Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1053914 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27240936.fastq.gz | Fastqsanger.gz | |||
| SRR27240937.fastq.gz | Fastqsanger.gz | |||
| SRR27240938.fastq.gz | Fastqsanger.gz | |||
| SRR27240939.fastq.gz | Fastqsanger.gz | |||
| SRR27240940.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
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Project description:Synthesizing the cellular proteome is a demanding process that is regulated by numerous signaling pathways and RNA modifications. How these orchestrate the protein synthesis machinery to generate specific proteome subsets remains unclear. We found when mTORC1 was inactive, tRNA wobble uridine-modifying enzymes (U34-enzymes) Elongator and Ctu1/2 became essential for cell growth in vitro and in tumors. Using ribosome profiling, RNA seq and other methods, we interrogated the functional interplay between U34-enzymes and mTORC1.
2025-02-19 | GSE250593 | GEO
Project description:mTORC1 cooperates with tRNA wobble modification to sustain the protein synthesis machinery
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Project description:5-Formylcytidine (f5C) is one type of post-transcriptional RNA modifi-cations, which is known at the wobble position of tRNA in mitochon-dria and essential for mitochondrial protein synthesis. Here, we show a method to detect f5C modifications in RNA and a transcriptome-wide f5C mapping technique, named f5C-seq. It is developed based on the treatment of pyridine borane, which can reduce f5C to 5,6-dihydrouracil (DHU), thus inducing C-to-T transition in f5C sites during PCR to achieve single-base resolution detection. Thousands of f5C sites were identified after mapping in Saccharomyces cerevisiae by f5C-seq. Moreover, codon composition demonstrated a preference for f5C within wobble sites in mRNA, suggesting the potential role in regulation of translation. These findings expand the scope of the understanding of cytosine modifications in mRNA. Reference build: S288C_reference_genome_R64-2-1_20150113
2021-12-01 | GSE133138 | GEO
Project description:The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth that stimulates macromolecule synthesis via insulin, growth factors, and oncogenic signals. mTORC1 activates anabolic pathways by inducing posttranslational modifications of metabolic enzymes, and by regulating expression through transcription and mRNA processing. However, mechanisms of how mTORC1 orchestrates these tightly connected processes remain unclear. Here, we identify FAM120A as a transcriptional co-activator that couples transcription and splicing of lipid synthesis enzymes downstream of mTORC1-SRPK2 signaling. Mechanistically, the mTORC1-activated SRPK2 phosphorylates a splicing factor SRSF1, enhancing its binding to FAM120A. FAM120A directly interacts with a lipogenic transcription factor SREBP1 at active promoters, thereby bridging newly transcribed lipogenic genes to the RNA splicing machinery. This multi-protein complex regulated by mTORC1 promotes efficient splicing and stability of lipogenic transcripts, resulting in fatty acid synthesis and cancer cell proliferation. These results elucidate FAM120A as a critical transcription co-factor that connects mTORC1-dependent gene regulation programs for anabolic cell growth.
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Project description:Here we report Total RNA seq and RiboSeq on MEF cells treated with halofuginone. Halofuginone is a competitive inhibitor of the Prolyl-tRNA synthetase that results in an accumulation of uncharged Prolyl-tRNA upon treatment that leads to an activation of the protein kinase Gcn2.
2021-05-26 | GSE156850 | GEO
Project description:Proteins begin to fold as they emerge from translating ribosomes. The kinetics of ribosome transit along a given mRNA can influence nascent chain folding, but the extent to which individual codon translation rates impact proteome integrity remains unknown. Here, we show that slower decoding of discrete codons elicits widespread protein aggregation in vivo. Using ribosome profiling, we find that loss of anticodon wobble uridine (U34) modifications in a subset of tRNAs leads to ribosome pausing at their cognate codons in S. cerevisiae and C. elegans. Yeast cells lacking U34 modifications exhibit gene expression hallmarks of proteotoxic stress and accumulate aggregates of endogenous proteins with key cellular functions. Moreover, these cells are severely compromised in clearing stress-induced protein aggregates. Overexpression of hypomodified tRNAs alleviates ribosome pausing, concomitantly restoring protein homeostasis. Our findings demonstrate that modified U34 is an evolutionarily conserved accelerator of decoding and reveal an unanticipated role for tRNA anticodon modifications in maintaining proteome integrity. Ribosome profiling of wild-type and tRNA modification-deficient yeast and nematodes. Yeast samples were generated in various growth conditions (rich medium versus stress induced by treatment with diamide or rapamycin) and paired mRNA-Seq was performed on a subset of samples. Dataset contains three biological replicates for yeast samples and two biological replicates for nematode samples.
