Total tRNA level and tRNA charged fraction in DLD-1 cells treated with 4-hydroxytamoxefen and compared to untreated cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE116812 | GEO | 2019/04/20
REPOSITORIES: GEO
Similar Datasets
Project description:Total tRNA level and tRNA charged fraction in DLD-1 cells treated with 4-hydroxytamoxefen and compared to untreated cells
| PRJNA480290 | ENA
Project description: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. In HEK293T cells, most cytosolic tRNAs are charged at >90% levels, whereas tRNASer and tRNAThr are generally charged at lower levels. These low charging levels were validated using acid denaturing gels. Our method should be widely applicable for investigations of tRNA charging as a parameter for biological regulation.
2017-06-15 | GSE97259 | GEO
Project description: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. We find that sequencing caveats affect quantitation of only a subset of human tRNA genes. Unexpectedly, we detect several cases where the differences in tRNA expression among samples do not involve variations at the level of isoacceptor tRNA sets (tRNAs charged with the same amino acid but using different anticodons); but rather among tRNA genes within the same isodecoder set (tRNAs having the same anticodon sequence). Because isodecoder tRNAs are functionally equal in terms of genetic translation, their differential expression may be related to non-canonical tRNA functions. We show that several instances of differential tRNA gene expression result in changes in the abundance of tRNA-derived fragments (tRFs) but not of mature tRNAs. Examples of differentially expressed tRFs include: PIWI-associated RNAs, tRFs present in tissue samples but not in cells cultured in vitro, and somatic tissue-specific tRFs. Our data support that differential expression of tRNA genes regulate non-canonical tRNA functions performed by tRFs.
2019-04-17 | GSE114904 | GEO
Project description:In this study, we identify leucyl-tRNA synthetase (LARS) as a breast tumor suppressor. To identify the mechanism underlying LARS-mediated breast tumor suppression, we first conducted charged tRNA profiling to assess charged and total tRNA-Leu expression in cell lines with high and low LARS expression. Expression of select charged and total tRNA-Leu isoacceptors were reduced in cell lines with lower LARS expression. We then conducted RNA-Seq and translation profiling including ribosome profiling (Ribo-Seq), polysome profiling in LARS-depleted cell lines. To test our hypothesis in vivo, we also performed RNA-Seq of ribosome-associated RNAs in Lars depleted PyMT tumors within RiboTag mice. The analyses implicate LARS as a regulator of leucine-rich translation.
2022-01-05 | GSE176130 | GEO
Project description:During mRNA translation, tRNAs are charged by aminoacyl-tRNA synthetases (aaRS) and subsequently used by ribosomes. A multi-enzyme aminoacyl-tRNA synthetase complex (MSC) has long been proposed to increase protein synthesis efficiency by passing charged tRNAs directly to ribosomes. An alternative is that the MSC repurposes specific synthetases for ex-translational functions that are activated by cues that direct specific enzymes to novel targets. To explore this question, we generated mammalian cell clones in which ArgRS and GlnRS were absent from the MSC to give a stable complex lacking the two enzymes (MSCΔRQ). Protein synthesis, under a variety of stress conditions, was unchanged in MSCΔRQ cells. Most strikingly, levels of charged tRNAGln and tRNAArg remained unchanged and no ribosome pausing was observed at codons for Arg and Gln. Thus, increasing or regulating protein synthesis efficiency is not dependent on ArgRS and GlnRS in the MSC. Alternatively, and consistent with previously reported ex-translational roles, we found manipulations that do not affect protein synthesis but instead MSC cellular localization.
