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Lineage-specific functions of TET1 in the post-implantation mouse embryo.: RNA-Seq of in vitro converted primed epiblast-like cells

ABSTRACT: The mammalian TET dioxygenases contribute to global waves of DNA demethylation in the zygote and in primordial germ cells, but their involvement during de novo DNA methylation at peri/post-implantation development is unknown. Here, we investigate the role

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Bram Boeckx

PROVIDER: E-MTAB-4578 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Epigenetic regulation and transcriptional repression by Tet1 in the early post-implantation mouse embryo: Methylation data.

Project description:The mammalian TET dioxygenases contribute to global waves of DNA demethylation in the zygote and in primordial germ cells, but their involvement during de novo DNA methylation at peri/post-implantation development is unknown. Here, we show novel physiological functions of Tet1 in the pre-primitive streak stage mouse embryo, where it is expressed not only in the primed-state epiblast, but also in the extra-embryonic ectoderm. In the epiblast, Tet1 contributes to DNA methylation patterning, which indirectly results in dominant transcriptional repression involving a Jumonji-family gene Jmjd8. In the extra-embryonic ectoderm, Tet1 suppresses expression of metabolic genes involved in oxidative phosphorylation. These lineage-specific gene repressive functions, involving distinct modes of regulation by DNA methylation, counteract precocious differentiation of the embryo prior to the onset of gastrulation. Such dysregulation in the absence of Tet1 are surprisingly tolerated in an inbred strain but results in full embryonic lethality in non-inbred mice, thus implicating a complex but essential role of Tet1 in normal gestational development.

2017-05-15 | E-MTAB-4581 | biostudies-arrayexpress

Epigenetic regulation and transcriptional repression by Tet1 in the early post-implantation mouse embryo: ChIP seq

2017-05-15 | E-MTAB-5562 | biostudies-arrayexpress

ChIP-seq analysis with an antibody directed against the human Rad21 protein in Raji cells (Genbank: KF717093.1) prior to and post induction of BZLF1.

Project description:Peaks were identified in both the human and viral (EBV (Human Herpesvirus 4; GenBank accession KF717093.1) genome.

2021-06-22 | E-MTAB-8424 | biostudies-arrayexpress

ChIP-seq analysis with an antibody directed against the human H3K4me1 protein in Raji cells (Genbank: KF717093.1) prior to and post induction of BZLF1.

Project description:Peaks were identified in both the human and viral (EBV (Human Herpesvirus 4 GenBank accession KF717093.1) genome.

2021-02-07 | E-MTAB-8425 | biostudies-arrayexpress

ChIP-seq against the CTCF protein in Raji cells with inducible BZLF1 protein (KF717093.1) prior to and post induction of BZLF1.

Project description:Peaks were identified in both the human and viral (EBV (Human Herpesvirus 4; GenBank accession KF717093.1) genome.

2019-04-01 | E-MTAB-7787 | biostudies-arrayexpress

ChIP-seq analysis with an antibody directed against the human H3K4me3 protein in Raji cells (Genbank: KF717093.1) prior to and post induction of BZLF1.

Project description:Peaks were identified in both the human and viral (EBV (Human Herpesvirus 4; GenBank accession KF717093.1) genome.

2021-06-22 | E-MTAB-8419 | biostudies-arrayexpress

ChIP-seq analysis with an antibody directed against the human H3K27ac protein in Raji cells (Genbank: KF717093.1) prior to and post induction of BZLF1.

Project description:ChIP peaks were identified in both the human and viral genomes (genome assembly GRCh37 (hg19) and Epstein-Barr virus, Human Herpesvirus 4; GenBank accession KF717093.1).

2021-06-22 | E-MTAB-8421 | biostudies-arrayexpress

ChIP-seq analysis with an antibody directed against the H3K27me3 protein in Raji cells (Genbank: KF717093.1) prior to and post induction of BZLF1.

Project description:Peaks were identified in both the human and viral (EBV (Human Herpesvirus 4; GenBank accession KF717093.1) genome.

2021-06-22 | E-MTAB-8423 | biostudies-arrayexpress

ChIP-seq analysis with an antibody directed against the human SMC1 protein in Raji cells (Genbank: KF717093.1) prior to and post induction of BZLF1

Project description:Peaks were identified in both the human and viral (EBV (Human Herpesvirus 4; GenBank accession KF717093.1) genome.

2021-06-22 | E-MTAB-8428 | biostudies-arrayexpress

Establishment of a primed pluripotent epiblast stem cell in FGF4-based conditions.

Project description:Several mouse pluripotent stem cell types have been established either from mouse blastocysts and epiblasts. Among these, embryonic stem cells (ESCs) are considered to represent a "naïve", epiblast stem cells (EpiSCs) a "primed" pluripotent state. Although EpiSCs form derivatives of all three germ layers during in vitro differentiation, they rarely incorporate into the inner cell mass of blastocysts and rarely contribute to chimera formation following blastocyst injection. Here we successfully established homogeneous population of EpiSC lines with efficient chimera-forming capability using a medium containing fibroblast growth factor (FGF)-4. The expression levels of Rex1 and Nanog was very low although Oct4 level is comparable to ESCs. EpiSCs also expressed higher levels of epiblast markers, such as Cer1, Eomes, Fgf5, Sox17, and T, and further showed complete DNA methylation of Stella and Dppa5 promoters. However, the EpiSCs were clustered separately from E3 and T9 EpiSC lines and showed a completely different global gene expression pattern to ESCs. Furthermore, the EpiSCs were able to differentiate into all three germ layers in vitro and efficiently formed teratomas and chimeric embryos (21.4%) without germ-line contribution.

| S-EPMC4268649 | biostudies-literature

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