Here, we show that tRF-GG plays a role in production of a wide variety of noncoding RNAs normally synthesized in Cajal bodies. Among these noncoding RNAs, tRF-GG regulation of the U7 snRNA modulates heterochromatin-mediated transcriptional repression of MERVL elements by supporting an adequate supply of histone proteins. Importantly, the effects of inhibiting tRF-GG on histone mRNA levels, activity of a histone 3’ UTR reporter, and ultimately on MERVL regulation could all be suppressed by the U7 RNA. We show that the related RNA-binding proteins hnRNPF and H bind directly to tRF-GG, and are required for Cajal body biogenesis. Together, our data reveal a conserved mechanism for 5’ tRNA fragment control of noncoding RNA biogenesis and, consequently, in global chromatin organization.
2020-01-17 | GSE127247 | GEO
Project description:To identify the downstream genes of tRF-20-S998LO9D, we transfected HEC-1-A and RL-95-2 cells with tRF-20-S998LO9D mimics or negative control of mimics, and send the cells for RNA-Seq. Differentially expressed tsRNAs were identified using DESeq2.
2022-07-23 | GSE208381 | GEO
Project description:Context: Papillary thyroid cancer (PTC) is the most common thyroid cancer with dramatically increasing worldwide. Accurate diagnosis is crucial to avoid unnecessary overtreatment for low-risk patients, but the currently available markers are still insufficient. tRNA-derived fragments (tRFs) are emerging as a new class of small non-coding RNAs due to their potential roles as novel biomarkers and therapeutic targets in cancer. However, their involvement in papillary thyroid carcinoma (PTC) is still unclear. Objectives: This study was performed to identify differentially expressed tRFs in PTC and investigate the role of serum tRFs to discriminate PTC from nodular goiters (NGs).Methods and Materials: tRF expression profiles were measured in pooled sera from patients with PTCs (n=6), NGs (n=6) and healthy subjects (n=6) using high-throughput sequencing (cohort1). One selected tRF candidate was validated in the same individual samples (cohort1) by qRT-PCR. The confirmed tRF was further validated in a larger second cohort including patients with PTCs (n=30), NGs (n=20) and healthy individuals (n=18).Results: Our sequencing results showed that circulating tRFs were differentially expressed in patients with PTC compared with those with NG and healthy people. After the validation in individual samples, tRF-Pro-AGG-018 was confirmed as differentially elevated in serum samples of patients with PTC. These results were further confirmed in a larger second cohort. Moreover, tRF-Pro-AGG-018 exhibited good diagnostic performance with a sensitivity of 0.7222 and a specificity of 0.8846 for PTC and it was associated with several targeted genes of PTC. Conclusions: Our study identified that the serum tRFs were differentially expressed in PTC compared with NG and healthy individuals. Notably, circulating tRF-Pro-AGG-018 was found to have a significant elevation in patients with PTC and exhibited good diagnostic performance with relatively high sensitivity and specificity for PTC. Our findings suggest tRFs might serve as novel circulating biomarkers in predicting patients with PTC, which may prevent unnecessary thyroid surgeries for low-risk and benefit from optimal
2019-11-09 | GSE140144 | GEO
Project description:Our previous study identified that a novel tRNA-derived fragment (tRF) termed AS-tDR-007333 was up-regulated in non-small cell lung cancer (NSCLC), but the molecular mechanisms of AS-tDR-007333 in NSCLC were unclear. Here, we used RNA-seq for high-throughput profiling of transcriptomes in A549 cells transfected with AS-tDR-007333, in order to find differentially expressed genes regulated by AS-tDR-007333.
2022-05-25 | GSE184690 | GEO
Project description:tRNA fragments (tRFs) are small non-coding RNA molecules that are generated through the cleavage of tRNAs and have been implicated in various biological processes. Among the different types of tRFs, the 3′-tRFs have attracted considerable scientific interest due to their regulatory role in gene expression. In this study, we investigated the role of 3′-tRF-CysGCA, a tRF derived from cleavage in the T-loop of tRNACysGCA, in the regulation of gene expression in HEK-293 cells. Previous studies have shown that 3′-tRF-CysGCA is incorporated into the RISC complex and interacts with Argonaute proteins, suggesting its involvement in the regulation of gene expression. However, the general role and effect of the deregulation of 3′-tRF-CysGCA levels in human cells have not been investigated so far. To address this gap, we stably overexpressed 3′-tRF-CysGCA in HEK-293 cells and performed transcriptomics and proteomics experiments. Moreover, we validated the interaction of this tRF with putative targets whose levels were affected after 3′-tRF-CysGCA overexpression. Last, we investigated the implication of 3′-tRF-CysGCA in various pathways using extensive bioinformatics analysis. Our results indicate that 3′-tRF-CysGCA overexpression led to changes in the cell expression profile, and we identified multiple pathways that were affected by the deregulation of this tRF. Additionally, our reporter assays demonstrated that 3′-tRF-CysGCA directly interacted with TMPO and ERGIC1, leading to changes in their expression levels. Taken together, these findings suggest that 3′-tRF-CysGCA plays a significant role in the regulation of gene expression and highlight the potential importance of this tRF in cellular processes.
2023-11-30 | PXD044218 | Pride
Project description:Next generation sequencing was used to assess the changes along a diurnal cycle in the transcriptome of Drosophila head, periphery (entire body except the head) or the heart at 3, 5 or 7 weeks of age under ad libitum feeding (ALF) or time-restricted feeding (TRF). Next generation sequencing was used to assess the changes along a diurnal cycle in the transcriptome of Drosophila head, periphery (entire body except the head) or the heart at 3, 5 or 7 weeks of age under ad libitum feeding (ALF) or time-restricted feeding (TRF).
2015-02-18 | E-GEOD-64108 | biostudies-arrayexpress