2015-06-04 | E-GEOD-67387 | biostudies-arrayexpress
Project description:Alternative macrophages are critical in parasites defense, the resolution of inflammation and wound healing. RNA modifications, which are defined as post-transcriptional changes in the chemical composition of RNA molecules, are involved in the immune response.Among tRNA-modifying enzymes which target the tRNA anticodon, Elongator and Cytosolic thiouridylase (Ctu)-1/2 complexes exclusively modify the wobble uridine (U34) base in cytosolic tRNAs. However, the full picture of how mRNA translational factors maintain protein synthesis accuracy and co-translational protein folding are far from being fully understood.To address this question,we evaluated the role of Elp3 on protein in the IL4 induced alternative bone marrow derived macrophages (BMDMs). The BMDMs from widetype and Elp3 myeloid specific knockout mice were treated by IL-4 for 24h or not. Then the aggregates were isolated from these BMDMs and performed by MS.
2022-09-12 | PXD023588 | Pride
Project description:In response to a variety of upstream growth and oncogenic signals, the mechanistic target of rapamycin complex 1 (mTORC1) promotes anabolic metabolism, in part, through activation of downstream transcription factors. The transcription factor activating transcription factor 4 (ATF4) has been previously shown to function downstream of mTORC1 signaling to promote de novo purine synthesis and this activation of ATF4 can occur independently of the canonical activation of ATF4 through the integrated stress response (ISR). Here, we show that ATF4 activation through mTORC1 signaling drives a specific transcriptional program through ATF4 which is comprised of only a subset of genes involved in the broader cellular stress response. We find genes involved in amino acid uptake, biosynthesis, and charging by tRNA synthetases display transcriptional changes downstream of both mTORC1 and ATF4. We discovered that ATF4 activation contributes to the mTORC1-stimulated increase in protein synthesis, highlighting the importance of these transcriptional changes. Additionally, we observe regulation of the cystine transporter SLC7A11 by ATF4. We show that SLC7A11 is important for cell survival and is one mechanism by which cells with active mTORC1 signaling produce glutathione. Thus, ATF4 downstream of mTORC1 signaling regulates protein and glutathione synthesis.
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Project description:Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay [RiboSeq]
| PRJNA757962 | ENA
Project description:Transfer RNAs (tRNAs) are one of the most conserved components of protein synthesis machinery. An effective strategy for microbes to defend against viruses or competitors is to employ anticodon nucleases (ACNases) to deplete essential tRNAs and thereby shut off global protein synthesis, but this strategy has not been observed in multicellular eukaryotes. Here, we report that human SAMD9 is a virus-activatable ACNase that specifically depletes phenylalanine tRNA (tRNAPhe), causing codon-specific ribosomal pausing and inducing stress signaling. SAMD9 ACNase can be activated by poxvirus infection or by SAMD9 mutations associated with a spectrum of developmental or immunological disorders, implicating tRNAPhe deficiency as a major toxic effect in these human diseases and suggesting a new therapeutic strategy. The specificity of the ACNase, located to an N-terminal effector domain of SAMD9, is largely determined by a eukaryotic tRNAPhe specific 2’-O-methylation at the wobble position, making eukaryotic tRNAPhe a universal but specific target for SAMD9. The SAMD9 ACNase differs from the microbial ACNases in structure and substrate specificity, suggesting convergent evolution resulted in a universal immune defense strategy targeting tRNAs.
2023-06-07 | GSE230043 | GEO