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Effect of the simultaneous knockdown of TET1, TET2 and TET3 on the transcriptome of HEK293 cells

ABSTRACT: We compared TET triple knockdown cells to control cells treated with non-targeting siRNAs to determine global gene expression changes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE67348 | GEO | 2015/07/16

SECONDARY ACCESSION(S): PRJNA279568

REPOSITORIES: GEO

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Effect of the simultaneous knockdown of TET1, TET2 and TET3 on the transcriptome of HEK293 cells

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2015-07-16 | E-GEOD-67348 | biostudies-arrayexpress

Effect of the simultaneous knockdown of TET1, TET2 and TET3 on DNA methylation levels of HEK293 cells

Project description:We compared TET triple knockdown cells to control cells treated with non-targeting siRNAs to determine DNA methylation changes.

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Effect of TET1 and TET3 overexpression on the transcriptome of HEK293 cells

Project description:We compared TET1 and TET3 overexpressing cells to uninduced cells with endogenous levels of the respective transcript to determine global gene expression changes. TET1 overexpression, TET3 overexpression

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Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency

Project description:Cytosine DNA bases can be methylated by DNA methyltransferases and subsequently oxidized by TET proteins. The resulting 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) are considered demethylation intermediates as well as stable epigenetic marks. To dissect the contribution of these cytosine modifying enzymes, we generated combinations of Tet knockout (KO) embryonic stem cells (ESCs) and systematically measured protein and DNA modification levels at the transition from naive to primed pluripotency. Whereas the increase of genomic 5-methylcytosine (5mC) levels during exit from pluripotency correlated with an upregulation of the de novo DNA methyltransferases DNMT3A and DNMT3B, the subsequent oxidation steps turned out to be far more complex. The strong increase of oxidized cytosine bases (5hmC, 5fC, and 5caC) was accompanied by a drop in TET2 levels, yet the analysis of KO cells suggested that TET2 is responsible for most 5fC formation. The comparison of modified cytosine and enzyme levels in Tet KO cells revealed distinct and differentiation-dependent contributions of TET1 and TET2 to 5hmC and 5fC formation arguing against a processive mechanism of 5mC oxidation. The apparent independent steps of 5hmC and 5fC formation suggest yet to be identified mechanisms regulating TET activity and may constitute another layer of epigenetic regulation.

2020-07-24 | PXD019514 | Pride

Loss of TET2 and TET3 in regulatory T cells unleashes effector function

Project description:We studied the effects of loss of TET proteins in regulatory T cells in mice and compared the transcriptional profiles in Treg cells and CD4+ T cells isolated from WT and Tet2/3 DKO mice

2019-03-15 | GSE113694 | GEO

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