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Tet1 controls maintenance DNA methylation via the regulation of Dppa3

ABSTRACT: Tet1 controls maintenance DNA methylation via the regulation of Dppa3

PROVIDER: PRJEB34996 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3606900.fastq.gz	Fastqsanger.gz
	ERR3606910.fastq.gz	Fastqsanger.gz
	ERR3606901.fastq.gz	Fastqsanger.gz
	ERR3606911.fastq.gz	Fastqsanger.gz
	ERR3606902.fastq.gz	Fastqsanger.gz

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TET1 controls maintenance DNA methylation

Project description:TET1 controls maintenance DNA methylation via the regulation of Dppa3

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Tet1 controls maintenance DNA methylation via the regulation of Dppa3

Project description:Dissection of catalytic and non-catalytic functions of Tet1. DNA methylation (RRBS) profiling of wild type, Tet1 knockout and catalytic mutants during EpiLC differentiation.

2020-09-30 | E-MTAB-6785 | biostudies-arrayexpress

TETs controls maintenance DNA methylation via the regulation of Dppa3

Project description:TETs controls maintenance DNA methylation via the regulation of Dppa3

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DNA methylation profiling to investigate how Tet1 controls maintenance DNA methylation via the regulation of Dppa3 in ESCs

Project description:DNA methylation profiling to investigate how Tet1 controls maintenance DNA methylation via the regulation of Dppa3 in ESCs

| PRJEB34995 | ENA

DNA methylation profiling to investigate how Tet1 controls maintenance DNA methylation via the regulation of Dppa3 in ESCs

Project description:DNA methylation profiling using RRBS in wild type and Dppa3 knockout ESCs.

2020-09-30 | E-MTAB-6800 | biostudies-arrayexpress

TETs controls maintenance DNA methylation via the regulation of Dppa3

Project description:Dissection of catalytic and non-catalytic functions of Tet1 and Tet2. Transcriptome profiling of wild type, Tet1 catalytic mutants, Tet2 and Tet1/2 catalytic mutant catalytic during EpiLC differentiation.

2020-10-05 | E-MTAB-6797 | biostudies-arrayexpress

LINE-1 DNA methylation levels in DPPA3 KO overexpressing DPPA3 mutants

Project description:DPPA3 mutants were overexpressed using a doxycycline system to identify regions in DPPA3 necessary for DNA methylation maintenance suppression

2020-10-22 | E-MTAB-9653 | biostudies-arrayexpress

Amplicon bisulfite sequencing of LINE-1 elements in TET catalytic mutants and DPPA3 KO ESCs rescued by doxycylin induced overexpression

Project description:Tet1, Tet2 and Tet1/Tet2 catalytic mutants as well as DPPA3 KO ESCs harboring a doxycyclin inducible Dppa3 transgene were induced for several days to monitor LINE-1 methylation levels.

2020-10-23 | E-MTAB-9654 | biostudies-arrayexpress

ChIP-MS of DPPA3/STELLA in mouse embryonic stem cells

Project description:Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. So far, it was unclear how mammals specifically achieve global DNA hypomethylation, given the high conservation of the DNA (de-)methylation machinery among vertebrates. We found that DNA demethylation requires TET activity but mostly occurs at sites where TET proteins are not bound suggesting a rather indirect mechanism. Among the few specific genes bound and activated by TET proteins was the naïve pluripotency and germline marker Dppa3 (Pgc7, Stella), which undergoes TDG dependent demethylation. The requirement of TET proteins for genome-wide DNA demethylation could be bypassed by ectopic expression of Dppa3. We show that DPPA3 binds and displaces UHRF1 from chromatin and thereby prevents the recruitment and activation of the maintenance DNA methyltransferase DNMT1. We demonstrate that DPPA3 alone can drive global DNA demethylation when transferred to amphibians (Xenopus) and fish (medaka), both species that naturally do not have a Dppa3 gene and exhibit no post-fertilization DNA demethylation. Our results show that TET proteins are responsible for active and - indirectly also for - passive DNA demethylation; while TET proteins initiate local and gene-specific demethylation in vertebrates, the recent emergence of DPPA3 introduced a unique means of genome-wide passive demethylation in mammals and contributed to the evolution of epigenetic regulation during early mammalian development.

2020-10-12 | PXD019794 | Pride

TET1 interactome in mESCs (via ChIP-MS)

Project description:Precise regulation of DNA methylation in mammals is critical for genome stability and epigenetic regulation. The discovery of the ten-eleven translocation (TET) proteins catalyzing the oxidation from 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) revolutionized the perspective on the complexity and regulation of DNA modifications. Despite accumulating knowledge about the role of TET1, it remains unclear to what extent these can be attributed to its catalytic activity. Here, we use genome engineering and quantitative multi-omics approaches to dissect the role and mechanism of TET1 in mESCs. Our study identifies TET1 as an essential interaction hub for multiple chromatin modifying complexes and as a global regulator of histone modifications. Strikingly, we find that the majority of transcriptional regulation depends on non-catalytic functions of TET1. Moreover, we show that the establishment of H3K9me3 and H4K20me3 at ERV1, ERVK, and ERVL is mediated by TET1 independent of DNA demethylation. We provide evidence that repression of endogenous retroviruses depends on the interaction between TET1 and SIN3A. In summary, we demonstrate that the non-catalytic functions of TET1 are critical for regulation of gene expression and the silencing of endogenous retroviruses in mESCs.

2022-08-31 | PXD028850 | Pride

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