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Loss of TET2 results in gene expression represssion in mouse naïve B-cells and lymphoma cells [RNA-seq]

ABSTRACT: Loss of TET2 results in gene expression represssion in mouse naïve B-cells and lymphoma cells [RNA-seq]

PROVIDER: PRJNA548518 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9278220.fastq.gz	Fastqsanger.gz
	SRR9278230.fastq.gz	Fastqsanger.gz
	SRR9278221.fastq.gz	Fastqsanger.gz
	SRR9278231.fastq.gz	Fastqsanger.gz
	SRR9278222.fastq.gz	Fastqsanger.gz

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Loss of TET2 results in gene expression represssion in mouse naïve B-cells and lymphoma cells

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Loss of TET2 results in gene expression represssion in mouse GC B-cells and lymphoma cells (RNA-Seq data set)

Project description:Absence of Tet2 at mouse cells results in reduced gene expression

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OGT, H2B S112GlcNAc, TET2 ChIP-seq results

Project description:TET2 directly interacts with OGT, which is important for the chromatin association of OGT in vivo. Although this specific interaction does not regulate the enzymatic activity of TET2, it facilitates OGT-dependent histone O-GlcNAcylation. Moreover, OGT associates with TET2 at transcription starting sites (TSS). Down-regulation of TET2 reduces the amount of H2B S112 GlcNAc marks in vivo, which are associated with gene transcription regulation. We found that OGT interacts with TET2 tightly. Using ChIP-seq with specific antibodies, we tested the co-localization of TET2 and OGT in genome level.

2012-12-11 | E-GEOD-41720 | biostudies-arrayexpress

Rescue of Tet2 KO ES cells in primed or naïve state

Project description:Endogenous retroviruses (ERVs), which are responsible for 10% of spontaneous mouse mutations, are kept under control via several epigenetic mechanisms. The H3K9 histone methyltransferase SETDB1 is essential for ERV repression in embryonic stem cells (ESCs), with DNA methylation also playing an important role. It has been suggested that SETDB1 protects ERVs from TET-dependent DNA demethylation, but the relevance of this mechanism for ERV expression remains unclear. Moreover, previous studies have been performed in primed ESCs, which are not epigenetically or transcriptionally representative of preimplantation embryos. We used naïve ESCs to investigate the role of SETDB1 in ERV regulation and, in particular, its relationship with TET-mediated DNA demethylation. Naïve ESCs show an increased dependency on SETDB1 for ERV silencing when compared to primed ESCs, including at the highly mutagenic intracisternal A particles (IAPs). We found that, in the absence of SETDB1, TET2 activates IAP elements in a catalytic-dependent manner. Surprisingly, however, TET2 does not drive changes in DNA methylation levels at IAPs, suggesting that it regulates these transposons indirectly.

2017-09-25 | GSE100863 | GEO

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