Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of queuosine-modified RNAs in S. pombe using metabolic labelling with preQ1-L1 (Q-RIP-Seq)

ABSTRACT: In most eukaryotes and bacteria, queuosine (Q) replaces the guanosine at the wobble position of tRNAs harboring a GUN anticodon. To investigate whether other RNAs are also Q-or preQ1-modified in Schizosaccharomyces pombe, Q-RIP-Seq was established and applied to RNAs from WT (AEP1) and qtr2∆ cells (AEP288). Metabolic labeling of RNAs with azido-propyl-preQ1 (preQ1-L1), chemical clicking of a biotin-alkyne followed by immunoprecipitation on streptavidin beads and sequencing of enriched RNAs in WT compared to qtr2∆ allowed identification of Q-modified RNAs.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE210404 | GEO | 2022/09/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Detection of queuosine and queuosine precursors in tRNAs by direct RNA sequencing

Project description:Queuosine (Q) is a complex tRNA modification found at position 34 of four tRNAs with a GUN anticodon, and it regulates the translational efficiency and fidelity of the respective codons that differ at the Wobble position. In bacteria, the biosynthesis of Q involves two precursors, preQ0 and preQ1, whereas eukaryotes directly obtain Q from bacterial sources. The study of queuosine has been challenging due to the limited availability of high-throughput methods for its detection and analysis. Here, we have employed direct RNA sequencing using nanopore technology to detect the modification of tRNAs with Q and Q precursors. These modifications were detected with high accuracy on synthetic tRNAs as well as on tRNAs extracted from Schizosaccharomyces pombe and Escherichia coli by comparing unmodified to modified tRNAs using the tool JACUSA2. Furthermore, we present an improved protocol for the alignment of raw sequence reads that gives high specificity and recall for tRNAs ex cellulo that, by nature, carry multiple modifications. Altogether, our results show that such 7-deazaguanine-derivatives are readily detectable using direct RNA sequencing. This advancement opens up new possibilities for investigating these modifications in native tRNAs, furthering our understanding of their biological function.

2023-09-19 | GSE236838 | GEO

Detection of Q-modification in RNAs from S. pombe and S. flexneri via reverse transcription using RT-KTq I614Y (Q-MaP-Seq)

Project description:In most eukaryotes and bacteria, queuosine (Q) replaces the guanosine at the wobble position of tRNAs harboring a GUN anticodon. To faithfully detect Q-modification in RNAs from Schizosaccharomyces pombe and Shigella flexneri, Q-MaP-Seq was established and applied to tRNAs from S. pombe WT (AEP1) cells and Shigella flexneri WT cells and tgt∆ cells. Q-modification of in vitro-transcribed RNAs and RNAs isolated from S. pombe and S. flexneri followed by reverse transcription using the RT-active DNA polymerase variant RT-KTq I614Y and sequencing of unmodified compared to modified RNAs allowed identification of Q-sites within tRNAs.

2023-03-15 | GSE216921 | GEO

Global fine-tuning of translation by queuosinylation and Dnmt2-dependent tRNA methylation

Project description:In most eukaryotes, the wobble position of tRNA with a GUN anticodon is queuosine-modified (Q34). Q is synthesized exclusively by eubacteria and salvaged by eukaryotes as a nutrient to replace G34 in tRNAs. Q34 modification stimulates Dnmt2/Pmt1-dependent C38 methylation in the tRNAAsp anticodon loop in Schizosaccharomyces pombe. Due to the location of both modification in the anticodon loop, we anticipated an influence on translation. Our experimental setup allowed for the analysis of effects from each modification alone or a combination of both.

2019-02-13 | GSE102376 | GEO

Queuosine modification protects cognate tRNAs against ribonuclease cleavage

Project description:Eukaryotic transfer RNAs (tRNA) contain on average 13 modifications that perform a wide range of roles in translation and in the generation of tRNA fragments that regulate gene expression. Queuosine (Q) modification occurs in the wobble anticodon position of tRNAs for amino acids His, Asn, Tyr, and Asp. In eukaryotes, Q modification is fully dependent on diet or on gut microbiome in multi-cellular organisms. Despite decades of study, cellular roles of Q modification remain to be fully elucidated. Here we show that in human cells, Q modification specifically protects its cognate tRNAHis and tRNAAsn against cleavage by ribonucleases. We generated cell lines that contain completely depleted or fully Q-modified tRNAs. Using these resources, we found that Q modification significantly reduces angiogenin cleavage of its cognate tRNAs in vitro. Q modification does not change the cellular abundance of the cognate full-length tRNAs, but alters the cellular content of their fragments in vivo in the absence and presence of stress. Our results provide a new biological aspect of Q modification and a mechanism of how Q modification alters small RNA pool in human cells.

