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TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions [MMS/RRHP]

ABSTRACT: TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions [MMS/RRHP]

PROVIDER: PRJNA641869 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12091113_1.fastq.gz	Fastqsanger.gz
	SRR12091113_2.fastq.gz	Fastqsanger.gz
	SRR12091114_1.fastq.gz	Fastqsanger.gz
	SRR12091114_2.fastq.gz	Fastqsanger.gz
	SRR12091115_1.fastq.gz	Fastqsanger.gz

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TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions [MMS/RRHP]

Project description:Estrogen receptor-a (ER) drives tumour development and metastasis in ER positive (ER+) breast cancer. GATA3 is a transcription factor that has been closely linked to ER function, but the role of GATA3 in ER transcriptional activity is not clear. We sought to identify the contribution of GATA3 to the ER complex by conducting quantitative multiplexed rapid immunoprecipitation mass spectrometry of endogenous proteins (qPLEX-RIME) to assess changes to the ER complex in response to GATA3 depletion. Unexpectedly, very few proteins were dissociated from the ER complex in the absence of GATA3, with the only major change being depletion of TET2 from the ER complex. In breast cancer cells and Patient-Derived Xenograft (PDX) tissue, TET2 binding events were shown to constitute a near-total subset of ER binding events, and loss of TET2 was functionally associated with reduced activation of proliferative pathways. To investigate the TET2-ER relationship, the role of TET2 in regulating DNA modifications in ER+ breast cancer cells was examined. TET2 knockdown did not appear to result in changes to global DNA methylation, however, oxidation of methylated DNA to 5-hydroxymethylcytosine (5hmC) was significantly reduced after TET2 depletion and these events occurred at ER enhancers. These findings implicate TET2 in the production and maintenance of 5hmC at ER sites, providing a potential mechanism for TET2-mediated regulation of ER target genes.

2021-02-10 | GSE153252 | GEO

TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions

Project description:Estrogen receptor-alpha (ER) drives tumour development and metastasis in ER positive (ER+) breast cancer. GATA3 is a transcription factor that has been closely linked to ER function, but the role of GATA3 in ER-transcriptional activity is not clear. We sought to identify the contribution of GATA3 to the ER complex, by conducting quantitative multiplexed rapid immunoprecipitation mass spectrometry of endogenous proteins (qPLEX-RIME), to assess changes to the ER complex in response to GATA3 depletion. Unexpectedly, very few proteins were dissociated from the ER complex in the absence of GATA3, with the only major change being loss of TET2 in the ER complex. In breast cancer cells and Patient-Derived Xenograft (PDX) tissue, TET2 binding events were shown to constitute a near-total subset of ER binding events, and loss of TET2 was functionally associated with reduced activation of proliferative pathways. To investigate the TET2-ER relationship, the role of TET2 in regulating DNA modifications in ER+ breast cancer cells was examined. TET2 knockdown did not appear to result in changes to global DNA methylation, however, oxidation of methylated DNA to 5-hydroxymethylcytosine (5hmC) was significantly reduced after TET2 depletion and these events occurred at ER enhancers. These findings implicate TET2 in the production and maintenance of 5hmC at ER sites, providing a potential mechanism for TET2-mediated regulation of ER target genes.

2021-02-10 | PXD019438 | Pride

TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions [ChIP-Seq]

2021-02-10 | GSE153251 | GEO

TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions [RNA-Seq]

2021-02-10 | GSE153250 | GEO

TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions

Project description:TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions

| PRJNA641866 | ENA

TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions [RNA-Seq]

Project description:TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions [RNA-Seq]

| PRJNA641867 | ENA

TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions [ChIP-Seq]

Project description:TET2 is a component of the ER complex and controls 5mC to 5hmC conversion at ER cis-regulatory regions [ChIP-Seq]

| PRJNA641868 | ENA

Methylome of 5mC and 5hmC regulated by NEIL2

Project description:To elucidate the role of DNA glycosylase NEIL2 in regulation of DNA methylome, we performed genome sequencing of epigenetic marker 5mC and 5hmC in genome-wide using enyme-based library methods of TAPS and CAPS. The 5mC and 5hmC profile in CpG contect was further extracted and analysed.

2023-12-13 | GSE240177 | GEO

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [snhmCseq]

Project description:Oxidative modification of 5-methylcytosine (5mC) by TET DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here we present Joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A towards 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from the mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multi-modal single-cell data integration, enable accurate identification of neuronal subtypes, and uncover context-specific regulatory effects of cell-type-specific genes by TET enzymes.

2023-07-14 | GSE236776 | GEO

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [snRNAseq]

2023-07-14 | GSE236769 | GEO