GEO DataSets

(Submitter supplied) 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. more...

Organism:

Homo sapiens; Escherichia coli

Type:

Other

Platforms:

GPL21433 GPL24676

29 Samples

Download data: TSV

(Submitter supplied) 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. more...

Organism:

Escherichia coli; synthetic construct; Schizosaccharomyces pombe

Type:

Other

Platforms:

GPL30119 GPL25738 GPL31123

14 Samples

Download data: XLSX

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15433

4 Samples

Download data: TXT, XLSX, ZIP

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21626

20 Samples

Download data: CSV, TXT

(Submitter supplied) 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:

Schizosaccharomyces pombe

Type:

Other

Platform:

GPL16192

12 Samples

Download data: TXT

(Submitter supplied) Post-transcriptional modification of tRNAs is critical for protein synthesis. Queuosine (Q), a 7-deaza-guanosine derivative, is present at the first position of anticodons of several tRNA species. In vertebrate tRNAs for Tyr and Asp, Q is further glycosylated with galactose and mannose to generate galactosyl-queuosine (galQ) and mannosyl-queuosine (manQ), respectively. However, the biogenesis and physiological relevance of Q-glycosylation remain poorly understood. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

5 Samples

Download data: TXT

(Submitter supplied) Regulation of protein translation is a key feature of many biological processes. Global protein translation as well as translation at the codon level can be regulated by RNA modifications. These modifications are particularly enriched in tRNAs, where they represent an additional regulatory layer on top of the primary RNA sequence. In eukaryotes, levels of tRNA queuosinylation reflect the bioavailability of the precursor queuine, which is salvaged from the gut microbiota and absorbed in the intestine. more...

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL11154

20 Samples

Download data: TXT

(Submitter supplied) Purpose: to observe differences in E. coli transcripts levels due to the absence of the tRNA modification queuosine and due to exposure to excess nickel. Methods: RNAseq was performed using the total RNA isolated from E. coli MG1655 WT and Δtgt strains grown in LB medium only or in LB added by 2 mM NiCl2. Results: in nickel-treated WT compared to untreated WT (WT_Ni/WT_LB) 734 genes were found up-regulated and 1,642 genes down-regulated in the treated cells; in the tgt mutant compared to the WT strain (tgt_LB/WT_LB), 417 genes were found up regulated and 1,053 genes down regulated in the tgt mutant. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18133

12 Samples

Download data: XLSX

(Submitter supplied) We report the identification and quantification of Watson-Crick modifications in tRNA and rRNA through the use of high throughput sequencing. We apply the recently published DM-tRNA-Seq method to generate demethylase treated and untreated 293T samples, and using computational methods we are able to flag sites using a modification index. This index allows us to generate site-resolved information about modification that we can use to identify and quantify Watson-Crick face modifications in tRNA and rRNA. more...

Organism:

Homo sapiens

Type:

Other; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL15433

5 Samples

Download data: TXT

(Submitter supplied) Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced due to the abundant presence of post-transcriptional modifications and extensive structure that interfere with cDNA synthesis and adapter ligation. We achieve efficient and quantitative tRNA sequencing by removing base methylations using engineered demethylases and using a highly processive thermo-stable reverse transcriptase without the need for adapter ligation (DMTRT-tRNA-seq). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

8 Samples

Download data: TXT

(Submitter supplied) The human genome encodes hundreds of tRNA genes but their individual contribution to the tRNA pool is not fully understood. Deep sequencing of tRNA transcripts (tRNA-Seq) can estimate tRNA abundance at single gene resolution, but tRNA structures and post-transcriptional modifications impair these analyses. Here we present a bioinformatics strategy to investigate differential tRNA gene expression and use it to compare tRNA-Seq datasets from cultured human cells and human brain. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: XLS

(Submitter supplied) Amebiasis is an intestinal disease transmitted by the protist parasite, Entamoeba histolytica, following the ingestion of contaminated food and water. Many infected patients (90%) are asymptomatic but for unknown reasons, these trophozoites can become virulent and invasive, cause amebic dysentery, and migrate to the liver, via the portal veins, where they cause hepatocellular damage. We have recently reported that Escherichia coli can modulate E.histolytica 's virulence and resistance to oxidative stress (OS) via the production of oxaloacetate. more...

Organism:

Entamoeba histolytica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24064

11 Samples

Download data: XLS

(Submitter supplied) 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. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13988 GPL20584

36 Samples

Download data: TXT

(Submitter supplied) Transfer RNAs (tRNA) are quintessential in deciphering the genetic code; disseminating nucleic acid triplets into correct amino acid identity. While this decoding function is clear, an emerging theme is that tRNA abundance and functionality can powerfully impact protein production rate, folding, activity, and messenger RNA stability. Importantly, however, the expression pattern of tRNAs (in even simple systems) is obliquely known. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21626 GPL21697

29 Samples

Download data: CSV

(Submitter supplied) tRNAs are heavily decorated with post-transcriptional modifications (tRNA modifications). Profile of tRNA modifications in non-model organisms are largely uncharacterized. Here using high-throughput sequencing, sites and frequency of tRNA modifications are predicted in Vibrio cholerae and Escherichia coli. During cDNA synthesis, some modifications cause misincorporation of a wrong base or termination of reverse transcription (RT). more...

Organism:

Escherichia coli; Vibrio cholerae

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21022 GPL16085

16 Samples

Download data: TXT

(Submitter supplied) Mitochondria are organelles that generate most of the energy in eukaryotic cells in the form of ATP via oxidative phosphorylation in eukaryote. Twenty-two species of mitochondrial (mt-)tRNAs encoded in mtDNA are required to translate essential subunits of the respiratory chain complexes involved in oxidative phosphorylation. mt-tRNAs contain post-transcriptional modifications introduced by nuclear-encoded tRNA-modifying enzymes. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20301

4 Samples

Download data: TXT

(Submitter supplied) Here we develop a high throughput sequencing method that enables accurate determination of charged tRNA fractions at single base resolution (Charged tRNA-seq). Our method takes advantage of the recently developed DM-tRNA-seq method, but includes additional chemical steps that specifically remove the 3'A residue in the uncharged tRNA. Charging fraction is obtained by counting the fraction of A-ending reads versus A+C-ending reads for each tRNA species. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT, XLSX

(Submitter supplied) RNA modifications have a substantial impact on tRNA function. While modifications in the anticodon loop play an important role in translational fidelity, modifications in the tRNA core influence tRNA structural stability. In bacteria, tRNA modifications play important roles in the stress response and expression of virulence factors. While tRNA modifications are well characterized in a few model organisms, our knowledge of tRNA modifications in human pathogens, such as Pseudomonas aeruginosa is lacking. more...

Organism:

Pseudomonas aeruginosa PA14; Escherichia coli BW25113

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL25344 GPL33546 GPL30881

27 Samples

Download data: CSV, FA, TXT

(Submitter supplied) The success of bacterial pathogens depends on the coordinated expression of virulence determinants. Regulatory circuits that drive pathogenesis are complex, multilayered, and incompletely understood. Here, we reveal that alterations in tRNA modifications define pathogenic phenotypes in the opportunistic pathogen Pseudomonas aeruginosa. We demonstrate that the enzymatic activity of GidA leads to the introduction of a carboxymethylaminomethyl modification in selected tRNAs. more...

Organism:

Pseudomonas aeruginosa UCBPP-PA14

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL27892

12 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Pseudomonas aeruginosa UCBPP-PA14; Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18287 GPL27892

18 Samples

Download data: BED