2020-11-18 | GSE158212 | GEO
Project description:During mRNA translation, tRNAs are charged by aminoacyl-tRNA synthetases (aaRS) and subsequently used by ribosomes. A multi-enzyme aminoacyl-tRNA synthetase complex (MSC) has long been proposed to increase protein synthesis efficiency by passing charged tRNAs directly to ribosomes. An alternative is that the MSC repurposes specific synthetases for ex-translational functions that are activated by cues that direct specific enzymes to novel targets. To explore this question, we generated mammalian cell clones in which ArgRS and GlnRS were absent from the MSC to give a stable complex lacking the two enzymes (MSCΔRQ). Protein synthesis, under a variety of stress conditions, was unchanged in MSCΔRQ cells. Most strikingly, levels of charged tRNAGln and tRNAArg remained unchanged and no ribosome pausing was observed at codons for Arg and Gln. Thus, increasing or regulating protein synthesis efficiency is not dependent on ArgRS and GlnRS in the MSC. Alternatively, and consistent with previously reported ex-translational roles, we found manipulations that do not affect protein synthesis but instead MSC cellular localization.
2020-12-23 | PXD021527 | Pride
Project description:Comparison of overall tRNA level and fraction of charged tRNAs of different variants
2021-08-19 | GSE137567 | GEO
Project description:Protein translation depends on mRNA-specific initiation, elongation, and termination rates. While the regulation of ribosome elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here, we combined ribosome and tRNA profiling to investigate the relations between ribosome elongation rates, (aminoacyl-) tRNA levels and codon usage in mammals. We modeled codon-specific ribosome dwell times and translation fluxes from ribosome profiling, considering pair-interactions between ribosome sites. In mouse liver, the model revealed site and codon specific dwell times, as well as codon pair-interactions clustering by amino acids. While translation fluxes varied significantly across diurnal time and feeding regimen, codon dwell times were highly stable, and conserved in human. Fasting had no effect on codon dwell times in mouse liver. Profiling of total and aminoacylated tRNAs revealed highly heterogeneous levels with specific isoacceptor patterns and a correlation with codon usage. tRNAs for isoleucine, asparagine, aspartate and arginine were lowly loaded and conserved in fasted mice. Finally, codons with low levels of charged tRNAs and high codon usage relative to tRNA abundance exhibited long dwell times. Together, these analyses pave the way towards understanding the complex relation between tRNA loading, codon usage and ribosome dwell times in mammals.
2020-03-26 | GSE126382 | GEO
Project description:Here we report that the spatial organization of yeast tRNA genes depends upon both locus position and tRNA identity; supporting the idea that the genomic organization of tRNA loci utilizes tRNA dependent signals within the nucleoprotein-tRNA complexes that form into clusters. We use high-throughput sequencing coupled to Circular Chromosome Conformation Capture to detect interactions with two wild type tRNAs and these same positions replaced with suppressor tRNAs (SUP4-1). Detect DNA-DNA interactions (Circular chromosome conformation capture; 4C) with two wild type tRNAs and these same positions replaced with suppressor tRNAs (SUP4-1) Supplementary files: Alignment files generated by Topography v1.19 software.
2012-06-13 | E-GEOD-30103 | biostudies-arrayexpress
Project description:Increased proliferation and elevated levels of protein synthesis are characteristic of transformed and tumor cells. Though components of the translation machinery are often misregulated in cancers, how tRNA plays a role in cancer cells has not been explored. We compare genome-wide tRNA expression in tumorigenic versus non-tumorigenic breast cell lines, as well as tRNA expression in breast tumors versus normal breast tissues. In tumorigenic versus non-tumorigenic cell lines, nuclear-encoded tRNAs increase by up to 3-fold and mitochondrial-encoded tRNAs increase by up to 5-fold. In tumors versus normal breast tissues, both nuclear and mitochondrial-encoded tRNAs increase by up to 10-fold. This tRNA over-expression is selective and coordinates with the properties of cognate amino acids. Nuclear- and mitochondrial-encoded tRNAs exhibit distinct expression patterns, indicating that tRNAs can be used as biomarkers for breast cancer. We analyzed tRNA expression levels in 2 non-tumorigenic breast cell lines, 6 tumorigenic breast cancer cell lines, 3 normal breast tissue samples, and 9 breast tumor samples. We used a non-tumorigenic breast cell line (MCF10A) as a reference sample in all hybridizations. All data is dye-swapped.
2010-05-22 | E-GEOD-17945 | biostudies-arrayexpress