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Nucleolus assembly impairment leads to two-cell transcriptional repression via NPM1-mediated PRC2 recruitment

ABSTRACT: We report the high-throughput sequencing of RNA expression in control embryos ,LoNA KO embryos, control 2c like mESC and LoNA KD 2c like mESC

ORGANISM(S): Mus musculus

PROVIDER: GSE166142 | GEO | 2023/03/31

REPOSITORIES: GEO

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NPM1 directs PIDDosome-dependent caspase-2 activation in the nucleolus.

Project description: Not available

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RNA-seq of Maternal Kdm1a mutant 2C embryos

Project description:2C embryos were generated from Kdm1a FL/Fl Zp3Cre females mated to wild type males for RNA-seq analysis using the Nugen Ovation RNA-seq system V2 3 replicates of maternal Kdm1a mutant 2C embryos were collected for RNA-seq , compared to wt 2C embryos and wt oocyte samples from Macfarlan TS et al, Nature 2012 (GEO acession GSE33923)

2015-03-10 | E-GEOD-66547 | biostudies-arrayexpress

ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress [ChIP-Seq]

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NR5A2 connects genome activation to the first lineage segregation in totipotent embryos

Project description:Zygotic genome activation (ZGA) marks the beginning of the embryonic program for a totipotent embryo, which gives rise to inner cell mass (ICM), where pluripotent epiblast arises, and extraembryonic trophectoderm. While much has been learned about pluripotency regulation, how ZGA is connected to the first lineage segregation in early embryos remains elusive. Here, we investigated the role of nuclear receptor transcription factors (NR TFs), whose motifs are highly enriched in accessible chromatin at the 2-cell (2C) to 8-cell (8C) stages after ZGA. We found NR5A2, an NR TF highly induced upon ZGA, is required for early development. Genome-wide chromatin binding in 2C and 8C embryos showed NR5A2 bound cis-regulatory elements which strongly enrich B1 elements where its motif is embedded. RNA-seq showed while the zygotic genome was largely activated at the 2C stage, 4-8C-specific gene activation was substantially impaired in Nr5a2 KD embryos. At the 8C stage, NR5A2 preferentially regulated its targets including a subset of early ICM genes. Consistently, NR5A2 was required for opening 8C-specific binding sites. Interestingly, while NR5A2’s 2C-binding sites are largely closed in blastocyst, 8C-specific binding sites tend to stay open and are bound by master pluripotency TFs (NANOG, SOX2, and OCT4) in blastocyst or ESC. Further analyses showed NR5A2 regulates early ICM genes at the 8C stage, master pluripotency TFs regulate both early and late ICM genes at later stages. Taken together, these data identify NR5A2 as a key regulator in totipotent embryos that connects ZGA to the first lineage segregation in early mouse development.

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Project description:Zscan4 regulates chromatin accessibility and 2C in early embryos or 2C-like state in ESC cultures.

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Zscan4 mediates ubiquitination and degradation of co-repressor complex to promote chromatin accessibility in two-cell embryos and ESCs

Project description:Zscan4 regulates chromatin accessibility and 2C in early embryos or 2C-like state in ESC cultures.

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Four Hi-C datasets from mESCs and 2C-like cells generated by knocking down the histone chaperone CAF-1 in mESCs

Project description:In this experiment, we've examined chromatin conformation of mESCs and 2C-like cells generated from a CAF-1 knockdown. The method to generate the knockdown was described in (). We performed a modified in situ Hi-C protocol from (Rao et al., 2014) and that can be found in detail at (Díaz et al., 2017, under revision). Samples were digested with MboI restriction enzyme having as starting material 100k cells with two biological replicates per sampling point. The aim of the experiment was to analyze the potential chromatin conformational changes that accompany the mESC to 2C-like transition.

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2C::tomato ES cells, 2-cell embryos and wild type oocytes

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Molecular Mechanisms Directing PRC2 Recruitment and H3K27 Methylation.

Project description: Not available

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Unique Patterns of H3K4me3 and H3K27me3 in 2-Cell-like Embryonic Stem Cells (ESCs)

Project description:A small subgroup of embryonic stem cells (ESCs) exhibit molecular features similar to those of 2-cell (2C) embryos. These so-called 2C-like cells display highly relaxed chromatin architecture and expanded developmental potential. However, it remains elusive whether 2C-like cells and 2-cell embryos share similar epigenetic features. Here, we map the genome-wide profiles of histone H3K4me3 and H3K27me3 in 2C-like cells. We integrated transcriptome and epigenome data to conduct a detailed comparison of 2-cell embryos and 2C-like cells. We found that the majority of genes in 2C-like cells inherit their histone status from ESCs. Among the genes showing a switch in their histone methylation status during 2C-like transitions, only a small number acquire a 2-cell-embryo epigenetic signatures. In contrast, broad H3K4me3 domains display extensive loss in 2C-like cells. Most of differentially expressed genes display decreased H3K4me3 and H3K27me3 levels in 2C-like cells whereas de novo H3K4me3 deposition is closely linked with the expression levels of upregulated 2C-embryo-specific genes. Taken together, our study reveals the unique epigenetic profiles of 2C-like cells, facilitating the further exploration of totipotency in the future.

2021-01-23 | GSE164486 | GEO

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