Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

47 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transfer RNA (tRNA) processing and RNA m5C-methylation profiles of mouse skin squamous tumours

ABSTRACT: Purpose: High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, such those derived from tRNAs. Also recent advances in high-throughput RNA sequencing has revealed the complex RNA modification landscape and the complex role these nucleosides modifactions have in cell signalling, stem cell biology, development and cancer. The goal of this study is to establish how m5C-tRNA methylation and tRNA-derived small RNAs can affect stem cell fucntion in cancer. Methods: four replicates of tRNAs and RNA buisulphite sequencing of wild-type (WT) and NSun2 -/- mouse skin squamous tumours were generated by deep sequencing, using Illumina HiSeq platform. Results: Our analyses reveal that inhibition of post-transcriptional cytosine-5 methylation locks stem cells in this distinct translational inhibition programme that results in tumour progression but that also sentizes cancer cells to genotoxic stress. Transfer RNA (tRNA) sequencing and RNA Bisulphite sequencing of wild-type (WT) and NSun2 -/- mouse skin squamous tumours

ORGANISM(S): Mus musculus

SUBMITTER: Sabine Dietmann

PROVIDER: E-GEOD-72065 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Loss of cytosine-5 methylation in tRNA triggers stress responses in a disease model for Intellectual Disability

Project description:Mutations in the cytosine-5 RNA methyltransferase NSun2 can cause Intellectual Disability (ID) and symptoms commonly found in patients with Dubowitz syndrome. By analysing gene expression data with the global cytosine-5 RNA methylome in NSun2-deficient mice, we find that loss of cytosine-5 RNA methylation increases the fragmentation of transfer RNAs (tRNA) leading to an accumulation of 5M-bM-^@M-^Y halves. Cleavage of tRNAs by Angiogenin is a common cellular stress response to silence translational programmes, and we show that Angiogenin binds tRNAs lacking site-specific NSun2-methylation with higher affinity. Furthermore, cells lacking functional NSun2 up-regulate stress markers, and deletion of NSun2 compromises cellular survival in response stress stimuli including UV-light and oxidative stress. The decreased tolerance of NSun2 null cells towards oxidative stress can be rescued through inhibition of Angiogenin. In conclusion, cytosine-5 RNA methylation is an essential post-transcriptional mechanism during cellular stress responses and NSun2-mediated tRNA methylation protects from Angiogenin-dependent stress-induced RNA cleavage. RNA Methylation profiling by high throughput sequencing small non-coding RNA profiling by high throughput sequencing Pol III Chromatin-IP profiling by high throughput sequencing

2014-11-06 | E-GEOD-44746 | biostudies-arrayexpress

Transfer RNA (tRNA) processing profiles of mouse embryonic frontal lobes at E13.5/E18.5

Project description:Purpose: High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, such those derived from tRNAs. Also recent advances in high-throughput RNA sequencing has revealed the complex RNA modification landscape and the complex role these nucleosides modifactions have in cell signalling, stem cell biology and development. The goal of this study is to establish how tRNA-derived small RNAs can affect stem cell function. Methods: four replicates of tRNAs sequencing of wild-type (WT) and NSun2 -/- mouse embryonic frontal lobes at E18.5 were generated by deep sequencing, using Illumina HiSeq platform. Results: Our analyses reveal that deletion of the cytosine-5 tRNA methylase NSUN2 increases tRNA cleaveage of NSUN2 tRNA substrates.

2017-01-02 | GSE82162 | GEO

Identification of nascent peptides of peptidyl-tRNA dissociated from ribosome in the early elongation stage in Escherichia coli pthts cells

Project description:Accurate translation of mRNAs into functional proteins is a fundamental process in all living organisms. In bacteria, in the early stage of translation elongation, peptidyl-tRNAs (pep-tRNAs) with short nascent chains frequently dissociate from the ribosome (pep-tRNA drop-off). The dissociated pep-tRNAs are deacylated and recycled by peptidyl-tRNA hydrolase (PTH), which is an essential enzyme in bacteria. Here, we establish a highly sensitive method for direct profiling of pep-tRNAs using RNA isolation method and mass spectrometry. We isolated each tRNA species with peptide from Escherichia coli pthts cells using reciprocal circulating chromatography and precisely analyzed their nascent peptides. As a result, we successfully detected 703 peptides consisted of 402 cognate peptides and 301 non-cognate peptides with single amino-acid substitution. Detailed analysis of individual pep-tRNAs revealed that most of the substitutions in the miscoded peptides take place at the C-terminal drop-off site. We further examined this observation using a reporter construct and found that the non-cognate pep-tRNAs produced by mistranslation rarely participate in the next round of elongation but dissociate from the ribosome, suggesting that pep-tRNA drop-off is an active mechanism by which the ribosome rejects miscoded pep-tRNAs in the early elongation, thereby contributing to quality control of protein synthesis after peptide bond formation.

2023-05-18 | PXD030806 | Pride

Identification of nascent peptides of peptidyl-tRNA dissociated from ribosome in the early elongation stage in Escherichia coli pthts cells

2023-05-18 | PXD030808 | Pride

Identification of nascent peptides of peptidyl-tRNA dissociated from ribosome in the early elongation stage in Escherichia coli pthts cells

2023-05-18 | PXD030807 | Pride

Identification of nascent peptides of peptidyl-tRNA dissociated from ribosome in the early elongation stage in Escherichia coli pthts cells

2023-05-18 | PXD030805 | Pride

tRNA gene identity acts as a determinant of gene positioning

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

Loss of cytosine-5 methylation in tRNA triggers stress responses in a disease model for Intellectual Disability

Project description:Mutations in the cytosine-5 RNA methyltransferase NSun2 can cause Intellectual Disability (ID) and symptoms commonly found in patients with Dubowitz syndrome. By analysing gene expression data with the global cytosine-5 RNA methylome in NSun2-deficient mice, we find that loss of cytosine-5 RNA methylation increases the fragmentation of transfer RNAs (tRNA) leading to an accumulation of 5’ halves. Cleavage of tRNAs by Angiogenin is a common cellular stress response to silence translational programmes, and we show that Angiogenin binds tRNAs lacking site-specific NSun2-methylation with higher affinity. Furthermore, cells lacking functional NSun2 up-regulate stress markers, and deletion of NSun2 compromises cellular survival in response stress stimuli including UV-light and oxidative stress. The decreased tolerance of NSun2 null cells towards oxidative stress can be rescued through inhibition of Angiogenin. In conclusion, cytosine-5 RNA methylation is an essential post-transcriptional mechanism during cellular stress responses and NSun2-mediated tRNA methylation protects from Angiogenin-dependent stress-induced RNA cleavage.

2014-11-06 | GSE44746 | GEO

Genome-Wide Translation Profiling by Ribosome-Bound tRNA Capture

Project description:In the ribosome complex, tRNA is a critical element of mRNA translation. We reported a new technology for profiling ribosome-embedded tRNAs and their modifications. With the method, we generated a comprehensive survey of the quanity and quality of intra-ribosomal tRNAs (Ribo-tRNA-seq). Ribo-tRNA-seq can provide new insights on translation control mechanism in diverse biological contexts.

2018-03-19 | E-MTAB-6576 | biostudies-arrayexpress

Comparison of tRNA expression between HEK293 and HeLa cells

Project description:To associate the amount of tRNAs with codon usage, we perform hydro-tRNA sequencing (Gogakos et al. 2017) and quantify tRNA expression in HEK293 and HeLa cells.

2020-02-28 | E-MTAB-8144 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data