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

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

ORGANISM(S): Homo sapiens

PROVIDER: GSE67350 | GEO | 2015/07/16

SECONDARY ACCESSION(S): PRJNA279566

REPOSITORIES: GEO

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

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

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

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

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

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Reduced representation bisulfite sequencing (RRBS) of WT, Tet1-/-, Tet2-/-, Tet1-/-:Tet2-/- (DKO), and Tet1-/-:Tet2-/-:Tet3-/- (TKO) murine embryonic stem under normal culture conditions.

Project description:RRBS was used to investigate the methylation status of CpG dinucleotides in different Tet knockouts.

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Endogenous epitope-tagging of Tet1, Tet2 and Tet3 identifies TET2 as a naive pluripotency marker.

Project description:Tet1, Tet2, and Tet3 encode DNA demethylases that play critical roles during stem cell differentiation and reprogramming to pluripotency. Although all three genes are transcribed in pluripotent cells, little is known about the expression of the corresponding proteins. Here, we tagged all the endogenous Tet family alleles using CRISPR/Cas9, and characterised TET protein expression in distinct pluripotent cell culture conditions. Whereas TET1 is abundantly expressed in both naïve and primed pluripotent cells, TET2 expression is restricted to the naïve state. Moreover, TET2 is expressed heterogeneously in embryonic stem cells (ESCs) cultured in serum/leukemia inhibitory factor, with expression correlating with naïve pluripotency markers. FACS-sorting of ESCs carrying a Tet2Flag-IRES-EGFP reporter demonstrated that TET2-negative cells have lost the ability to form undifferentiated ESC colonies. We further show that TET2 binds to the transcription factor NANOG. We hypothesize that TET2 and NANOG co-localise on chromatin to regulate enhancers associated with naïve pluripotency genes.

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RNA-seq of WT, Tet1-/-, Tet2-/-, Tet1-/-:Tet2-/- (DKO), and Tet1-/-:Tet2-/-:Tet3-/- (TKO) murine embryonic stem cells following six days of LIF withdrawal.

Project description:The goal of this study was to identify transcriptional differences between varying combinations of Tet deletion clones following six days of LIF withdrawal. These libraries were generated from cells under normal culture conditions.

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Project description:To analyze the role of Tet proteins on global gene expression, we profiled the transcriptome of Xenopus tropicalis blastula embryos upon knockdown of Tet2 and Tet3 using Morpholino antisense oligonucleotides.

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Simultaneous deletion of the methylcytosine oxidases Tet1 and Tet3 increases transcriptome variability in early embryogenesis.

Project description:Dioxygenases of the TET (Ten-Eleven Translocation) family produce oxidized methylcytosines, intermediates in DNA demethylation, as well as new epigenetic marks. Here we show data suggesting that TET proteins maintain the consistency of gene transcription. Embryos lacking Tet1 and Tet3 (Tet1/3 DKO) displayed a strong loss of 5-hydroxymethylcytosine (5hmC) and a concurrent increase in 5-methylcytosine (5mC) at the eight-cell stage. Single cells from eight-cell embryos and individual embryonic day 3.5 blastocysts showed unexpectedly variable gene expression compared with controls, and this variability correlated in blastocysts with variably increased 5mC/5hmC in gene bodies and repetitive elements. Despite the variability, genes encoding regulators of cholesterol biosynthesis were reproducibly down-regulated in Tet1/3 DKO blastocysts, resulting in a characteristic phenotype of holoprosencephaly in the few embryos that survived to later stages. Thus, TET enzymes and DNA cytosine modifications could directly or indirectly modulate transcriptional noise, resulting in the selective susceptibility of certain intracellular pathways to regulation by TET proteins.

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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

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2020-07-24 | PXD019514 | Pride

Epigenomic profiling of Glioblastoma Stem Cells (U3117) subjected to TET1, TET2 or TET3 protein knockouts and subsequent treatment with ascorbic acid.

Project description:Glioblastoma (GBM) is a fatal disease with a poor prognosis, whose aetiology involves profound molecular alterations. Given the limited progress made in recent years, research into new therapeutic avenues may improve the treatment of GBM patients. In this work, we have characterised the epigenomic landscape of patient-derived glioblastoma stem cells in the context of a proneural GBM subtype (U31117). We performed a systematic knockdown of each of the TET proteins (TET1, TET2 and TET3) and explored the consequences of their deletion at the level of DNA methylation (5mC) and hydroxymethylation (5hmC). Global 5hmC levels were then restored using a low dose of ascorbic acid, and the epigenetic landscape of all these conditions was examined using high-content DNA methylation microarrays (Illumina MethylationEPIC Beadchip platform).

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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

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