Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic profiling of human pancreatic cell lines hPNE/hTert stably over-expressing DNMTs compared to GFP-hPNE/hTert over-expressing control cells after lentiviral transduction

ABSTRACT: The overexpression of DNA methyltransferases (DNMTs) is a common hallmark of numerous cancers. These aberrant changes in DNA methylation profiles are correlated to the overexpression of DNMTs. Although this association is clearly demonstrated, the causal role of DNMT overexpression in pancreatic cancer has not been clearly established. Consequently, we decided to determine whether DNMT overexpression induces diffrent methylation patterns in non-cancerous pancreatic cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE148913 | GEO | 2023/04/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Nanopore sequencing on yeast expressing 4 murine DNMTs

Project description:Localisation of CpG methylation in yeast expressing murine DNMTS Genomic DNA was purified from a control strain and a strain expressing murine DNMTs

2020-09-30 | E-MTAB-9356 | biostudies-arrayexpress

WGBS on yeast expressing 3 or 4 murine DNMTs

Project description:Localisation of CpG methylation in yeast expressing murine DNMTS Genomic DNA was purified from a control strain and a strain expressing murine DNMTs, treated with Bisulfite and sequenced on a hiseq 2000

2020-09-30 | E-MTAB-9258 | biostudies-arrayexpress

Nucleosome positioning in Yeast expressing active or inactive murine DNMTs

Project description:Effect of induced Methylation on Nucleosome positioning in yeast. Mnase digested DNA from a control strain, a strain expressing the 4 murine DNMTs or a strain expressing catalytically inactive murine DNMTs were extracted and sequenced on a hiseq 2000

2021-04-01 | E-MTAB-10254 | biostudies-arrayexpress

Nanopore sequencing on yeast expressing 4 murine DNMTs

Project description:Nanopore sequencing on yeast expressing 4 murine DNMTs

| PRJEB39412 | ENA

WGBS on yeast expressing 3 or 4 murine DNMTs

Project description:WGBS on yeast expressing 3 or 4 murine DNMTs

| PRJEB39061 | ENA

Expression data from mouse wild type, PRDM14-overexpressing and Dnmts KO embryonic stem cells (ESCs).

Project description:Germline cells reprogram extensive epigenetic modifications to ensure the cellular totipotency of the next generation and prevent accumulation of epimutations. Primordial germ cells (PGCs)1, the common source of both oocytes and sperm, erase genome-wide DNA methylation and histone H3 lysine 9 dimethylation (H3K9me2), a process called genome-wide epigenetic reprogramming2,3. However, little is known about the molecular mechanism of DNA demethylation by developing PGCs. Here we show that overexpression of PRDM14, a critical regulator for specification and early differentiation of PGCs, promotes global DNA demethylation in embryonic stem cells (ESCs). PRDM14 directly represses transcription of de novo DNA methyltransferase, Dnmt3b, but its repression is not sufficient for global DNA demethylation. Comparison of global gene expression profiles between PRDM14-overexpressing ESCs and Dnmts triple mutant ESCs clearly demonstrates that overexpression of PRDM14 activates about half of the genes silenced by DNA methylation in ESCs. Furthermore, PRDM14 directly interacts with TET1, which converts 5-methylcytosine to 5-hydroxymethylcytosine, and DNA demethylation by overexpression of PRDM14 is strongly disturbed by pharmacological inhibitors of the base excision repair (BER) pathway. We propose that formation of a PRDM14/TET1 complex triggers the activation of BER-dependent active demethylation across the whole genome of developing PGCs.

2021-02-17 | GSE36371 | GEO

Nucleosome positioning in Yeast expressing active or inactive murine DNMTs

Project description:Nucleosome positioning in Yeast expressing active or inactive murine DNMTs

| PRJEB43847 | ENA

Pivotal role for S-nitrosylation of DNA methyltransferase in epigenetic regulation

Project description:DNMTs catalyze the methylation of cytosine with SAM. DNA methylation affects key cellular processes by regulating gene expression, thus serving a variety of physiological and pathophysiological roles. However, the chemical mechanisms of DNA methylation by which its enzymatic activity is regulated have not been fully elucidated. We found that a critical cysteine residue in DNMT is the target of protein S-nitrosylation, leading to the attenuation of DNMT enzymatic activity and consequent aberrant regulation of gene expression during neoplastic cell proliferation. Our results demonstrate that de novo DNA methylation mediated by DNMT3 is regulated by NO, which is involved in tumor formation.

2023-03-11 | PXD039437 | Pride

Transcription profiling of mouse Dicer-null cell lines vs. wt ES cells and Dicer-null cell lines vs. Dicer-null cells overexpressing Dnmt1 or Dnmt3a/3b

Project description:Dicer initiates RNA interference by generating small RNAs involved in various silencing pathways. Dicer participates in centromeric silencing, but its role in the epigenetic regulation of other chromatin domains has not been explored. Here we show that Dicer1 deficiency in Mus musculus leads to decreased DNA methylation, concomitant with increased telomere recombination and telomere elongation. These DNA-methylation defects correlate with decreased expression of Dnmt1, Dnmt3a and Dnmt3b DNA methyltransferases (Dnmts), and methylation levels can be recovered by their overexpression. We identify the retinoblastoma-like 2 protein (Rbl2) as responsible for decreased Dnmt expression in Dicer1-null cells, suggesting the existence of Dicer-dependent small RNAs that target Rbl2. We identify the miR-290 cluster as being downregulated in Dicer1-deficient cells and show that it silences Rbl2, thereby controlling Dnmt expression. These results identify a pathway by which miR-290 directly regulates Rbl2-dependent Dnmt expression, indirectly affecting telomere-length homeostasis. Experiment Overall Design: Two-condition experiments. 6 comparisons. One dye-swap technical replicate for all samples. 2-color platform.

2008-06-19 | E-GEOD-11229 | biostudies-arrayexpress

De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs) [BiSulfite-seq]

Project description:We engineered combinatorial knock-in of human DNMTs in Komagataella phaffii, a yeast species lacking endogenous DNA methylation, to characterize methylation preferences and functional consequences of individual de-novo DNMTs as well as their combinations. Methylation preferences were determined through whole-genome bisulfite sequencing (WGBS) experiments. Effects of knock-in on gene expression were determined by RNA-seq. Measurements of genome-wide methylation produced by distinct de-novo DNMTs permitted determination of methylation preferences and aversions specific to individual DNMTs. Combining methylation and gene expression data provided insight about cellular response to the stress of DNA methylation and about the association between gene methylation patterns and changes in transcriptional output.

2020-02-28 | GSE139062 | GEO

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