Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA bisulfite sequencing of candidate tRNAs in Drosophila melanogaster

ABSTRACT: Dnmt2 and NSun2 are (cytosine-5) RNA methyltransferases. Using CRISPR/Cas9 we created null mutations in Dnmt2 and NSun2 genes in Drosophila melanogaster. We also ectopically expressed a wild type and catalytically inactive Dnmt2 form in the Dnmt2 mutant background. RNA bisulfite sequencing was used to follow RNA methylation at partical tRNA substrates.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE109133 | GEO | 2018/01/16

SECONDARY ACCESSION(S): PRJNA430044

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Site-specific cytosine-5 methylation by the mouse RNA methyltransferases Dnmt2 and NSun2 promotes tRNA stability and protein synthesis

Project description:Mouse embryonic fibroblast (MEFs) cell lines and liver samples from Dnmt2 and Nsun2 single mutant, double mutant and wildtype mice were used to identify potential mRNA substrates of both proteins. MEFs were derived from day 13.5 embryos and immortalized by transfection with a plasmid expressing the SV40 large-T antigen. Total RNA of MEFs cell line at passage 9 and total RNA extracted from 2 months old mouse liver tissues of Dnmt2, Nsun2 single mutant, double mutant and wildtype mice were arrayed on Illumina MouseRef8 v2 chips.

2012-07-03 | E-GEOD-36918 | biostudies-arrayexpress

The mouse cytosine-5 RNA methyltransferase NSun2 is a component of the chromatoid body and required for testis differentiation

Project description:Post-transcriptional regulatory mechanisms are crucial for protein synthesis during spermatogenesis and often organized by the chromatoid body. Chromatoid bodies are large cytoplasmic ribonucleoprotein granules, whose precise function and composition remain unclear. Here, we identify NSun2 as a novel component of the chromatoid body, and further show that this RNA methylase is essential for germ cell differentiation in the mouse testis. Lack of NSun2 leads to down-regulation of genes controlling RNA processing and post-transcriptional repression pathways, including Ddx4, Mili, Piwil1 (Miwi) and Tudor domain containing (Tdrd) proteins. Germ cell differentiation was blocked specifically at the pachytene stage by lack of NSun2, as spermatogonial and Sertoli cells were unaffected in knockout mice. We observed the same phenotype when we simultaneously deleted NSun2 with Dnmt2, the only other characterized cytosine-5 RNA methyltransferase to date, indicating that Dnmt2 was not functionally redundant for NSun2 in spermatogonial stem cells or Sertoli cells. Thus, our data indicate that RNA methylation pathways play an essential role in male germ cell differentiation. Four sample groups: Testes from Wild-type and NSun2 knock out mice at 15 and 49 days; 6 samples in each group

2013-02-07 | E-GEOD-39480 | biostudies-arrayexpress

Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns [Drosophila melanogaster]

Project description:Dnmt2 is a widely conserved protein, which is closely related to eukaryotic DNA methyltransferases. However, Dnmt2 shows a robust tRNA methyltransferase activity and only limited activity towards DNA. Interestingly, a recent study has provided evidence for a biologically important function of Dnmt2-dependent DNA methylation in the blood fluke Schistosoma mansoni, which seemed to contradict the weak activity of the enzyme in other organisms. We now used whole-genome bisulfite sequencing to comprehensively analyze the methylome of adult worms and could not detect any evidence for biologically relevant DNA methylation patterns. We also characterized the methylome of Drosophila melanogaster embryos and did not find any evidence for DNA methylation. Unconverted cytosine residues were detectable only at very low levels and shared many attributes with bisulfite deamination artifacts. Our results thus strongly argue against a DNA methyltransferase activity of Dnmt2 and suggest that Dnmt2-dependent phenotypes are caused by reduced tRNA methylation. Whole genome methylation analysis of D. melanogaster. Two samples were analyzed, one sample containing DNA from WT embryos, one sample containing DNA from Dnmt2-/- embryos.

2013-05-06 | E-GEOD-39996 | biostudies-arrayexpress

The mouse cytosine-5 RNA methyltransferase NSun2 is a component of the chromatoid body and required for testis differentiation

2013-02-07 | GSE39480 | GEO

RNA bisulfite sequencing of candidate tRNAs in Drosophila melanogaster

Project description:RNA bisulfite sequencing of candidate tRNAs in Drosophila melanogaster

| PRJNA430044 | ENA

Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns [Drosophila melanogaster]

2013-05-06 | GSE39996 | GEO

Site-specific cytosine-5 methylation by the mouse RNA methyltransferases Dnmt2 and NSun2 promotes tRNA stability and protein synthesis

2012-07-04 | GSE36918 | GEO

High-throughput sequencing of HMW RNAs (4-10 kb) from Drosophila Dnmt2 mutants during heat shock recovery

Project description:Dnmt2 genes are highly conserved tRNA methyltransferases with biological roles in cellular stress responses. Dnmt2 has recently been implicated in transposon silencing in Drosophila but the exact molecular mechanisms are unclear. Adult Dnmt2 mutants were heat shocked and RNA sequencing was performed on visible high-molecular weight RNAs to determine the identity of up-regulated transposons. Dnmt2 mutants accumulated almost all families of transposons after heat shock, indicating a general mis-regulation of transposon silencing in Dnmt2 mutants during the stress response.

2014-12-01 | GSE40432 | GEO

High-throughput sequencing of small RNAs (25-70 nt) from Drosophila wild-type and Dnmt2 mutants

Project description:Dnmt2 genes are highly conserved tRNA methyltransferases with biological roles in cellular stress responses. The absence of obvious mutant phenotypes under laboratory conditions suggested a function for Dnmt2 under non-physiological conditions. Indeed, Dnmt2 has recently been implicated in various aspects of the cellular stress response and the tRNA methyltransferase activity of Dnmt2 has been shown to interfere with stress-induced fragmentation of various tRNAs. We used adult animals and small RNA sequencing during a heat stress experiment to determine the tRNA fragment abundance and identities in wild-type and Dnmt2 mutant somatic tissues. Dnmt2 mutants produced tRNA fragments with different identities when compared to wild-type controls, indicating the accumulation of non-physiological tRNA-derived molecules in tissues without Dnmt2. 6 samples examined: heterozygous and Dnmt2 mutant under control, heat shock and recovery conditions

2012-11-12 | E-GEOD-35981 | biostudies-arrayexpress

Neuronal Nsun2 deficiency is associated with codon-specific epitranscriptomic dysregulation of Gly-tRNAs and corresponding proteomic shift impacting synaptic signaling and behavior

Project description:The role of transfer (t)RNA cytosine methyl-transferases as epitranscriptomic regulators of brain proteomes remains unexplored. We report that fear memory and antidepressant-like behaviors are highly sensitive to bi-directional changes in Nsun2 tRNA methyltransferase activity in prefrontal cortex (PFC) neurons. Nsun2-deficient mutant cortex showed a selective deficit in multiple glycine tRNAs, resulting in codon-specific shifts in translational efficiencies and a distorted proteomic landscape with deficits in glycine-rich neuronal proteins impacting synaptic signaling and behavior.

2021-07-02 | PXD023437 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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