2018-08-10 | GSE102570 | GEO

Arsenic toxicity is regulated by queuine availability and oxidation- induced reprogramming of the human tRNA epitranscriptome

Project description:Cells respond to environmental stress by regulating gene expression at the level of both transcription and translation. The ~50 modified ribonucleotides of the human epitranscriptome contribute to the latter, with mounting evidence that dynamic regulation of tRNA wobble modifications leads to selective translation of stress response proteins from codon-biased genes. Here we show that the response of human HepG2 cells to arsenite exposure is regulated by the availability of queuine, a micronutrient and essential precursor to the wobble modification queuosine (Q) on tRNAs reading GUN codons. Among oxidizing and alkylating agents at equitoxic concentrations, arsenite exposure caused an oxidant-specific increase in Q that correlated with up-regulation of proteins from codon-biased genes involved in energy metabolism. Limiting queuine increased arsenite-induced cell death, altered translation, increased reactive oxygen species levels, and caused mitochondrial dysfunction. In addition to revealing a new epitranscriptomic facet of arsenite toxicity and response, our results highlight the mechanistic links between environmental exposures, stress tolerance, and micronutrients.

2022-06-03 | GSE205332 | GEO

Identification of queuosine-modified RNAs in S. pombe using metabolic labelling with preQ1-L1 (Q-RIP-Seq)

Project description:Identification of queuosine-modified RNAs in S. pombe using metabolic labelling with preQ1-L1 (Q-RIP-Seq)

| PRJNA865659 | ENA

Arsenic toxicity is regulated by queuine availability and oxidation-induced reprogramming of the human tRNA epitranscriptome

2022-08-27 | PXD030726 | Pride

Queuosine-tRNA promotes sex-dependent learning and memory formation by maintaining codon-biased translation elongation speed.

Project description:Queuosine (Q) is a modified nucleoside at the wobble position of specific tRNAs. In mammals, queuosinylation is facilitated by queuine uptake from the gut microbiota and is introduced into tRNA by the QTRT1-QTRT2 enzyme complex. By establishing a Qtrt1 knockout mouse model, we discovered that the loss of QtRNA leads to learning and memory deficits. Ribo-Seq analysis in the hippocampus of Qtrt1-deficient mice revealed not only stalling of ribosomes on Q-decoded codons but also a global imbalance in translation elongation speed between codons that engage in weak and strong interactions with their cognate anticodons. While Qdependent molecular and behavioral phenotypes were identified in both sexes, female mice were affected more severely than males. Proteomics analysis confirmed deregulation of synaptogenesis and neuronal morphology. Together, our findings provide a link between tRNA modification and brain functions and reveal an unexpected role of protein synthesis in sex-dependent cognitive performance.

2023-08-16 | GSE180766 | GEO

Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing

Project description:Queuosine (Q) is a conserved tRNA modification at the wobble anticodon position of tRNAs that read the codons of amino acids Tyr, His, Asn, and Asp. Q-modification in tRNA plays important roles in the regulation of translation efficiency and fidelity. Queuosine tRNA modification is synthesized de novo in bacteria, whereas the substrate for Q-modification in tRNA in mammals is queuine, the catabolic product of the Q-base of gut bacteria. This gut microbiome dependent tRNA modification may play pivotal roles in translational regulation in different cellular contexts, but extensive studies of Q-modification biology are hindered by the lack of high throughput sequencing methods for its detection and quantitation. Here, we describe a periodate-treatment method of biological RNA samples that enables single base resolution profiling of Q-modification in tRNAs by Nextgen sequencing. Periodate oxidizes the Q-base, which results in specific deletion signatures in the RNA-seq data. Unexpectedly, we found that periodate-treatment also enables the detection of several 2-thio-modifications including τm5s2U, mcm5s2U, cmnm5s2U, and s2C by sequencing in human and E. coli tRNA. We term this method Periodate-dependent analysis of queuosine and thio modification sequencing (PAQS-seq). We assess Q- and 2-thio-modifications at the tRNA isodecoder level, and 2-thio modification changes in stress response. PAQS-seq should be widely applicable in the biological studies of Q- and 2-thio-modifications in mammalian and microbial tRNAs.

2022-06-22 | GSE196016 | GEO

Detection of queuosine and queuosine precursors in tRNAs by direct RNA sequencing

Project description:Detection of queuosine and queuosine precursors in tRNAs by direct RNA sequencing

| PRJNA992497 | ENA